Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a Feruloyl Esterase from Lactobacillus plantarum

ABSTRACT Lactobacillus plantarum is frequently found in the fermentation of plant-derived food products, where hydroxycinnamoyl esters are abundant. L. plantarum WCFS1 cultures were unable to hydrolyze hydroxycinnamoyl esters; however, cell extracts from the strain partially hydrolyze methyl ferulate and methyl p-coumarate. In order to discover whether the protein Lp_0796 is the enzyme responsible for this hydrolytic activity, it was recombinantly overproduced and enzymatically characterized. Lp_0796 is an esterase that, among other substrates, is able to efficiently hydrolyze the four model substrates for feruloyl esterases (methyl ferulate, methyl caffeate, methyl p-coumarate, and methyl sinapinate). A screening test for the detection of the gene encoding feruloyl esterase Lp_0796 revealed that it is generally present among L. plantarum strains. The present study constitutes the description of feruloyl esterase activity in L. plantarum and provides new insights into the metabolism of hydroxycinnamic compounds in this bacterial species.
Mapping-varied modulation with labeling optimization for secure transmission in mode-division-multiplexed fiber-optic systems

To improve the physical-layer security of mode-division multiplexing (MDM) systems, a simple security scheme named mapping-varied modulation (MVM) is proposed in this paper by combining cryptographic and information-theoretic security. Specifically, on top of the information-theoretic security provided by the less-conditioned wiretap channel due to the larger mode-dependent loss induced by fiber-bend tapping, the proposed MVM security method varies the mapping rules of the adopted constellations for the subchannels (one subchannel corresponds to one mode) by using the inherently time-varying random channel state information (CSI) of the MDM fiber, under the assumption that an eavesdropper does not know the exact instantaneous CSI of the legitimate link. To maximize the difference among the binary labels of the constellation points in the same position for each subchannel, a labeling optimization method is proposed as well. Numerical results demonstrate the effectiveness of the proposed MVM method via bit-error ratio performance and secrecy rate, showing a potential way to improve the security of the MDM link for high-speed data transmission.
Association Between Highly-Sensitive C- Reactive Protein and Neutrophil to Lymphocyte Ratio as Markers of Inflammation Among Adult Nigerians with Essential Hypertension

Background: Hypertension is a medical condition with global public health importance that is associated with significant morbidity and mortality in both developed and developing countries. It is important to identify readily available parameters that may indicate the level of inflammation that is associated with hypertension. Objective: To assess the relationship between highly-sensitive C-Reactive Protein (hs-CRP) and neutrophil-to-lymphocyte ratio (NLR) in hypertensive adults. Methods: Three hundred and sixty adults comprising 240 hypertensive and 120 healthy normotensive subjects (control) were studied. The full blood count (FBC) and highly-sensitive C-Reactive Protein (hs-CRP) levels were determined using standard methods. Results: The mean values of Total White Blood Cells count (WBC) (p = 0.03), absolute neutrophil count (p = 0.03), absolute lymphocyte count (p = 0.01), NLR (p = 0.001) and hs-CRP (p <0.001) in the hypertensive subjects were significantly higher than in the normotensive subjects. The mean values also differed significantly with increasing severity of hypertension. There was a significant but weak positive correlation between NLR and hs-CRP (r = 0.248, p <0.001). The Areas Under the Curve (AUC) of the Receiver Operating Characteristic (ROC) of NLR and hs-CRP (p = 0.01) were 0.68 and 0.639 respectively. Conclusion: NLR is closely associated with hs- CRP among hypertensive subjects. Therefore, NLR may be utilised routinely instead of hs-CRP as a screening test for inflammation in essential hypertension.
optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks

