Miracle-dz/UniFAR-FTUs huggingface dataset:
A dose and time response Markov model for the in-host dynamics of infection with intracellular bacteria following inhalation: with application to Francisella tularensis

In a novel approach, the standard birth–death process is extended to incorporate a fundamental mechanism undergone by intracellular bacteria, phagocytosis. The model accounts for stochastic interaction between bacteria and cells of the immune system and heterogeneity in susceptibility to infection of individual hosts within a population. Model output is the dose–response relation and the dose-dependent distribution of time until response, where response is the onset of symptoms. The model is thereafter parametrized with respect to the highly virulent Schu S4 strain of Francisella tularensis, in the first such study to consider a biologically plausible mathematical model for early human infection with this bacterium. Results indicate a median infectious dose of about 23 organisms, which is higher than previously thought, and an average incubation period of between 3 and 7 days depending on dose. The distribution of incubation periods is right-skewed up to about 100 organisms and symmetric for larger doses. Moreover, there are some interesting parallels to the hypotheses of some of the classical dose–response models, such as independent action (single-hit model) and individual effective dose (probit model). The findings of this study support experimental evidence and postulations from other investigations that response is, in fact, influenced by both in-host and between-host variability.
Life-Cycle Cost Analysis of Pay Adjustment for Initial Smoothness of Asphalt Pavement Overlay

This study aims at developing pay adjustments for initial smoothness of asphalt pavement overlay using life-cycle cost analysis (LCCA). The relationship between the initial International Roughness Index (IRI) and pavement life based on the threshold of surface distress index (SDI) was developed to calculate the pay adjustment using LCCA. It was found that the terminal IRI values when pavement overlay life was reached based on the SDI threshold of poor condition had an average value of 128 in. /mile (2.02 m/km) with standard deviation of 15 in. /mile (0.24 m/km). The pay adjustments were significantly affected by the assumption of analysis period in LCCA considering single or successive overlay applications. The Bayesian approach with Markov Chain Monte Carlo (MCMC) methods was used to develop the probabilistic model between the expected pavement life and the initial IRI. The probabilistic distribution of pay adjustments was presented when the uncertainty was considered with respect to the effect of initial IRI on pavement life and the assumption of overlay sequence. Compared with the pay adjustment obtained from the deterministic approach, the probabilistic analysis resulted in a similar pay adjustment for the case of single overlay but a greater pay adjustment for the case of successive overlays. The proposed analysis approach can be implemented by agencies in decision making of quality assurance based on actual practice of maintenance strategy.
Robotically Assisted Laparoscopic Radical Hysterectomy Compared With Open Radical Hysterectomy

Background: Radical hysterectomy is a common and effective treatment of early cervical cancer. Modern advances include the use of robotic assistance to perform equivalent minimally invasive procedures. The purpose was to compare surgical and short-term outcomes, as well as margins, between robotic-assisted laparoscopic radical hysterectomy and open radical hysterectomy. Methods: The first 30 cases of robotically assisted type III radical hysterectomy for cervical cancer were compared with the 30 previous cases of open type III radical hysterectomy. Body mass index, length of operation, nodal yield, margins, estimated blood loss, hospital stay, and complications were all documented and compared. Results: The 30 patients undergoing robotically assisted laparoscopic radical hysterectomy were similar in body mass index to the women undergoing open radical hysterectomy (34 kg/m2 robotic, 32 kg/m2 open, P = 0.22). The mean operating time was 154 minutes compared with 166 minutes in the open arm (P = 0.36). The mean blood loss was 165 mL compared with 323 mL in the open arm (P = 0.001). The mean pelvic nodal yield was 25 nodes compared with 26 nodes in the open group (P = 0.45). The mean parametrial margin size was not significantly different between groups. The mean postoperative length of stay was 1.4 days compared with 2.8 days for the open cases (P < 0.001). Urinary retention was significantly more common in the robotic arm. Conclusions: Radical surgery for cervical cancer can be accomplished using the da Vinci surgical system (Intuitive Surgical, Sunnyvale, Calif) with acceptable blood loss, operating time, parametrial margins, and nodal yield. Future studies need to address long-term outcomes.
A qualitative study of health-related quality of life and psychosocial adjustments of Thai adolescents with repaired cleft lips and palates.

