Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-invasive mapping of fluid temperature and flow in microsystems

Currently available temperature and fluid flow measurement methods have shown limitations in microscale systems. This research concerns the development of a non-invasive optical measurement technique and sensor for mapping two-dimensional temperature fields and, ultimately fluid flows. The system is based on the Shack-Hartmann wave-front sensor. Analytical considerations underlying the mapping technique and preliminary experimental results are presented. Two experimental rigs involved in this study are also discussed.
A Bayesian Reformulation of the Extended Drift-Diffusion Model in Perceptual Decision Making

Perceptual decision making can be described as a process of accumulating evidence to a bound which has been formalized within drift-diffusion models (DDMs). Recently, an equivalent Bayesian model has been proposed. In contrast to standard DDMs, this Bayesian model directly links information in the stimulus to the decision process. Here, we extend this Bayesian model further and allow inter-trial variability of two parameters following the extended version of the DDM. We derive parameter distributions for the Bayesian model and show that they lead to predictions that are qualitatively equivalent to those made by the extended drift-diffusion model (eDDM). Further, we demonstrate the usefulness of the extended Bayesian model (eBM) for the analysis of concrete behavioral data. Specifically, using Bayesian model selection, we find evidence that including additional inter-trial parameter variability provides for a better model, when the model is constrained by trial-wise stimulus features. This result is remarkable because it was derived using just 200 trials per condition, which is typically thought to be insufficient for identifying variability parameters in DDMs. In sum, we present a Bayesian analysis, which provides for a novel and promising analysis of perceptual decision making experiments.
Memory consolidation from seconds to weeks: a three-stage neural network model with autonomous reinstatement dynamics

Declarative long-term memories are not created in an instant. Gradual stabilization and temporally shifting dependence of acquired declarative memories in different brain regions—called systems consolidation—can be tracked in time by lesion experiments. The observation of temporally graded retrograde amnesia (RA) following hippocampal lesions points to a gradual transfer of memory from hippocampus to neocortical long-term memory. Spontaneous reactivations of hippocampal memories, as observed in place cell reactivations during slow-wave-sleep, are supposed to drive neocortical reinstatements and facilitate this process. We propose a functional neural network implementation of these ideas and furthermore suggest an extended three-state framework that includes the prefrontal cortex (PFC). It bridges the temporal chasm between working memory percepts on the scale of seconds and consolidated long-term memory on the scale of weeks or months. We show that our three-stage model can autonomously produce the necessary stochastic reactivation dynamics for successful episodic memory consolidation. The resulting learning system is shown to exhibit classical memory effects seen in experimental studies, such as retrograde and anterograde amnesia (AA) after simulated hippocampal lesioning; furthermore the model reproduces peculiar biological findings on memory modulation, such as retrograde facilitation of memory after suppressed acquisition of new long-term memories—similar to the effects of benzodiazepines on memory.
A simple and efficient implemantation of interleaved boost converter

Recently, DC-DC boost converters are usually required in many applications which has low output voltage, such as renewable energy sources. The interleaved boost converters consists of several identical boost converters connected in parallel and controlled by the interleaved method which has the same switching frequency and phase shift. The advantages of interleaved boost converters include increased efficiency, reduced size and improved reliability. This paper presents, simple design and implementation of a two phase interleaved boost converter.
Efficacy of the Novel Antibiotic POL7001 in Preclinical Models of Pseudomonas aeruginosa Pneumonia

