Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelers' Perception of Mathematical Modeling in Epidemiology: A Web-Based Survey

BACKGROUND Mathematical modeling in epidemiology (MME) is being used increasingly. However, there are many uncertainties in terms of definitions, uses and quality features of MME. METHODOLOGY/PRINCIPAL FINDINGS To delineate the current status of these models, a 10-item questionnaire on MME was devised. Proposed via an anonymous internet-based survey, the questionnaire was completed by 189 scientists who had published in the domain of MME. A small minority (18%) of respondents claimed to have in mind a concise definition of MME. Some techniques were identified by the researchers as characterizing MME (e.g. Markov models), while others-at the same level of sophistication in terms of mathematics-were not (e.g. Cox regression). The researchers' opinions were also contrasted about the potential applications of MME, perceived as highly relevant for providing insight into complex mechanisms and less relevant for identifying causal factors. The quality criteria were those of good science and were not related to the size and the nature of the public health problems addressed. CONCLUSIONS/SIGNIFICANCE This study shows that perceptions on the nature, uses and quality criteria of MME are contrasted, even among the very community of published authors in this domain. Nevertheless, MME is an emerging discipline in epidemiology and this study underlines that it is associated with specific areas of application and methods. The development of this discipline is likely to deserve a framework providing recommendations and guidance at various steps of the studies, from design to report.
Analysis of the human immunodeficiency virus type 1 M group Vpu domains involved in antagonizing tetherin

Zoonosis of chimpanzee simian immunodeficiency virus cpz to humans has given rise to both pandemic (M) and non-pandemic (O, N and P) groups of human immunodeficiency virus type-1 (HIV). These lentiviruses encode accessory proteins, including Vpu, which has been shown to reduce CD4 levels on the cell surface, as well as increase virion release from the cell by antagonizing tetherin (CD317, BST2). Here, we confirm that O group Vpus (Ca9 and BCF06) are unable to counteract tetherin or downregulate the protein from the cell surface, although they are still able to reduce cell-surface CD4 levels. We hypothesize that this inability to antagonize tetherin may have contributed to O group viruses failing to achieve pandemic levels of human-to-human transmission. Characterization of chimeric O/M group Vpus and Vpu mutants demonstrate that the Vpu–tetherin interaction is complex, involving several domains. We identify specific residues within the transmembrane proximal region that, along with the transmembrane domain, are crucial for tetherin counteraction and enhanced virion release. We have also shown that the critical domains are responsible for the localization of M group Vpu to the trans-Golgi network, where it relocalizes tetherin to counteract its function. This work sheds light on the acquisition of anti-tetherin activity and the molecular details of pandemic HIV infection in humans.
Duration of Nocturnal Hypoglycemia Before Seizures

OBJECTIVE—Despite a high incidence of nocturnal hypoglycemia documented by the use of continuous glucose monitoring (CGM), there are no reports in the literature of nocturnal hypoglycemic seizures while a patient is wearing a CGM device. RESEARCH DESIGN AND METHODS—In this article, we describe four such cases and assess the duration of nocturnal hypoglycemia before the seizure. RESULTS—In the cases where patients had a nocturnal hypoglycemic seizure while wearing a CGM device, sensor hypoglycemia (<60 mg/dl) was documented on the CGM record for 2.25–4 h before seizure activity. CONCLUSIONS—Even with a subcutaneous glucose lag of 18 min when compared with blood glucose measurements, glucose sensors have time to provide clinically meaningful alarms. Current nocturnal hypoglycemic alarms need to be improved, however, since patients can sleep through the current alarm systems.
The effect of morphine on formalin‐evoked behaviour and spinal release of excitatory amino acids and prostaglandin E2 using microdialysis in conscious rats

