Miracle-dz/UniFAR-FTUs huggingface dataset:
Role for Influenza Virus Envelope Cholesterol in Virus Entry and Infection

ABSTRACT Enveloped viruses are highly dependent on their lipid envelopes for entry into and infection of host cells. Here, we have examined the role of cholesterol in the virus envelope, using methyl-β-cyclodextrin depletion. Pretreatment of virions with methyl-β-cyclodextrin efficiently depleted envelope cholesterol from influenza virus and significantly reduced virus infectivity in a dose-dependent manner. A nonenveloped virus, simian virus 40, was not affected by methyl-β-cyclodextrin treatment. In the case of influenza virus, infectivity could be partially rescued by the addition of exogenous cholesterol. Influenza virus morphology, binding, and internalization were not affected by methyl-β-cyclodextrin depletion, whereas envelope cholesterol depletion markedly affected influenza virus fusion, as measured by a specific reduction in the infectivity of viruses induced to fuse at the cell surface and by fluorescence-dequenching assays. These data suggest that envelope cholesterol is a critical factor in the fusion process of influenza virus.
On Leveraging Partial Paths in Partially-Connected Networks

Mobile wireless network research focuses on scenarios at the extremes of the network connectivity continuum where the probability of all nodes being connected is either close to unity, assuming connected paths between all nodes (mobile ad hoc networks), or it is close to zero, assuming no multi-hop paths exist at all (delay-tolerant networks). In this paper, we argue that a sizable fraction of networks lies between these extremes and is characterized by the existence of partial paths, i.e., multi-hop path segments that allow forwarding data closer to the destination even when no end-to-end path is available. A fundamental issue in such networks is dealing with disruptions of end-to-end paths. Under a stochastic model, we compare the performance of the established end-to-end retransmission (ignoring partial paths), against a forwarding mechanism that leverages partial paths to forward data closer to the destination even during disruption periods. Perhaps surprisingly, the alternative mechanism is not necessarily superior. However, under a stochastic monotonicity condition between current vs. future path length, which we demonstrate to hold in typical network models, we manage to prove superiority of the alternative mechanism in stochastic dominance terms. We believe that this study could serve as a foundation to design more efficient data transfer protocols for partially-connected networks, which could potentially help reducing the gap between applications that can be supported over disconnected networks and those requiring full connectivity.
Carotid Intima‐Media Thickness Measurement Promises to Improve Cardiovascular Risk Evaluation in Head and Neck Cancer Patients

Radiation‐treated head and neck cancer (HNC) patients are at high risk for developing radiation vasculopathy, as evidenced by an increased stroke risk. The benefits of screening and assessing the cardiovascular (CV) risk of HNC patients using carotid intima‐media thickness (CIMT) ultrasound are not known. Our objective was to determine the prevalence of high CV risk in patients without known CV diseases who received radiation for HNC, determine the percentage of screened patients who had a change in clinical management as a result of an increased CIMT, and to compare this risk‐assessment tool to patients' risk classification using the Framingham Risk Score (FRS) and Pooled Cohort Atherosclerotic Cardiovascular Disease (ASCVD) Risk Equation (recommended by American College of Cardiology/American Heart Association Guidelines on the Assessment of Cardiovascular Risk).
Onset detection in pitched non-percussive music using warping-compensated correlation

Automatically extracting temporal information from musical recordings is inarguably one of the most critical subtasks of many music information retrieval systems. In this paper we present a system for automatic note onset detection in pitched non-percussive (PNP) musical sounds, which is the most challenging audio signal group for this task. We propose a new approach based on stable pitch cues and signal energy. A computationally inexpensive method for feature extraction, which efficiently suppresses vibrato, is combined with information derived from the signal energy in the feature space. Onsets are localized by a median filter based peak picking method. The proposed method is tested against a database of annotated violin recordings, covering a wide range of tempo and playing styles like vibrato and staccato. Our system outperforms prior state of the art systems with results for true positives of 91.2% and false positives of 9.2%.
Genomic imprinting in plants