Constraint-based models of metabolic networks are typically underdetermined, because they contain more reactions than metabolites. Therefore the solutions to this system do not consist of unique flux rates for each reaction, but rather a space of possible flux rates. By uniformly sampling this space, an estimated probability distribution for each reaction’s flux in the network can be obtained. However, sampling a high dimensional network is time-consuming. Furthermore, the constraints imposed on the network give rise to an irregularly shaped solution space. Therefore more tailored, efficient sampling methods are needed. We propose an efficient sampling algorithm (called optGpSampler), which implements the Artificial Centering Hit-and-Run algorithm in a different manner than the sampling algorithm implemented in the COBRA Toolbox for metabolic network analysis, here called gpSampler. Results of extensive experiments on different genome-scale metabolic networks show that optGpSampler is up to 40 times faster than gpSampler. Application of existing convergence diagnostics on small network reconstructions indicate that optGpSampler converges roughly ten times faster than gpSampler towards similar sampling distributions. For networks of higher dimension (i.e. containing more than 500 reactions), we observed significantly better convergence of optGpSampler and a large deviation between the samples generated by the two algorithms. Availability: optGpSampler for Matlab and Python is available for non-commercial use at: http://cs.ru. nl/~wmegchel/optGpSampler/.
Synergistic induction of apoptosis in human myeloid leukemia cells by phorbol 12-myristate 13-acetate and flavopiridol proceeds via activation of both the intrinsic and tumor necrosis factor-mediated extrinsic cell death pathways.

Previous studies have shown that coexposure to marginally toxic concentrations of phorbol 12-myristate 13-acetate (PMA; 10 nM) and the cyclin-dependent kinase inhibitor flavopiridol (FP; 100-200 nM) synergistically induces apoptosis in human myeloid leukemia cells U937 and HL-60 (i.e., >50% apoptotic at 24 h). Attempts have now been made to characterize the cell death pathway(s) involved in this phenomenon. In contrast to cytochrome c release and caspase-3 activation, which occur within 2.5 h of PMA/FP coexposure, caspase-8 activation and Bid cleavage appeared as later events. Such findings implicate the mitochondria-dependent pathway in the initial induction of apoptosis by PMA/FP. However, U937 cells ectopically expressing CrmA, dominant-negative caspase-8, or dominant-negative Fas-associated death domain that were highly resistant to tumor necrosis factor (TNF)/cycloheximide-induced lethality displayed significant, albeit incomplete, resistance to PMA/FP-induced apoptosis after 24 h. Furthermore, coadministration of TNF soluble receptor significantly attenuated PMA/FP-induced apoptosis in U937 (p < 0.02) and HL-60 (p < 0.03) cells at 24 h. PMA/FP coadministration also triggered substantial increases in TNFalpha mRNA and protein secretion compared with the effects of PMA administered alone. The protein kinase C (PKC) inhibitor bisindolylmaleimide (1 microM) completely blocked PMA/FP-induced TNFalpha secretion in U937 cells and attenuated apoptosis. Taken together, these results suggest that coadministration of PMA with FP in myeloid leukemia cells initially triggers mitochondrial damage, an event followed by the PKC-dependent induction and release of TNFalpha, supporting a model in which the synergistic induction of leukemic cell apoptosis by this drug combination proceeds via both mitochondrial- and TNF receptor-related apoptotic pathways.
Primal Congestion Control Algorithms for Multimedia Streams

We investigate in this paper congestion control algorithms that are TCP-friendly and media-friendly at the same time, so they are more suitable for multimedia streaming than TCP's AIMD. We use in this investigation the optimization framework developed by Kelly et al. in. Kelly et al. derived two gradient-like algorithms, a primal algorithm and a dual one, to control the congestion in a computer network in an end-to-end way and to obtain optimal bandwidth allocation among competing sources. Starting with Kelly et. al's paper, several other papers proposed different variants of the original primal and dual algorithms, but none of these considers the specific characteristics of multimedia streams. The aim of this paper is to build window-based, primal congestion control algorithms for optimizing the perceived quality of multimedia streams in best-effort networks. We build these media-friendly primal congestion control algorithms using the following recipe: 1) first we construct a window-based congestion control algorithm that is TCP-friendly, but has a much more stable throughput and then 2) we shape this stable throughput according to media characteristics (e.g. bitrate). We present two such primal congestion control algorithms and prove their stability around the equilibrium.
Magnetic resonance imaging of the entorhinal cortex and hippocampus in mild cognitive impairment and Alzheimer's disease