OBJECTIVE The purposes of the present study were (1) to study the meaning of Health-Related Quality of Life (HRQoL) from the insider's perspective and (2) to explore the relevant psychosocial adjustments involved in the HRQoL of Thai 12-to-17-year-old adolescents with repaired cleft lip and cleft palate (CLP). MATERIAL AND METHOD The study included a sample of 18 adolescents with non-syndromic repaired CLP and 6 parents of these adolescents. The participants were recruited from an orthodontic clinic in the Faculty of Dentistry, Mahidol University, and all were in-depth interviewed. RESULTS HRQoL can be categorized into four domains: physical symptoms,functional limitations, emotional well-being and social well-being. In the affected group they were striking differences in psychological assets, psychosocial resources and socioeconomic disparities. The majority of these participants were well-adjusted and able to cope with the adversities they experienced as a result of their conditions; hence it was noted that, participants with consistent support from parents,friends and professionals were likely to have a positive health status and satisfaction with treatment. CONCLUSION These findings have important implications in measuring a multidimensional HRQoL construct, and will enhance issues regarding adaptation strategies which have an impact on HRQoL of adolescents with CLP.
A COMPARATIVE STUDY OF ASYMMETRIC MIGRATION EVENTS ACROSS A MARINE BIOGEOGRAPHIC BOUNDARY

Abstract In many nonclonal, benthic marine species, geographic distribution is mediated by the dispersal of their larvae. The dispersal and recruitment of marine larvae may be limited by temperature gradients that can affect mortality or by ocean currents that can directly affect the movements of pelagic larvae. We focus on Point Conception, a well-known biogeographic boundary between the Californian and Oregonian biogeographic provinces, to investigate whether ocean currents affect patterns of gene flow in intertidal marine invertebrates. The predominance of pelagically dispersing species with northern range limits at Point Conception suggests that ocean currents can affect species distributions by erecting barriers to the dispersal of planktonic larvae. In this paper, we investigate whether the predominantly southward currents have left a recognizable genetic signature in species with pelagically dispersing larvae whose ranges span Point Conception. We use patterns of genetic diversity and a new method for inferring cladistic migration events to test the hypothesis that southward currents increase southward gene flow for species with pelagically dispersing larvae. We collected mitochondrial DNA (mtDNA) sequence data for the barnacles Balanus glandula and Chthamalus fissus and also reanalyzed a previously published mtDNA dataset (Strongylocentrotus purpuratus, Edmands et al. 1996). For all three species, our cladistic approach identified an excess of southward migration events across Point Conception. In data from a fourth species with nondispersing larvae (Nucella emarginata, Marko 1998), our method suggests that ocean currents have not played a role in generating genetic structure.
Analysis of software rejuvenation using Markov Regenerative Stochastic Petri Net

In a client-server type system, the server software is required to run continuously for very long periods. Due to repeated and potentially faulty usage by many clients, such software "ages" with time and eventually fails. (Huang et al., 1995) proposed a technique called "software rejuvenation" in which the software is periodically stopped and then restarted in a "robust" state after proper maintenance. This "renewal" of software prevents (or at least postpones) the crash failure. As the time lost (or the cost incurred) due to the software failure is typically more than the time lost (or the cost incurred) due to rejuvenation, the technique reduces the expected unavailability of the software. We present a quantitative analysis of software rejuvenation. The behavior of the system is represented through a Markov Regenerative Stochastic Petri Net (MRSPN) model which is solved both for steady state as well as transient conditions. We provide a closed-form analytical solution for the steady state expected down time (and the expected cost incurred) due to system unavailability. We also evaluate the optimal rejuvenation interval which minimizes the expected unavailability of the software.
3-Phenylcoumarins as Inhibitors of HIV-1 Replication