Genomic imprinting attracted particular attention in the 1980’s following the discovery that the parental origin of genetic information is essential for normal development of eutherians,1,2 for review see.3 The term imprinting was first introduced in the 1960s to describe the elimination of the paternal chromosomes during spermatogenesis in the Sciarid fly.4‑6Today the term genomic imprinting mainly refers to parent‑of‑origin specific effects distinguishing each parental genome which can be regarded as memories, or “imprints”. 7,8 Breaking the rules of Mendel, genomic imprinting is an epigenetic phenomenon per se. Epigenetics is currently defined as the study of mitotically or meiotically heritable changes in gene expression without any change in DNA sequence9,10 and it is intimately linked to the study of inheritance of chromatin states.11 Gene imprinting currently refers to differential expression of autosomal genes according to their parent of origin.12The phenomenon of genomic imprinting explains several cases of parent‑specific human disorders.13 To date over 80 imprinted genes have been described in mammals14 and their parent‑of‑origin specific expression can correlate with changes in DNA methylation patterns, antisense noncoding RNAs and chromatin folding.3 Epigenetic imprints can either activate or silence the “imprinted” allele, and hence imprinting can be associated with either an expressed or silenced allele.15 In mammals, the number of paternally expressed imprinted genes is almost equivalent to the number of maternally expressed genes and the imprinted status can differs according to tissue, developmental stage and species. It is then crucial for our understanding to clearly indicate the status of imprinting (i.e., paternally or maternally expressed) and the context (e.g., species, developmental stage, tissue).
Two-B or not Two-B?: Design Patterns for Hybrid Metaheuristics

Real world search problems, characterised by nonlinearity, noise and multidimensionality, are often best solved by hybrid algorithms. Techniques embodying different necessary features are triggered at specific iterations, in response to the current state of the problem space. In the existing literature, this alternation is managed either statically (through pre-programmed policies) or dynamically, at the cost of high coupling with algorithm inner representation. We extract two design patterns for hybrid metaheuristic search algorithms, the All-Seeing Eye and the Commentator patterns, which we argue should be replaced by the more flexible and loosely coupled Simple Black Box (Two-B) and Utility-based Black Box (Three-B) patterns that we propose here. We recommend the Two-B pattern for purely fitness based hybridisations and the Three-B pattern for more generic search quality evaluation based hybridisations.
EPIDEMIOLOGY OF ROTAVIRUS DIARRHEA AMONG CHILDREN AGED LESS THAN 5 YEARS IN RURAL SOUTHERN ETHIOPIA.

The objective of this study was to determine the epidemiological and clinical features of rotavirus infection among children aged less than 5 years in rural southern Ethiopia. We conducted a hospital-based, prospective study among children aged less than 5 years with acute diarrhea and moderate to severe dehydration attending the outpatient department of Gambo Rural Hospital, Ethiopia during September-November 2012. Three hundred fourteen children were included in the study, of whom 137 (43.6%) had rotavirus infection. The average age of children with rotavirus infection was lower than those without it [odds ratio (OR): 0.94]. Finding severe dehydration on skin pinch test (adjusted OR: 3.76) and having diarrhea for ! 3 days (adjusted OR: 2.50) were associated with rotavirus infection. The mortality rate was 4.4% among rotavirus infection children and 0% among non-rotavirus diarrhea cases (p=0.006). Rotavirus infection should be suspected in children with severe dehydration on a skin pinch test and among those presenting with diarrhea for 3 days in rural southern Ethiopia.
Evaluating POS Tagging under Sub-optimal Conditions . Or : Does Meticulousness Pay ?