OBJECTIVES To explore volume changes of the entorhinal cortex (ERC) and hippocampus in mild cognitive impairment (MCI) and Alzheimer's disease (AD) compared with normal cognition (NC); to determine the powers of the ERC and the hippocampus for discrimination between these groups. METHODS This study included 40 subjects with NC, 36 patients with MCI, and 29 patients with AD. Volumes of the ERC and hippocampus were manually measured based on coronal T1 weighted MR images. Global cerebral changes were assessed using semiautomatic image segmentation. RESULTS Both ERC and hippocampal volumes were reduced in MCI (ERC 13%, hippocampus 11%, p<0.05) and AD (ERC 39%, hippocampus 27%, p<0.01) compared with NC. Furthermore, AD showed greater volume losses in the ERC than in the hippocampus (p<0.01). In addition, AD and MCI also had cortical grey matter loss (p< 0.01) and ventricular enlargement (p<0.01) when compared with NC. There was a significant correlation between ERC and hippocampal volumes in MCI and AD (both p<0.001), but not in NC. Using ERC and hippocampus together improved discrimination between AD and CN but did not improve discrimination between MCI and NC. The ERC was better than the hippocampus for distinguishing MCI from AD. In addition, loss of cortical grey matter significantly contributed to the hippocampus for discriminating MCI and AD from NC. CONCLUSIONS Volume reductions in the ERC and hippocampus may be early signs of AD pathology that can be measured using MRI.
Real-Time Rendering Of Mesostructures

In this thesis, we describe an efficient technique for rendering rich geometric details (e.g., surface mesostructure) of complex surfaces. We use sphere-tracing aided by directional distance maps (DDMs) for quickly finding ray-mesostructure intersections. High accuracy is achieved by analytically detecting such intersections. Further, space requirement is kept low by adaptively sampling the distance field, and employing off-the-shelf hardware texture compression. Our rendering technique can handle complex detailed scenes containing mesostructures in real time with correct self-occlusion, self-shadow, interpenetrations and silhouettes. We demonstrate our algorithm on a variety of test scenarios.
Memory Ordering in Modern Microprocessors

Summary of Memory Ordering When it comes to how memory ordering works on dif-ferent CPUs, there is good news and bad news.The bad news is that each CPU’s memory ordering isa bit different. The good news is that there are a fewthings you can count on:• A given CPU will always perceive its own memoryoperations as occurring in program order. That is,memory ordering issues arise only when a CPU isobserving other CPUs’ memory operations. • An operation will be reordered with a store only ifthe operation accesses a different location than doesthe store. • Aligned simple loads and stores are atomic. • Linux-kernel synchronization primitives containany needed memory barriers (which is a good rea-son to use these primitives! ). The most important differences are called out in Ta-ble 1. More detailed descriptions of speciﬁc CPUs’features are called out in following sections. The cellsmarked with a ”Y” indicate weak memory ordering; themore ”Y”s, the more reordering is possible. In general, itis easier to port SMP code from a CPU with many ”Y”sto a CPU with fewer ”Y”s, though your mileage mayvary. However, note that code that uses standard syn-chronization primitives (spinlocks, semaphores, RCU)Draft: 2007/09/19 15:15 Page: 2
REVIEW: Treatment of hypothyroidism with combinations of levothyroxine plus liothyronine.