1 In the present study, the object was to examine the effects of morphine on spinal release in vivo of excitatory amino acids (EAA), prostaglandin E2 (PGE2), and a marker for nitric oxide (NO) synthesis, citrulline (Cit), evoked by a protracted noxious stimulus produced by the injection of formalin into the paw. Spinal release was monitored in conscious rats using a microdialysis probe implanted into the subarachnoid space with the active site placed at the level of the lumbar enlargement. In split dialysate samples, EAAs were measured by high performance liquid chromatography (h.p.l.c.) and PGE2 was determined by radioimmunoassay. 2 Resting concentrations in nmol ml−1 for the amino acids (mean ± s.e.mean, n = 21) were: 4.8 ± 0.4 for glutamate (Glu), 0.8 ± 0.1 for aspartate (Asp), 8.8 ± 0.8 for taurine (Tau), 24 ± 3 for glycine (Gly), 19 ± 3 for serine (Ser), 5.2 ± 0.8 for asparagine (Asn), 64 ± 4 for glutamine (Gln) and 5.2 ± 0.4 for Cit. Mean basal release for PGE2 was 12 ± 1 pmol ml−1. 3 Subcutaneous (s.c.) injection of 5% formalin evoked a biphasic flinching behaviour (phase 1: 0–9 min and phase 2: 10–60 min) of the injected paw. Corresponding to phase 1 behaviour, there was a significant increase (50–100%) in spinal levels of Glu, Asp, Tau, Gly, Cit and PGE2, but not Ser, Asn and Gln. A significant (P<0.01) second phase increase in release was observed only for Cit and PGE2. However, Glu and Asp levels were increased by approximately 45%. 4 Injection of morphine sulphate (3 mg kg−1, s.c.) had no effect on resting release, but produced a significant suppression of the formalin‐evoked behaviour and release of Glu, Asp, Tau, Gly, Cit and PGE2. The effect of morphine was reversed by pretreatment with 1 mg kg−1 naloxone. Naloxone by itself did not change the release or behaviour of the formalin test. 5 This study demonstrates that both spinal EAA and PGE2 release patterns correlate with behavioural nociceptive responses in the formalin test and that morphine suppresses the formalin‐evoked behaviours and spinal release. The reversal by naloxone of the morphine effect indicates mediation via an opioid receptor.
Synthesis of Reduced Equivalent Circuits for Transmission Lines

This paper presents a method for generating lumped models for symmetrical transmission-line two-ports. These models consist of an ideal transformer and frequency-domain approximations for two physical driving-point impedances. The lumped element values are obtained directly from the distributed parameters or propagation constant and characteristic impedance. The method is applied to dispersive transmission lines, skin effect and waveguides. It is shown that the equivalent circuit is superior in accuracy and number of elements compared to spatial discretizations like ladder approximation
How Can Regulators Set Nonarbitrary Interim Rates? The Case of Local Loop Unbundling in Ireland

During a period of substantial regulatory change, as in the case of network unbundling in telecommunications, regulators often face the challenge of setting “interim” rates for services. How, in the face of inherently imperfect information and the need to proceed according to what is invariably an expeditious plan of deregulation or industry restructuring, can the regulator select an interim rate that is the least arbitrary? In this Article, we answer that questions using, as a case study, local loop unbundling (LLU) in the Republic of Ireland in 2001. We analyze the interim prices set by the Office of the Director of Telecommunications Regulation (ODTR) for access by competitors to the local network of the incumbent carrier, eircom. The ODTR's interim prices are based on a simple average of the prices in ten European Union countries for the same service. That methodology is flawed because, with minimal effort, the regulator could have used publicly available data to produce a considerably less arbitrary interim rate. A simple average does not produce good in-sample predictions when the sample variance is large relative to the sample mean – as is the case with the prices of unbundled loops in the EU countries. Using a simple multiple regression model, we find that the ODTR's methodology ignores relevant information, such as population, wage rate, population density, and the degree of urbanization, which, in a sample of the fifty U.S. states and ten European countries, explains roughly 25 percent of the cross-sectional variation in unbundled loop prices over and above that which can be explained by the sample mean alone. The regression model would produce an interim rate that is 42 percent higher than the rate set by the ODTR. Finally, we observe that interim rates that impose artificially low pricing of unbundled network elements will discourage facilities-based investment, to the long-run detriment of consumers.
Derivative based control for LPV system with unknown parameters: An application on a Permanent Magnet Synchronous Motors

