Miracle-dz/UniFAR-FTUs huggingface dataset:
Fabrication of Microfluidic Pump Using Conducting Polymer Actuator

In this paper, we present a low-power microfluidic pump based on polypyrrole- actuator. This polymeric microfluidic pump is fabricated with polypyrrole modified poly dimethylsiloxane (PDMS) membrane encased into a polymethylmethacrylate (PMMA) structure. The pumping action is induced by electro-chemically actuating the PPy- PDMS membrane while check valves at the inlet and outlet control the flow direction in the respective pump phases. This pump is self-priming. Accurate control of the output flow rate can be obtained by changing the actuation frequency. With this pump, a maximum pumping rate of 52 muL/min was achieved using an input power of 55 mW operated at plusmn1.5 volt.
Thoracic Pedicle Screw Placement: Analysis Using Anatomical Landmarks Without Image Guidance

Study Design: Prospective laboratory study analyzing the technique of pedicle screw placement in a cadaveric model. Objectives: To determine whether a freehand technique without image guidance can be used to safely place pedicle screws in the thoracic spine. Summary of Background Data: The use of thoracic pedicle screws for the treatment of spinal deformity has been gaining increased acceptance among surgeons. Although these implants improve deformity correction, there is still concern regarding the risks to neurological and vascular structures and regarding the experience level needed to use this implant. This study was designed to determine whether these implants could be placed safely without imaging modalities. Methods: Six fresh cadaveric specimens were instrumented from vertebral segments T4-T11. Ninety-six screws were placed along the anatomical axis of the pedicle. Pedicles were dissected to determine the wall violations, the position of neural structures, and the lateral coverage of the pedicle by the rib head. Results: Ninety-seven percent of screws had less than 1 mm of wall violation, with 84 screws (87.5%) fully contained within the pedicle. Four screws (4.16%) violated the medial cortex. No violations occurred superiorly, inferiorly, or anteriorly. Nerve roots were in contact with the inferior pedicle wall at all levels. The average distance from nerve to the superior pedicle ranged from 3.85 to 5.04 mm. Conclusions: Placing pedicle screws along the anatomical axis without image guidance produced a low level of pedicle wall disruption. This technique uses a reproducible start point at each level, and the results are equal to or better than those of other cadaveric studies that have used guidance systems.
Roughness as a Shape Measure

In this paper, we present a measure to quantify the multi-neighborhood level roughness of the surface using mean curvature. The surface is scaled to a unit sphere to enable comparison between different models with scale taken out of the comparison equation. Our roughness measure can be used as a shape indicator of the surface as it gives information regarding the vertex distribution at multiple neighborhood levels. In addition to computing the surface roughness, we use our measure as a unifying method to analyze different smoothing algorithms on different models including the effect of different vertex updating methods. We also use our measure to illustrate the differences in roughness at different neighborhood levels due to the irregular sampling of the surface. We specifically target triangle surface mesh representation for this paper, as it is the most common and other polygonal models can be converted to it by using local triangulation. Results are presented to demonstrate the usefulness of our roughness measure.
Exploring the Pharmacological Potential of Promiscuous Host-Defense Peptides: From Natural Screenings to Biotechnological Applications

In the last few years, the number of bacteria with enhanced resistance to conventional antibiotics has dramatically increased. Most of such bacteria belong to regular microbial flora, becoming a real challenge, especially for immune-depressed patients. Since the treatment is sometimes extremely expensive, and in some circumstances completely inefficient for the most severe cases, researchers are still determined to discover novel compounds. Among them, host-defense peptides (HDPs) have been found as the first natural barrier against microorganisms in nearly all living groups. This molecular class has been gaining attention every day for multiple reasons. For decades, it was believed that these defense peptides had been involved only with the permeation of the lipid bilayer in pathogen membranes, their main target. Currently, it is known that these peptides can bind to numerous targets, as well as lipids including proteins and carbohydrates, from the surface to deep within the cell. Moreover, by using in vivo models, it was shown that HDPs could act both in pathogens and cognate hosts, improving immunological functions as well as acting through multiple pathways to control infections. This review focuses on structural and functional properties of HDP peptides and the additional strategies used to select them. Furthermore, strategies to avoid problems in large-scale manufacture by using molecular and biochemical techniques will also be explored. In summary, this review intends to construct a bridge between academic research and pharmaceutical industry, providing novel insights into the utilization of HDPs against resistant bacterial strains that cause infections in humans.
Incidence, determinants, and prognostic value of reverse left ventricular remodelling after primary percutaneous coronary intervention: results of the Acute Myocardial Infarction Contrast Imaging (AMICI) multicenter study