CONTEXT Combined infusion of levothyroxine plus liothyronine, as opposed to levothyroxine alone, is the only way of restoring the concentrations of circulating TSH, T4, and T3 as well as those of both T4 and T3 in all tissues of thyroidectomized rats. Considering the substantial differences in thyroid hormone secretion, transport, and metabolism between rats and humans, whether or not combined levothyroxine plus liothyronine replacement therapy has advantages over treatment with levothyroxine alone in hypothyroid patients is still questioned. EVIDENCE ACQUISITION We conducted a systematic review of all the published controlled studies comparing treatment with levothyroxine alone with combinations of levothyroxine plus liothyronine in hypothyroid patients, identified through the Entrez-PubMed search engine. EVIDENCE SYNTHESIS Nine controlled clinical trials were identified that compared treatment with levothyroxine alone and treatment with combinations of levothyroxine plus liothyronine and included a sufficient number of adult hypothyroid patients to yield meaningful results. In only one study did the combined therapy appear to have beneficial effects on the mood, quality of life, and psychometric performance of the patients over levothyroxine alone. These results have not been confirmed by later studies using either T3 substitution protocols or approaches with fixed combinations of levothyroxine plus liothyronine, including those based on the physiological proportion in which T3 and T4 are secreted by the human thyroid. However, in some of these studies the patients preferred levothyroxine plus liothyronine combinations, for reasons not explained by changes in the psychological and psychometric tests employed. Yet patients' preference should be balanced against the possibility of adverse events resulting from the addition of liothyronine to levothyroxine, even in the small doses used in these studies. CONCLUSIONS Until clear advantages of levothyroxine plus liothyronine are demonstrated, the administration of levothyroxine alone should remain the treatment of choice for replacement therapy of hypothyroidism.
RhoA exerts a permissive effect on volume-regulated anion channels in vascular endothelial cells.

Cell swelling triggers in most cell types an outwardly rectifying anion current, I(Cl,swell), via volume-regulated anion channels (VRACs). We have previously demonstrated in calf pulmonary artery endothelial (CPAE) cells that inhibition of the Rho/Rho kinase/myosin light chain phosphorylation pathway reduces the swelling-dependent activation of I(Cl,swell). However, these experiments did not allow us to discriminate between a direct activator role or a permissive effect. We now show that the Rho pathway did not affect VRAC activity if this pathway was activated by transfecting CPAE cells with constitutively active isoforms of Galpha (a Rho activating heterotrimeric G protein subunit), Rho, or Rho kinase. Furthermore, biochemical and morphological analysis failed to demonstrate activation of the Rho pathway during hypotonic cell swelling. Finally, manipulating the Rho pathway with either guanosine 5'-O-(3-thiotriphosphate) or C3 exoenzyme had no effect on VRACs in caveolin-1-expressing Caco-2 cells. We conclude that the Rho pathway exerts a permissive effect on VRACs in CPAE cells, i.e., swelling-induced opening of VRACs requires a functional Rho pathway, but not an activation of the Rho pathway.
Challenges of Online Learning Faced by Working Parents in Urban Areas

This paper analyzed the challenges faced by working parents in guiding their children during online learning. It will focus on issues related to technology, time and parents' knowledge related to their children's online learning. Qualitative method was adopted and 41 parents were interviewed through Google form. Urban areas were chosen as there is a lack of studies conducted on parents' challenges in urban areas. Findings showed that parents have average to good knowledge on technology and they are willing to learn on the platforms used by schools and spend time to accompany their children’s learning at home. However, parents stated that this role has also affected their office work.
Human Development Dynamics : An Agent Based Simulation of Social Systems and Heterogeneous Evolutionary Games

Combining a system dynamics and agent based modeling approach, we formalize a simulation framework of the Human Development (HD) perspective. We first capture the core logic of HD theory in a asymmetric, coupled nonlinear system with empirically validated parameters from World Values Survey (WVS) data. Using evolutionary game theory, second we fuse these endogenously derived individual socio-economic attribute changes with Prisoner’s Dilemma in an agent based framework to model the interactive political-cultural effects of heterogeneous, spatial intra-societal economic transactions. We explore the model’s behavioral dynamics via simulation methods to identify paths and pitfalls towards economic development, cultural plasticity, and social change behavior. Our preliminary results suggest strong nonlinear path dependence in three areas: development processes, evolutionary intra-societal transactions and development trajectories, with significant implications for anticipating and managing positive development outcomes.
Multimodal system evaluation using modality efficiency and synergy metrics