This paper deals with the robust stabilization of a class of Linear Parameter Varying (LPV) systems in the continuous time case. Instead of using a state observer or searching for a dynamic output feedback, the controller is based on output derivative estimation. This allows the stabilization of the plant with very large parameter variation and uncertainties. The proof of stability is based on the polytopic representation of the closed loop, Lyapunov conditions and system transformations. The result is a control structure with only few parameters which are tuned via very simple conditions. This paper illustrates the usefulness on real application: Permanent Magnet Synchronous Motors (PMSM) position control.
Anisotropy of cell adhesive microenvironment governs cell internal organization and orientation of polarity

Control of the establishment of cell polarity is an essential function in tissue morphogenesis and renewal that depends on spatial cues provided by the extracellular environment. The molecular role of cell–cell or cell–extracellular matrix (ECM) contacts on the establishment of cell polarity has been well characterized. It has been hypothesized that the geometry of the cell adhesive microenvironment was directing cell surface polarization and internal organization. To define how the extracellular environment affects cell polarity, we analyzed the organization of individual cells plated on defined micropatterned substrates imposing cells to spread on various combinations of adhesive and nonadhesive areas. The reproducible normalization effect on overall cell compartmentalization enabled quantification of the spatial organization of the actin network and associated proteins, the spatial distribution of microtubules, and the positioning of nucleus, centrosome, and Golgi apparatus. By using specific micropatterns and statistical analysis of cell compartment positions, we demonstrated that ECM geometry determines the orientation of cell polarity axes. The nucleus–centrosome orientations were reproducibly directed toward cell adhesive edges. The anisotropy of the cell cortex in response to the adhesive conditions did not affect the centrosome positioning at the cell centroid. Based on the quantification of microtubule plus end distribution we propose a working model that accounts for that observation. We conclude that, in addition to molecular composition and mechanical properties, ECM geometry plays a key role in developmental processes.
Using a Mixed IRT Model to Assess the Scale Usage in the Measurement of Job Satisfaction

This study investigated the adequacy of a rating scale with a large number of response categories that is often used in panel surveys for assessing diverse aspects of job satisfaction. An inappropriate scale usage is indicative of overstraining respondents and of diminished psychometric scale quality. The mixed Item Response Theory (IRT) approach for polytomous data allows exploring heterogeneous patterns of inappropriate scale usage in form of avoided categories and response styles. In this study, panel data of employees (n = 7036) on five aspects of job satisfaction measured on an 11-point rating scale within the “Household, Income and Labor Dynamics in Australia” (wave 2001) were analyzed. A three-class solution of the restricted mixed generalized partial credit model fit the data best. The results showed that in no class the 11-point scale was appropriately used but that the number of categories used was reduced in all three classes. Respondents of the large class (40%) appropriately differentiate between up to six categories. The two smaller classes (33 and 27%) avoid even more categories and show some kind of extreme response style. Furthermore, classes differ in socio-demographic and job-related factors. In conclusion, a two- to six-point scale without the middle point might be more adequate for assessing job satisfaction.
Observer-based quantized output feedback control of nonlinear systems

This paper addresses the problem of stabilizing a nonlinear system by means of quantized output feedback. A framework is presented in which the control input is generated by an observer-based feedback controller acting on quantized output measurements. A stabilization result is established under the assumption that this observer-based controller possesses robustness with respect to output measurement errors in an input-to-state stability (ISS) sense. Designing such observers and controllers is a largely open problem, some partial results on which are discussed. The main goal of the paper is to encourage further work on this important topic.
Nocturnal oscillations: Understanding the brain through sleep