In this paper, we investigate the role of sub-optimality in training data for part-of-speech tagging. In particular, we examine to what extent the size of the training corpus and certain types of errors in it affect the performance of the tagger. We distinguish four types of errors: If a word is assigned a wrong tag, this tag can belong to the ambiguity class of the word (i.e. to the set of possible tags for that word) or not; furthermore, the major syntactic category (e.g. ‘N’ or ‘V’) can be correctly assigned (e.g. if a finite verb is classified as an infinitive) or not (e.g. if a verb is classified as a noun). We empirically explore the decrease of performance that each of these error types causes for different sizes of the training set. Our results show that those types of errors that are easier to eliminate have a particularly negative effect on the performance. Thus, it is worthwhile concentrating on the elimination of these types of errors, especially if the training corpus is large.
Breakdown of Friend virus-induced tolerance and development of runting syndrome in rats.

The effects of the inoculation of lymphoid cells into syngeneic rats made Friend virus (FV) tolerant by neonatal injections of FV were studied. The inoculation of lymphoid cells from immune donors brought about the runting syndrome in five of seven recipients, while the inoculation of lymphoid cells from normal donors induced the runting syndrome in one of five recipients. The titer of FV in the blood decreased markedly by the inoculation of lymphoid cells, but immunological tolerance to Friend lymphoma cells was not broken in the survivors. The repeated inoculation of lymphoid cells from immune rats induced the runting syndrome in all cases. The inoculation of immune lymphoid cells into young tolerant rats induced a low incidence of the runting syndrome and a high incidence of resistance to Friend lymphoma transplants. The major pathological findings in the runted rats were atrophy of the thymus and enlargement of the spleen with a depletion of lymphocytes. The pathogenic mechanism of the runting syndrome in the FV-tolerant rats induced by inoculation of syngeneic lymphoid cells was discussed.
Contributions of Ion Channel Currents to Ventricular Action Potential Changes and Induction of Early Afterdepolarizations During Acute Hypoxia

Rationale: Variability in delivery of oxygen can lead to electric instability in the myocardium and the generation of arrhythmias. In addition ischemic heart disease and angina are associated with an increase in circulating catecholamines that further increases the risk of developing ventricular tachyarrhythmias. Objective: We investigated the net effects of acute hypoxia and catecholamines on the cardiac action potential. Methods and Results: We incorporated all published data on the effects of hypoxia on the late Na+ current (INa-L), the fast Na+ current (INa), the basal L-type Ca2+ channel current (ICa-L), and the slow (IKs) and rapid components of the delayed rectifier K+-current (IKr) in the absence and presence of &bgr;-adrenergic receptor (&bgr;-AR) stimulation into the Luo–Rudy model of the action potential. Hypoxia alone had little effect on the action potential configuration or action potential duration. However in the presence of &bgr;-AR stimulation, hypoxia caused a prolongation of the action potential and early afterdepolarizations (EADs) and spontaneous tachycardia were induced. Experiments performed in guinea pig ventricular myocytes confirmed the modeling results. Conclusions: EADs occur predominantly because of the increased sensitivity of ICa-L to &bgr;-AR stimulation during hypoxia. &bgr;-AR stimulation is necessary to induce EADs as EADs are never observed during hypoxia in the absence of &bgr;-AR stimulation.
Optimizing Cancer Care Delivery through Implementation Science

The 2013 Institute of Medicine report investigating cancer care concluded that the cancer care delivery system is in crisis due to an increased demand for care, increasing complexity of treatment, decreasing work force, and rising costs. Engaging patients and incorporating evidence-based care into routine clinical practice are essential components of a high-quality cancer delivery system. However, a gap currently exists between the identification of beneficial research findings and the application in clinical practice. Implementation research strives to address this gap. In this review, we discuss key components of high-quality implementation research. We then apply these concepts to a current cancer care delivery challenge in women’s health, specifically the implementation of a surgery decision aid for women newly diagnosed with breast cancer.
Analysis of Productivity Gain in Incremental Effort Estimation