ABSTRACT The clinical development of antibiotics with a new mode of action combined with efficient pulmonary drug delivery is a priority against untreatable Pseudomonas aeruginosa lung infections. POL7001 is a macrocycle antibiotic belonging to the novel class of protein epitope mimetic (PEM) molecules with selective and potent activity against P. aeruginosa. We investigated ventilator-associated pneumonia (VAP) and cystic fibrosis (CF) as indications of the clinical potential of POL7001 to treat P. aeruginosa pulmonary infections. MICs of POL7001 and comparators were measured for reference and clinical P. aeruginosa strains. The therapeutic efficacy of POL7001 given by pulmonary administration was evaluated in murine models of P. aeruginosa acute and chronic pneumonia. POL7001 showed potent in vitro activity against a large panel of P. aeruginosa isolates from CF patients, including multidrug-resistant (MDR) isolates with adaptive phenotypes such as mucoid or hypermutable phenotypes. The efficacy of POL7001 was demonstrated in both wild-type and CF mice. In addition to a reduced bacterial burden in the lung, POL7001-treated mice showed progressive body weight recovery and reduced levels of inflammatory markers, indicating an improvement in general condition. Pharmacokinetic studies indicated that POL7001 reached significant concentrations in the lung after pulmonary administration, with low systemic exposure. These results support the further evaluation of POL7001 as a novel therapeutic agent for the treatment of P. aeruginosa pulmonary infections.
Regenerative potential and healing dynamics of the periodontium: a critical-size supra-alveolar periodontal defect study.

OBJECTIVES The nature and characteristics of the newly formed periodontium obtained following regenerative procedures remain a matter of controversy. The objective of this study was to evaluate the regenerative potential of the periodontal attachment and healing dynamics as observed from the spatial distribution of newly formed cementum, periodontal ligament (PDL) and alveolar bone following optimal circumstances for wound healing/regeneration in a discriminating animal model. MATERIAL AND METHODS Critical-size, 6-mm, supra-alveolar, periodontal defects were surgically created in six young adult Beagle dogs. Space-providing ePTFE devices with 300-microm laser-drilled pores were implanted to support wound stability and space provision in one jaw quadrant/animal. Treatments were alternated between left and right jaw quadrants in subsequent animals. The gingival flaps were advanced to submerge the defect sites for primary intention healing. Histometric analysis followed an 8-week healing interval. RESULTS Healing was uneventful in all animals. The histometric analysis showed that cementum regeneration (2.99 +/- 0.22 mm) was significantly greater than PDL (2.54 +/- 0.18 mm, p=0.03) and bone regeneration (2.46 +/- 0.26 mm, p=0.03). The wound area showed significant positive non-linear effect on cementum (log beta=1.25, p<0.001), PDL (log beta=1.24, p<0.001) and new bone formation (log beta=1.36, p<0.001). A high degree of concordance and significant linear relationship was observed between cementum, PDL and bone regeneration indicating that their formation virtually occurred in parallel. CONCLUSIONS Cementum, PDL and alveolar bone virtually regenerate in parallel under optimal circumstances for periodontal wound healing/regeneration. Moreover, space provision positively influences the extent of periodontal regeneration.
Algorithms for Molecular Biology

Background: Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient associations and are part of several complexes at different stages of a cellular process. A better understanding of this higher-order organization of proteins into overlapping complexes is an important step towards unveiling functional and evolutionary mechanisms behind biological networks. Results: We propose a new method for identifying and representing overlapping protein complexes (or larger units called functional groups ) within a protein interaction network. We develop a graph-theoretical framework that enables automatic construction of such representation. We illustrate the effectiveness of our method by applying it to TNF α /NF-κ B and pheromone signaling pathways. Conclusion: The proposed representation helps in understanding the transitions between functional groups and allows for tracking a protein's path through a cascade of functional groups. Therefore, depending on the nature of the network, our representation is capable of elucidating temporal relations between functional groups. Our results show that the proposed method opens a new avenue for the analysis of protein interaction networks.
Effects of therapeutic angiogenesis with plasmid VEGF165 on ventricular function in a canine model of chronic myocardial infarction.