This thesis explores the nature of sleep oscillations using behavioral and neurophysiological measures. The first experiment examines how the magnitude of different spectral frequencies in the sleep electroencephalography affect individual’s subjective emotional experience of positive and negative moods, as well as the emotional detriment associated with a full night of sleep deprivation, and its recovery after a daytime nap. The change in positive and negative moods across a night’s sleep is predicted by the magnitude of different oscillatory activity during rapid-eye-movement (REM) and non-REM (NREM) sleep. Experiment 2 uses EEG with simultaneous functional magnetic resonance imaging (fMRI) to examine the blood oxygen level dependent (BOLD) signal changes associated with sleep stage changes, and specifically investigates the functional connectivity changes within the basal ganglia network that occur across an early, slow-wave-rich sleep cycle. In NREM sleep, the functional connectivity of the globus pallidus and the striatum (composed of the putamen and caudate nucleus) show patterns supporting the tripartite division model, and lend support to existing studies of information processing during sleep, especially in the motor domain. Experiment 3 seeks to validate the hypothesis that different frequencies of oscillatory activity within the brain will differentially modulate the spatial profile of BOLD activity. This is achieved with applying transcranial alternating current stimulation (tACS) during fMRI acquisition, by artificially inducing oscillations of different frequencies in the brain while measuring the BOLD signal changes associated with the oscillatory activity. Stimulation to the primary visual cortex led to BOLD activity increases, relative to baseline, in different neural networks depending on the frequency of stimulation. The three experiments presented in the thesis shed light on the nature of neural network modulations caused by ongoing oscillatory activity, and bridge the gap between electrophysiological and haemodynamic findings of sleep-dependent information processing.
A General Boosting Method and its Application to Learning Ranking Functions for Web Search

We present a general boosting method extending functional gradient boosting to optimize complex loss functions that are encountered in many machine learning problems. Our approach is based on optimization of quadratic upper bounds of the loss functions which allows us to present a rigorous convergence analysis of the algorithm. More importantly, this general framework enables us to use a standard regression base learner such as single regression tree for fitting any loss function. We illustrate an application of the proposed method in learning ranking functions for Web search by combining both preference data and labeled data for training. We present experimental results for Web search using data from a commercial search engine that show significant improvements of our proposed methods over some existing methods.
Wideband radio propagation modeling for indoor geolocation applications

A framework for statistical modeling of the wideband characteristics of the frequency-selective fading multipath indoor radio channel for geolocation applications is presented. Multipath characteristics of the channel are divided into three classes according to availability and the strength of the direct line of sight (DLOS) path with respect to the other paths. Statistics of the error in estimating the time of arrival of the DLOS path in a building is related to the receiver's sensitivity and dynamic range. The effects of external walls on estimating the location of the DLOS path are analyzed.
Agreement between Electrocardiogram and Heart Rate Meter Is Low for the Measurement of Heart Rate Variability during Exercise in Young Endurance Horses

Analysis of the heart rate variability (HRV) gains more and more importance in the assessment of training practice and welfare in equine industry. It relies on mathematical analyses of reliably and accurately measured variations in successive inter-beat intervals, measured as RR intervals. Nowadays, the RR intervals can be obtained through two different techniques: a heart rate meter (HRM) or an electrocardiogram (ECG). The agreement and reliability of these devices has not been fully assessed, especially for recordings during exercise. The purpose of this study was to assess the agreement of two commercially available devices using the two mentioned techniques (HRM vs ECG) for HRV analysis during a standardized exercise test. Simultaneous recordings obtained during light exercise and during canter with both devices were available for 36 horses. Data were compared using a Bland–Altman analysis and the Lin’s coefficient. The agreement between the assessed HRV measures from the data obtained from the ECG and HRM was acceptable only for the mean RR interval and the mean heart rate. For the other studied measures (SDNN, root mean square of successive differences, SD1, SD2, low frequency, high frequency), the agreement between the devices was too poor for them to be considered as interchangeable in these recording conditions. The agreement tended also to be worse when speed of the exercise increased. Therefore, it is necessary to be careful when interpreting and comparing results of HRV analysis during exercise, as the results will depend upon recording devices. Furthermore, corrections and data processing included in the software of the devices affect largely the output used in the subsequent HRV analysis; this must be considered in the choice of the device.
‘Do we all get a PhD?' Attempting emancipatory research relating to disability in an academic environment.Relating to disability in an academic environment