We have synthesized fourteen 3-phenylcoumarin derivatives and evaluated their anti-HIV activity. Antiviral activity was assessed on MT-2 cells infected with viral clones carrying the luciferase gene as reporter. Inhibition of HIV transcription and Tat function were tested on cells stably transfected with the HIV-LTR and Tat protein. Six compounds displayed NF-κB inhibition, four resulted Tat antagonists and three of them showed both activities. Three compounds inhibited HIV replication with IC50 values < 25 µM. The antiviral effect of the 4-hydroxycoumarin derivative 19 correlates with its specific inhibition of Tat functions, while compound 8, 3-(2-chlorophenyl)coumarin, seems to act through a mechanism unrelated to the molecular targets considered in this research.
Circulating Progenitor Cells and Vascular Dysfunction in Chronic Obstructive Pulmonary Disease

Background In chronic obstructive pulmonary disease (COPD), decreased progenitor cells and impairment of systemic vascular function have been suggested to confer higher cardiovascular risk. The origin of these changes and their relationship with alterations in the pulmonary circulation are unknown. Objectives To investigate whether changes in the number of circulating hematopoietic progenitor cells are associated with pulmonary hypertension or changes in endothelial function. Methods 62 COPD patients and 35 controls (18 non-smokers and 17 smokers) without cardiovascular risk factors other than cigarette smoking were studied. The number of circulating progenitors was measured as CD45+CD34+CD133+ labeled cells by flow cytometry. Endothelial function was assessed by flow-mediated dilation. Markers of inflammation and angiogenesis were also measured in all subjects. Results Compared with controls, the number of circulating progenitor cells was reduced in COPD patients. Progenitor cells did not differ between control smokers and non-smokers. COPD patients with pulmonary hypertension showed greater number of progenitor cells than those without pulmonary hypertension. Systemic endothelial function was worse in both control smokers and COPD patients. Interleukin-6, fibrinogen, high sensitivity C-reactive protein, vascular endothelial growth factor and tumor necrosis factor were increased in COPD. In COPD patients, the number of circulating progenitor cells was inversely related to the flow-mediated dilation of systemic arteries. Conclusions Pulmonary and systemic vascular impairment in COPD is associated with cigarette smoking but not with the reduced number of circulating hematopoietic progenitors. The latter appears to be a consequence of the disease itself not related to smoking habit.
Maximum likelihood: extracting unbiased information from complex networks.

The choice of free parameters in network models is subjective, since it depends on what topological properties are being monitored. However, we show that the maximum likelihood (ML) principle indicates a unique, statistically rigorous parameter choice, associated with a well-defined topological feature. We then find that, if the ML condition is incompatible with the built-in parameter choice, network models turn out to be intrinsically ill defined or biased. To overcome this problem, we construct a class of safely unbiased models. We also propose an extension of these results that leads to the fascinating possibility to extract, only from topological data, the "hidden variables" underlying network organization, making them "no longer hidden. " We test our method on World Trade Web data, where we recover the empirical gross domestic product using only topological information.
Anomaly Detection for Data Reduction in an Unattended Ground Sensor (UGS) Field

Abstract : This report describes the design and implementation of a data reduction technique for video sensors that are part of a larger unattended ground sensor (UGS) network. The data reduction technique is based on anomaly detection in full-motion video and subsequent statistical analysis techniques that allow the system to identify abnormal or otherwise interesting behavior that acts as a notification trigger. These techniques have been integrated into an existing distributed sensor framework at the US Army Research Laboratory (ARL) that is based on the Open Standards for Unattended Sensors (OSUS), developed in collaboration with the Defense Intelligence Agency (DIA). Furthermore, the statistical technique applied to this problem does not require any training data, which are often impractical in battlefield environments. Instead, it operates by being bootstrapped on mission profiles and templates established by the user and supplemented by incremental and online learning algorithms. Overall, these techniques combine to provide an effective approach to monitoring large distributed sensor fields without network and operator overload.
Chapter 1 Liver Biopsy-Indications , Procedures , Results