OBJECTIVE Therapeutic angiogenesis is currently under investigation in ischemic heart disease. We examined the effect on left ventricular function induced by therapeutic angiogenesis by intramyocardial injection of plasmid VEGF(165), in a canine model of chronic myocardial infarction. METHODS Left thoracotomy was performed in 10 mongrel dogs, and myocardial infarction induced by ligation of the major diagonal coronary artery. At 7 postoperative (p.o.) day (pre-treatment), left ventricular ejection fraction was assessed by echocardiogram, and a second procedure was done: saline or plasmid VEGF(165) at 200 mg/mL was injected over 10 points of the ischemic areas of control or treated groups, respectively. Fourteen days later (post-treatment, day 21) a control echocardiogram was performed, the animals were sacrificed and histological examination was performed. RESULTS Ejection fraction was maintained in the treated group: 52.45 +/- 15.1% on day 7 and 48.53 +/-11.74% on day 21 (P=0.59), and tended to decrease in the control group, from 59.3 +/- 4% to 39.37 +/- 19.43% (P=0.04), although absolute values did not differ significantly between groups. Histological examination revealed a non significant increase in capillary vessels number in all areas in treated group. Paradoxically, arterioles were significantly less in number in all areas of treated dogs. CONCLUSION Intramyocardial injection of plasmid VEGF(165), in this canine model of chronic myocardial infarction, resulted in preservation of left ventricular ejection fraction, contrary to the control group where left ventricular ejection fraction showed continuous decline during the experiment. Histological examination, however, was unable to explain completely these results.
Comparison of permanent 125I seeds implants with two different techniques in 500 cases of prostate cancer

Purpose To perform a comparative study of 500 consecutive 125I seeds implants for intracapsular prostate carcinoma with two techniques differing in terms of both strand implantation and planning. Material and methods From 2002 to 2007 we performed 250 implants with fixed stranded seeds (RapidStrand™) and a preplanning system and from 2007 to 2010, 250 with real-time and ProLink™ system. Mean age was 68 and 66, respectively, median PSA (prostate-specific antigen) 7.3 and 7.2, stage T1-T2a in 98% and 94%, and Gleason ≤ 6 in 96% and 86%. Low risk cases were 81% and 71%. The prescribed dose was 145 Gy to the prostate volume, or 108 Gy plus EBRT 46 Gy in some intermediate risk cases. Hormonal treatment was given to 42% and 28%. Results Median follow-up was 48 and 47 months, respectively, 14 patients in the first group and 7 patients in the second developed biochemical failure (BF). Actuarial biochemical relapse-free survival (bRFS) at 5 years increased from 90.2% to 97.2% (low risk from 91.3% to 97.2%, intermediate risk from 84.2% to 97.1%). Biochemical failure was independent of hormone treatment. Rectal complications were G1-2 in 1.2% and 5.2%, respectively. A urinary catheter was necessary in 6.9% and 9.6%, and urethral resection in 1.9% and 4.4%. Genitourinary toxicity was G1-2 in 4.6% and 12%, G3-4 in 1.9% and 4.8%. An assessment of mean D90 in a sample of patients showed that the dosimetry in postoperative planning based on CT improved from a mean D90 of 143 Gy to 157 Gy. Conclusions The outcome of patients with low risk prostate carcinoma treated with 125I seed is very good with low complications rate. The real-time approach in our hands achieved a more precise seed implantation, better dosimetry, and a statistically non-significant better biochemical control. We have made this our standard technique.
pARIX: An index for causal induction as extended pARIs/JACCARD index

Intensity of human causal induction is expressed by statistical models in cognitive science. A statistical index, pARIs, which is one of the models of human causal induction, has good performance on some tests. The form of pARIs is nearly equal to one of Jaccard index. However, it has not been known yet why pARIs can be related to intensity of human causal induction. In this study, we propose pARIX (i.e. pARIs-eXtended), in which explanatory variables of pARIs are replaced from Bernoulli random variables to general continuous random variables. pARIX is applied to Gaussian random variables, and is compared with correlation coefficient and mutual information. Moreover, response of pARIX for parameter damping in which a cubic function gets close to a linear function is researched. When the given data pattern is regarded as the thing based on some function, high value of pARIX implies high degree of “single-valued-ness” and “injectivity (one-to-one-ness)” in neighborhood of a selected domain.
TO PEEL OR NOT TO PEEL THE INTERNAL LIMITING MEMBRANE IN IDIOPATHIC EPIRETINAL MEMBRANES