Within the model of emancipatory research, the researcher is situated as one member of a team. They are often conceptualised as providing methodological tools and skills to others involved in the research project but the definition of topic, data analysis and dissemination is presented as a joint enterprise. This model of research (deliberately) contradicts with the view of the expert researcher prevalent within higher education establishments and particularly with the individualised construction of research degrees such as PhDs which requires a thesis to be the exclusive product of one individual. The paper discusses attempts which have been made to reconcile the tensions inherent in adopting an emancipatory model within an academic environment including our own experiences of researching and supervising a doctoral thesis on citizenship and disability. The project is led by an advisory panel of disabled people who are involved in the preparation, selection and analysis of the interviews and pragmatic aspects of attempting such an emancipatory model of research from the viewpoint of the entire research team. It raises the question as to whether such models can only be completely adhered to in particular, probably non-academic settings.
Reducing task creation and termination overhead in explicitly parallel programs

There has been a proliferation of task-parallel programming systems to address the requirements of multicore programmers. Current production task-parallel systems include Cilk++, Intel Threading Building Blocks, Java Concurrency, . Net Task Parallel Library, OpenMP 3.0, and current research task-parallel languages include Cilk, Chapel, Fortress, X10, and Habanero-Java (HJ). It is desirable for the programmer to express all the parallelism intrinsic to their algorithm in their code for forward scalability and portability, but the overhead incurred by doing so can be prohibitively large in today's systems. In this paper, we address the problem of reducing the total amount of overhead incurred by a program due to excessive task creation and termination. We introduce a transformation framework to optimize task-parallel programs with finish, forall and next statements. Our approach includes elimination of redundant task creation and termination operations as well as strength reduction of termination operations (finish) to lighter-weight synchronizations (next). Experimental results were obtained on three platforms: a dual-socket 128-thread (16-core) Niagara T2 system, a quad-socket 16-way Intel Xeon SMP and a quad-socket 32-way Power7 SMP. The results showed maximum speedup of 66.7×, 11.25× and 23.1× respectively on each platform and 4.6×, 2.1× and 6.4×performance improvements respectively in geometric mean related to non-optimized parallel codes. The original benchmarks in this study were written with medium-grained parallelism; a larger relative improvement can be expected for programs written with finer-grained parallelism. However, even for the medium-grained parallel benchmarks studied in this paper, the significant improvement obtained by the transformation framework underscores the importance of the compiler optimizations introduced in this paper.
WiFi Network Virtualization to Control the Connectivity of a Target Service

This paper proposes a WiFi network virtualization technique to control the connectivity of a target service. The packet-level delay violation ratio can be reduced even in a congested situation by provisioning dedicated base station (BS) resources (a set of dedicated BSs) to the target service and allowing only the corresponding terminals to associate with the BSs. The proposed technique is novel in that BSs are specially configured to use the same MAC address, and thus all the decisions on BS selection and handover are separated from those BSs and terminals and are put together into a centralized controller, while consistent layer-2 data paths in a backhaul network are also cooperatively configured. Simulation results show that the proposed technique can control the delay violation ratio of a target VoIP service and keep the ratio extremely low and comparable to that under IEEE 802.11e. A proof-of-concept prototype including two multi-channel virtualization-capable WiFi BSs and a BS switch is developed using off-the-shelf WiFi modules and a commercial OpenFlow switch. Experimental results show that the terminals can make a handover to a dedicated BS in less than 65 ms without any packet drop and association break, and confirm that the effect of the managed handover is limited even in a VoIP application.