This paper presents the framework for incremental Effort based development in order to analysis the productivity gain in Effort based development. Effort estimation is a challenge in every software project. The estimates will impact costs and expectations on schedule, functionality and quality. While expert estimates are widely used, they are difficult to analyze and the estimation quality depends on the experience of experts from similar projects. Alternatively, more formal estimation models can be used. Traditionally, software size estimated in the number of Source Lines of Code (SLOC), Function Points (FP) and Object Points (OP) are used as input to these models. Models that predict product size as an exponential function of the development effort are used in the paper to explore the relationships between effort and the number of increments. The author mainly focus what will be effect on productivity rate on incremental development and how duration for incremental software development vary . For incremental development the author estimate the cumulative effort gain against effort estimation . This research paper will be helpful to get productivity rate against incremental effort estimation. General Terms Effort estimation, Productivity, Time duration.
Estimating frequency of three-phase power systems via widely-linear modeling and total least-squares

The frequency of a three-phase power system can be estimated from the parameters of a widely-linear predictive model for the complex-valued αβ signal of the system. Using the total least-squares (TLS) method, it is possible to estimate the model parameters while compensating for error in both input and output of the model when the voltage readings of the three phases are contaminated with noise. In this paper, we utilize the inverse power method to find a TLS estimate of the parameters of the assumed widely-linear predictive model in an adaptive fashion. Simulation results show that the resultant algorithm, called augmented inverse power iterations (AIPI), outperforms the recently proposed augmented complex Kalman filter (ACKF) and augmented complex extended Kalman filter (ACEKF) algorithms in estimating the frequency of the three-phase power systems. Unlike ACKF and ACEKF, AIPI requires no parameter tuning or prior knowledge of the noise variances. Computational complexity of AIPI is also similar to those of ACKF and ACEKF.
A Scalable Algorithm for Structured Kernel Feature Selection

Kernel methods are powerful tools for nonlinear feature representation. Incorporated with structured LASSO, the kernelized structured LASSO is an effective feature selection approach that can preserve the nonlinear input-output relationships as well as the structured sparseness. But as the data dimension increases, the method can quickly become computationally prohibitive. In this paper we propose a stochastic optimization algorithm that can efficiently address this computational problem on account of the redundant kernel representations of the given data. Experiments on simulation data and PET 3D brain image data show that our method can achieve superior accuracy with less computational cost than existing methods.
Predictors of influenza immunization in persons over age 65.

BACKGROUND Numerous individual characteristics have been found to be associated with rates of obtaining flu shots. This study creates a predictive model that assesses the relative impact of each of these factors on increasing rates of flu shots in a population. METHODS The Medicare beneficiary survey from 1998 and 1999 was used. Sixteen factors present in 1998 were compared between subjects who did and who did not receive flu shots. Significant factors were then used in a logistic regression to predict the probability of receiving a flu shot in 1998 and 1999. RESULTS Seven demographic and 7 health status measures were significantly different between subjects who did and who did not receive flu shots in 1998. Logistic regression showed that twelve of these variables were associated with a subject receiving a flu shot in 1998 and explained 11.4% of the variability in who did and who did not receive a flu shot. For the following year, 1999, 7 measures were significantly associated with receiving a flu shot and explained 64% of the variability in who did and who did not receive a flu shot. One variable, if the subject had received a flu shot in 1998, was highly predictive of a subject receiving a flu shot in 1999, explaining 63% of the observed variability in who did and who did not receive a flu shot in 1999. DISCUSSION The major predictor of getting a flu shot in future years is having received one in the current year (63% of predictive power). Six other behavior and demographic factors increase the predictive power modestly. Programs that target nonrecipients may increase the overall flu shot rates of a community.
A Multiple Targets Appearance Tracker Based on Object Interaction Models