Background: Epiretinal membranes (ERMs) have been described for more than 150 years. Currently, they are a common indication for vitreoretinal surgery. Recently, there has been an increasing trend to peel the internal limiting membrane (ILM). Although ILM peeling has generally been accepted as a fundamental step in macular hole repair, its current role in ERM remains controversial. Methods: Literature review. Results: Proponents of ILM peeling argue that peeling of the ILM reduces the recurrence rate and facilitates a greater resolution of retinal folds. Opponents of ILM peeling show that the visual outcomes between eyes that undergo ILM peeling and those that do not have their ILM peeled are the same. Stripping of the ILM removes the Müller cell footplates, so it is reasonable to expect some Müller cell dysfunction. Adverse events such as eccentric paracentral macular holes, macular microscotomata, and retinal dimpling have been associated with ILM peeling. Conclusion: Internal limiting membrane peeling does not improve the functional outcomes after ERM surgery. Internal limiting membrane peeling reduces ERM recurrences, but many recurrences are not clinically significant. It remains unclear what the long-term effects of ILM peeling are. We should err on the side of caution and avoid routine ILM peeling in primary idiopathic ERM cases and should reserve it for recurrent and high risk of recurrence cases.
Defining internal target volume using positron emission tomography for radiation therapy planning of moving lung tumors

Substantial disagreement exists over appropriate PET segmentation techniques for non‐small cell lung cancer. Currently, no segmentation algorithm explicitly considers tumor motion in determining tumor borders. We developed an automatic PET segmentation model as a function of target volume, motion extent, and source‐to‐background ratio (the VMSBR model). The purpose of this work was to apply the VMSBR model and six other segmentation algorithms to a sample of lung tumors. PET and 4D CT were performed in the same imaging session for 23 patients (24 tumors) for radiation therapy planning. Internal target volumes (ITVs) were autosegmented on maximum intensity projection (MIP) of cine CT. ITVs were delineated on PET using the following methods: 15%, 35%, and 42% of maximum activity concentration, standardized uptake value (SUV) of 2.5 g/mL, 15% of mean activity concentration plus background, a linear function of mean SUV, and the VMSBR model. Predicted threshold values from each method were compared to measured optimal threshold values, and resulting volume magnitudes were compared to cine‐CT‐derived ITV Correlation between predicted and measured threshold values ranged from slopes of 0.29 for the simplest single‐threshold techniques to 0.90 for the VMSBR technique. R2 values ranged from 0.07 for the simplest single‐threshold techniques to 0.86 for the VMSBR technique. The VMSBR segmentation technique that included volume, motion, and source‐to‐background ratio, produced accurate ITVs in patients when compared with cine‐CT‐derived ITV. PACS number: 87.57. nm
System-level reliability exploration framework for heterogeneous MPSoC

Power density of digital circuits increased at alarming rate for deep sub-micron CMOS technology, turning reliability into a serious design concern. On the other hand, ever-growing task complexity with strict performance budget forced designers to adopt complex, heterogeneous MPSoCs as the implementation choice. Several commercial system-level design platforms exist currently for design, exploration and implementation of MPSoC. In this paper, we propose a system-level reliability exploration framework by extending a commercial system-level design flow. Using this framework, a heterogeneous MPSoC is designed which can accept a custom mapping algorithm based on the MPSoC topology before the actual task deployment. The dynamic reliability-aware task management is able to consider the desired reliability constraints of tasks as well as reliability levels of the system components. We report our experimental findings using state-of-the-art benchmark applications.
Usage of agents in document management

EXtensible Java-based Agent Framework (XJAF) is a pluggable architecture of the hierarchical intelligent agents system with communication based on KQML. Workers, Inc. is a workflow management system implemented using mobile agents. It is especially suited for highly distributed and heterogeneous environments. The application of the above-mentioned systems will be considered in the area of Document Management Systems.
Using Homologous Recombination to Manipulate the Genome of Human Somatic Cells