In this paper, we propose two new objective metrics, relative modality efficiency and multimodal synergy, that can provide valuable information and identify usability problems during the evaluation of multimodal systems. Relative modality efficiency (when compared with modality usage) can identify suboptimal use of modalities due to poor interface design or information asymmetries. Multimodal synergy measures the added value from efficiently combining multiple input modalities, and can be used as a single measure of the quality of modality fusion and fission in a multimodal system. The proposed metrics are used to evaluate two multimodal systems that combine pen/speech and mouse/keyboard modalities respectively. The results provide much insight into multimodal interface usability issues, and demonstrate how multimodal systems should adapt to maximize modalities synergy resulting in efficient, natural, and intelligent multimodal interfaces.
A Complex Applications Framework Supporting Tolerant Dynamic Vehicle Dispatching

Mobile and wireless communication technologies encourage the development of complex real-time applications that require quality of service. However, the performance of such applications is likely to degrade at runtime due to the uncertainty of the environment. In the transportation domain, dynamic vehicle dispatching is found in many real-life applications including courier service and ambulance scheduling. Software architecture for such applications must be adaptive to achieve their required quality of service. Our design methodology, illustrated in the context of a dynamic vehicle dispatching problem, integrates experimental tests in the design phase, including simulation. Simulation experiments are carried out to evaluate the performance of two different strategies, maintaining the status quo on route planning or triggering a heuristic for route re-planning.
Optical interconnection system analysis using SPICE

With the increasing speed and capacity of data transfer systems, there is a growing interest for optical interconnection systems. In designing optical interconnection systems, reliable and easy-to-use CAD tools are required that can handle both electrical and optical devices. One approach for realizing such CAD tools is using SPICE, a widely used electrical circuit simulator, with equivalent circuit models for optical devices. In the paper, equivalent SPICE circuit models for a laser diode (LD) and a photodetector (PD) are implemented and system analysis is performed for a simple optical interconnection system having LD, LD driver circuitry, fiber, PD, and receiver circuitry.
Tumor characteristics of breast cancer in predicting axillary lymph node metastasis

Background Tumor characteristics was sought to be related to axillary lymph node metastasis (ALNM), the paramount prognostic factor in patients with invasive breast cancer. This study was aimed to identify the ALNM-associated tumor characteristics and to determine the predictive clinical pathway. Material/Methods Data from 1325 patients diagnosed with invasive breast cancer between January 2004 and January 2010 were retrospectively reviewed. The structure equation model (SEM) was used to build the predictive clinical pathway. Results Among the factors found in the final model, the status of human epidermal growth factor receptor 2 is the primary influence on ALNM through histology grade (β=0.18), followed by tumor size (β=0.16). Tumor size was highly relevant to lymphovascular invasion (LVI) and influenced ALNM through LVI (β=0.26), the strongest predictor of ALNM in the final model (β=0.46) and the highest risk of ALNM (odds ratio=9.282; 95% confidence interval: 7.218–11.936). Conclusions The structure equation model presented the relation of these important predictors, and might help physicians to assess axillary nodal condition and appropriate surgical procedures.
Cerebral Metabolic Responses of Hyperglycemic Immature Rats to Hypoxia-Ischemia

Abstract: Unlike adult rats, glucose supplementation of immature rats does not lead to accentuated hypoxicischemic brain damage. To explore the reason for this age-specific paradox, we subjected 7-day postnatal rats to unilateral common carotid artery occlusion followed by a subcutaneous injection of either 0.1 ml 50% glucose or normal saline. They were then exposed to hypoxia with 8% oxygen, during which they received 2.5 μCi 2-[14C]- glucose or were quick-frozen for brain metabolite analysis. During hypoxia-ischemia, glucose transport into the ipsilateral cerebral hemisphere of the hyperglycemic rats was greater (+100−150%) than in normoglycemic animals. However, glucose consumption was similar in the two groups. Glucose concentrations in brain were lower during hypoxia-ischemia in the normoglycemic animals, whereas lactate increased to similar levels in the two groups. The high-energy phosphate reserves, ATP and phosphocreatine, were depleted to a similar extent. Thus, hyperglycemia combined with hypoxia-ischemia, although associated with increased glucose transport into brain, does not lead to enhanced glucose utilization or lactate accumulation by brain over that of hypoxia-ischemia alone.