Kernel-based method has been proved to be effective in solving single-target tracking problem. However, facing more complicated multitarget tracking task, most classic kernel-based multitarget trackers do not model the interaction among targets successfully and simply track each target independently. Thus, they usually could not deal with “singularity” problem and fail in tracking the target when occlusions occur or distracters appear. Although multikernel methods may improve the performance by introducing more constraints, how to simulate the relationship and interaction among the tracked targets is still not fully investigated. In this paper, we discuss a very common scenario of multitarget tracking, in which a moving object's motion is not only determined by its virtual destination but also impacted by other neighboring objects. This phenomenon exists in many usual tracking applications such as human tracking, traffic monitoring, video surveillance, and so on, where an object usually moves toward a particular direction but meanwhile detours when close to others to avoid collision. Specifically, we propose a novel interaction model to explain the above phenomenon. Then by defining a new cost function, we embed this interaction model into a kernel-based tracker and further derive our interactive kernel-based multitarget tracker. Experimental results on various datasets demonstrate that our interaction model can alleviate “singularity” problem and, thus, the proposed tracking method could achieve superior performance in multitarget tracking.
The learning component in social software engineering

The interactions that occur in a software engineering context, both face-to-face and virtual and from the mundane to the professional have many purposes. Professional interactions can be planned or ad hoc, and their purposes are both varied and intertwined. They could serve to build trust, or be used to share or acquire knowledge or knowhow. In this paper, we contend that an important component of social software engineering is learning. A model, based on existing learning theory, is proposed to describe the knowledge and knowhow content of professional social software engineering. The model is applied within the context of an observational study in a professional environment where ad hoc interactions are audio-visually recorded. We found that 60% of the social software engineering occurring within this collocated team was aimed at improving knowhow on the use of tools, while 40% of the interactions were conducted for the purpose of acquiring knowledge on the application to be implemented.
Hidden Markov Tree Model in Dependency-based Machine Translation

We would like to draw attention to Hidden Markov Tree Models (HMTM), which are to our knowledge still unexploited in the field of Computational Linguistics, in spite of highly successful Hidden Markov (Chain) Models. In dependency trees, the independence assumptions made by HMTM correspond to the intuition of linguistic dependency. Therefore we suggest to use HMTM and tree-modified Viterbi algorithm for tasks interpretable as labeling nodes of dependency trees. In particular, we show that the transfer phase in a Machine Translation system based on tectogrammatical dependency trees can be seen as a task suitable for HMTM. When using the HMTM approach for the English-Czech translation, we reach a moderate improvement over the baseline.
The Empirically Corrected EP-TOMS Total Ozone Data Against Brewer Measurements at El Arenosillo (Southwestern Spain)

This paper focuses on the validation of the empirically corrected total ozone column (TOC) data provided by the Earth Probe Total Ozone Mapping Spectrometer (EP-TOMS) using ground-based measurements recorded by a well-calibrated Brewer spectroradiometer located at El Arenosillo (Spain). In addition, satellite TOC observations derived from the Ozone Monitoring Instrument (OMI) with the TOMS algorithm are also used in this paper. The agreement between EP-TOMS TOC data and Brewer measurements is excellent (R2 ~ 0.92) even for the period 2000-2005 when a higher EP-TOMS instrument degradation occurred. Despite its low magnitude, the EP-TOMS-Brewer relative differences depend on the solar zenith angle (SZA), showing a clear seasonal cycle with amplitude between ±2% and ±4%. Conversely, OMI-Brewer relative differences show a constant negative value around -1% with no significant dependence on SZA. No significant dependence on the ground-based to satellite-based differences with respect to the EP-TOMS scene or to the OMI crosstrack position is observed for either satellite retrieval algorithm. Finally, TOC, estimated by the two satellite instruments, have also been compared, showing a good agreement (R2 ~ 0.88). Overall, we conclude that the empirical correction of the EP-TOMS data record provides a reprocessed set of high quality. However, EP-TOMS data after year 2000 should not be used in calculations of global-ozone trending due to remaining errors in the data set and because it is no longer an independent data set.