Abbreviations: rAAV, recombinant adeno-associated virus; DNA, deoxyribonucleic acid; DSBs, doublestrand breaks; SDSA, synthesis dependent strand annealing; ES, embryonic stem; ESC, embryonic stem cell; HPRT, hypoxanthine phosphoribosyltransferase; HAT, hypoxanthine-aminopterin-thymidine; ITR, inverted terminal repeat; bp, basepair; ZFN, zinc finger nuclease; SCID, severe combined immunodeficiency. Biotechnology and Genetic Engineering Reviews Vol. 24, 195-212 (2007)
Black box for constant-time insertion in priority queues (note)

We present a simple black box that takes a priority queue <i>Q</i> which supports find-min, insert, and delete in x-time at most <i>t</i>. Here x-time may be worst-case, expected, or amortized. The black-box transforms <i>Q</i> into a priority queue <i>Q</i>* that supports find-min in constant time, insert in constant x-time, and delete in x-time <i>O</i>(<i>t</i>). Moreover, if <i>Q</i> supports dec-key in constant time, then so does <i>Q</i>*.
Rational Krylov subspace method (RKSM) for solving the Lyapunov equations of index-1 descriptor systems and application to balancing based model reduction

This paper focuses on the iterative method for solving Lyapunov equations to compute the low-rank Gramian factors. Such Lyapunov equations arise from large-scale sparse index-1 descriptor system. The technique is mainly based on rational Krylov subspace method (RKSM) which is introduced in [1]. However, there the proposed technique is applicable for the standard state space model. Here, we extend this idea for index-1 descriptor system to compute the low-rank Gramian factors. The Gramian factors are then applied to the balancing based model reduction to reduce the complexity of the underlying system. Several test examples are considered to show the efficiency of the proposed method numerically.
Improving Patient Safety of Acute Care Lumbar Punctures

Abstract Lumbar puncture (LP) is a common invasive procedure in the acute medical setting but is not without its risks and complications, making best clinical practice and correct documentation important for patient safety. Previous audit revealed poor levels of consistency in technique and documentation in the acute medical setting, highlighting it as an area for improvement. This project aims to identify current levels of documentation and improve upon these through the departmental education and the introduction of a documentation tool to create a safer clinical environment for LPs. Gold standards in clinical practice were identified through literature review and national guidelines, establishing 15 key parameters as essential areas for documentation. Patient notes were retrospectively analysed after LP over a two month period to identify levels of documentation in these areas, and the clinical technique used. Results of this initial audit were presented to the department along with an education session regarding current evidence based best practice for LPs and the important aspects relating to patient safety. A documentation tool was also introduced. A re-audit was then performed of the same parameters and assessing the use of the documentation tool. Results showed a significant increase in overall documentation from 44% up to 95% after intervention, with 85% of cases using the new proforma. We can conclude that the introduction of a documentation tool and departmental education has significantly improved upon LP documentation in the acute medical setting. This is important for both the protection of medical professionals, as well as patient safety and quality of care, and could be implemented in other clinical environments.
MiR-1271 Inhibits Ovarian Cancer Growth by Targeting Cyclin G1

Background Ovarian cancer is the most lethal gynecological malignant cancer in the female genital system. The dysfunction of miRNA contributes to ovarian cancer development. Material/Methods The miR-1271 level in ovarian cancer tissues and cells was assayed by qRT-PCR. The miR-1271 expression in cells was overexpressed by miRNA-mimic transfection and reduced by miRNA-antisense-oligonucleotide (ASO) transfection. Cell proliferation was analyzed by an MTT assay. The targeted genes were predicted by a bioinformatics algorithm and confirmed by a dual luciferase reporter assay. The protein level was assayed by Western blotting. Results The ovarian cancer tissue and cell lines showed low levels of miR-1271. Low levels of miR-1271 in ovarian cancer tissues were correlated with a low rate of patient survival, and the overexpression of miR-1271 inhibited the proliferation of ovarian cancer cells. The 3′ UTR of cyclin G1 (CCNG1) was targeted by miR-1271. Conclusions Low levels of miR-1271 in ovarian cancer tissues promoted cancer cell growth. MiR-1271 may be a new predictor of prognosis in ovarian cancer. MiR-1271 exerted its role by targeting CCNG1.