Liver biopsy (LB) is the most common procedure performed in clinical hepatology. His‐ tological assessment of the liver, and thus, LB is traditionally the “reference standard” in the diagnosis and management of parenchymal liver diseases. Definitive diagnosis of‐ ten depends on LB, and much of understanding of the characteristic features and natu‐ ral history of liver diseases is based on information obtained by serial liver biopsies. During the last 60 years as the result of a better understanding of liver disorders, ap‐ pearance of newer entities and advent of novel hepatic imaging techniques, the indica‐ tions for LB have evolved. Whereas in the past LB was often performed as the initial investigation in the workup of liver disease of unknown aetiology, today the most com‐ mon indication for LB includes staging of chronic hepatitis. A variety of methods exist for getting a liver tissue specimen. These take account of a percutaneous method, a transvenous (transjugular or transfemoral) approach, and intra-abdominal biopsy (laparo‐ scopic or laparotomic). All LB techniques require specific training so as to ensure appro‐ priate-sized specimen retrieval and the lowest rate of complications. However, because LB is an invasive procedure that carries a definite, albeit small, risk of complications, controversy persists with regard to its precise indications in various clinical situations, its clear contraindications, the optimal technique for its performance (and whether cer‐ tain modifications improve its safety), and training requirements for clinicians. The aim of this chapter will be summarize the existing clinical practice of LB with an emphasis on the technique, indications, contraindications, quality of LB specimens and risk of complications.
A novel location finding system for 3GPP LTE

We propose a novel location finding system exploiting the downlink reference signal of the Long Term Evolution (LTE) because of the absence of an efficient location finding system for the LTE. The proposed system is based on the correlation method and Chan's method for location sensing and positioning process, respectively. The conventional correlation method, however, is not matched to the LTE since the orthogonal gold sequence used for reference signal is assigned in frequency domain. Therefore, we estimate Time Difference Of Arrival (TDOA) data by cross-correlating the transmitted signal and received signal in the frequency domain. Simulation results show that the proposed system meets the Federal Communication Commission (FCC) requirement for typical Signal-to-Noise Ratio (SNR) region, and the performance can be further improved as more antennas are implemented in transmitter or receiver.
Collagen Fibrils Mechanically Contribute to Tissue Contraction in an In Vitro Wound Healing Scenario

Wound contraction is an ancient survival mechanism of vertebrates that results from tensile forces supporting wound closure. So far, tissue tension was attributed to cellular forces produced by tissue‐resident (myo‐)fibroblasts alone. However, difficulties in explaining pathological deviations from a successful healing path motivate the exploration of additional modulatory factors. Here, it is shown in a biomaterial‐based in vitro wound healing model that the storage of tensile forces in the extracellular matrix has a significant, so‐far neglected contribution to macroscopic tissue tension. In situ monitoring of tissue forces together with second harmonic imaging reveal that the appearance of collagen fibrils correlates with tissue contraction, indicating a mechanical contribution of tensioned collagen fibrils in the contraction process. As the re‐establishment of tissue tension is key to successful wound healing, the findings are expected to advance the understanding of tissue healing but also underlying principles of misregulation and impaired functionality in scars and tissue contractures.
Wideband Circularly Polarized Slotted-Patch Antenna With a Reflector

A design for wideband circularly polarized (CP) antennas with unidirectional radiation is described. The antenna structure is mainly composed of a rectangular slotted patch and a metallic reflector. First, an optimum CP design for the standalone slotted patch antenna is investigated, and a 3-dB-axial-ratio bandwidth of 53% is obtained. Then, the metallic reflector is placed at the rear of the slotted patch for generating unidirectional radiation, and the effects of various reflector sizes on CP performances are studied. Measured results show that the slotted patch antenna with a reflector has almost the same CP bandwidth as the standalone slotted patch antenna, and it has good impedance matching as well as stable radiation patterns across the CP operating frequencies.
Neural Signatures of Controlled and Automatic Retrieval Processes in Memory-based Decision-making

Decision-making often requires retrieval from memory. Drawing on the neural ACT-R theory [Anderson, J. R. , Fincham, J. M. , Qin, Y. , & Stocco, A. A central circuit of the mind. Trends in Cognitive Sciences, 12, 136–143, 2008] and other neural models of memory, we delineated the neural signatures of two fundamental retrieval aspects during decision-making: automatic and controlled activation of memory representations. To disentangle these processes, we combined a paradigm developed to examine neural correlates of selective and sequential memory retrieval in decision-making with a manipulation of associative fan (i.e., the decision options were associated with one, two, or three attributes). The results show that both the automatic activation of all attributes associated with a decision option and the controlled sequential retrieval of specific attributes can be traced in material-specific brain areas. Moreover, the two facets of memory retrieval were associated with distinct activation patterns within the frontoparietal network: The dorsolateral prefrontal cortex was found to reflect increasing retrieval effort during both automatic and controlled activation of attributes. In contrast, the superior parietal cortex only responded to controlled retrieval, arguably reflecting the sequential updating of attribute information in working memory. This dissociation in activation pattern is consistent with ACT-R and constitutes an important step toward a neural model of the retrieval dynamics involved in memory-based decision-making.
One‐Dimensional SDS Gel Electrophoresis of Proteins

Electrophoresis is used to separate complex mixtures of proteins (e.g., from cells, subcellular fractions, column fractions, or immunoprecipitates), to investigate subunit compositions, and to verify homogeneity of protein samples. It can also serve to purify proteins for use in further applications. In polyacrylamide gel electrophoresis, proteins migrate in response to an electrical field through pores in a polyacrylamide gel matrix; pore size decreases with increasing acrylamide concentration. The combination of pore size and protein charge, size, and shape determines the migration rate of the protein. In this unit, the standard Laemmli method is described for discontinuous gel electrophoresis under denaturing conditions, that is, in the presence of sodium dodecyl sulfate (SDS). Both full‐size and minigel formats are detailed. Several modifications are provided for specific applications. For separation of peptides and small proteins, the standard buffers are replaced with either a Tris‐tricine buffer system or a modified Tris buffer in the absence of urea. Continuous SDS‐PAGE is a simplified method in which the same buffer is used for both the gel and electrode solutions and the stacking gel is omitted. Other protocols cover the preparation and use of ultrathin gels and gradient gels, and the simultaneous preparation of multiple gels.
Learning Deep State Representations With Convolutional Autoencoders

Advances in artificial intelligence algorithms and techniques are quickly allowing us to create artificial agents that interact with the real world. However, these agents need to maintain a carefully constructed abstract representation of the world around them [9]. Recent research in deep reinforcement learning attempts to overcome this challenge. Mnih et al. [24] at DeepMind and Levine et al. [18] demonstrate successful methods of learning deep end-to-end policies from high-dimensional input. In addition, Böhmer et al. [1] and Mattner et al. [22] extract deep state representations that can be used with traditional value function approximation algorithms to learn policies. We present a model that discovers low-dimensional deep state representations in a similar fashion to the deep fitted Q algorithm [1]. A plethora of function approximation techniques can be used in the lower dimension space to obtain the Qfunction. To test our algorithms, we run several experiments on 80× 20 images taken from a 10 × 2 grid world and show that convolutional autoencoders can be trained to obtain deep state representations that are almost as good as knowing the ground-truth state.