Aims Few data are available on the extent and prognostic value of reverse left ventricular remodelling (r-LVR) after ST-elevation acute myocardial infarction (STEMI). We sought to evaluate incidence, major determinants, and long-term clinical significance of r-LVR in a group of STEMI patients treated with primary percutaneous coronary intervention (PPCI). In particular, the role of preserved microvascular flow within the infarct zone in inducing r-LVR has been investigated. Methods and results Serial echocardiograms (2DE) and myocardial contrast study were obtained within 24 h of coronary recanalization (T1) and at pre-discharge (T2) in 110 reperfused STEMI patients. Follow-up 2DE was scheduled after 6 months (T3). Two-year clinical follow-up was obtained. Reverse remodelling was defined as a reduction >10% in LV end-systolic volume (LVESV) at 6 months follow-up. r-LVR occurred in 39% of study population. At multivariable analysis, independent predictors of r-LVR were an effective microvascular reflow within the infarct zone, the in-hospital improvement of myocardial perfusion, an initial large LVESV, and a short time to reperfusion. Cox analysis identified r-LVR as the only independent predictor of 2-year event-free survival. Combined events rate was significantly higher among patients without compared to those with r-LVR (log-rank test P < 0.05). Conclusion r-LVR frequently occurs in STEMI patients treated with PPCI and it is an important predictor of favourable long-term outcome. A preserved microvascular perfusion within the infarct zone is the major determinant of r-LVR.
Multipole electrostatics in hydration free energy calculations

Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here, we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio method. We have compared two approaches to derive the atomic multipoles from quantum mechanical calculations: one directly from the new distributed multipole analysis and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6‐311G*, 6‐311++G(2d,2p), cc‐pVTZ, and aug‐cc‐pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug‐cc‐pVTZ). We conclude that aug‐cc‐pVTZ gives the best performance when used with AMOEBA, and 6‐311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long‐range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed‐charge water in the HFE calculation. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
EVIDENCE OF SIGNIFICANT CONTRIBUTION FROM CYP3A5 TO HEPATIC DRUG METABOLISM

CYP3A4 and CYP3A5 exhibit significant overlap in substrate specificity but can differ in product regioselectivity and formation activity. To further explore this issue, we compared the kinetics of product formation for eight different substrates, using heterologously expressed CYP3A4 and CYP3A5 and phenotyped human liver microsomes. Both enzymes displayed allosteric behavior toward six of the substrates. When it occurred, the “maximal” intrinsic clearance was used for quantitative comparisons. Based on this parameter, CYP3A5 was more active than CYP3A4 in catalyzing total midazolam hydroxylation (3-fold) and lidocaine demethylation (1.4-fold). CYP3A5 exhibited comparable metabolic activity as CYP3A4 (90-110%) toward dextromethorphan N-demethylation and carbamazepine epoxidation. CYP3A5-catalyzed erythromycin N-demethylation, total flunitrazepam hydroxylation, testosterone 6β-hydroxylation, and terfenadine alcohol formation occurred with an intrinsic clearance that was less than 65% that of CYP3A4. Using two sets of human liver microsomes with equivalent CYP3A4-specific content but markedly different CYP3A5 content (group 1, predominantly CYP3A4; group 2, CYP3A4 + CYP3A5), we assessed the contribution of CYP3A5 to product formation rates determined at low substrate concentrations (≤Km). Mean product formation rates for group 2 microsomes were 1.4- to 2.2-fold higher than those of group 1 (p < 0.05 for 5 of 8 substrates). After adjusting for CYP3A4 activity (itraconazole hydroxylation), mean product formation rates for group 2 microsomes were still significantly higher than those of group 1 (p < 0.05 for 3 substrates). We suggest that, under conditions when CYP3A5 content represents a significant fraction of the total hepatic CYP3A pool, the contribution of CYP3A5 to the clearance of some drugs may be an important source of interindividual variability.
Recent Advances in Converters and Control Systems for Grid- Connected Small Wind Turbines

In response to the introduction of feed-in tariffs around the world, an increasing number of small wind turbines are being grid connected [1]. Variable speed wind turbines, though ini‐ tially more costly, have several advantages over fixed speed systems: (i) average power pro‐ duction is typically 10% higher since the turbine operates more frequently near its ideal tipspeed-ratio, (ii) the turbine and mechanical transmission operate with reduced stresses, (iii) turbine and generator torque pulsations are reduced, and (iv) noise is reduced [2-4]. Varia‐ ble speed operation in general has only become possible over the last twenty years or so be‐ cause of major developments in power electronics and associated cost reductions [5]. This reference indicates that power electronic devices are reducing in cost at about 1-5% per year. This chapter will discuss the impact of these developments on small turbine design and op‐ eration along with some important aerodynamics issues related to turbine starting.
Capacity of Arbitrary Wireless Networks

In this work we study the problem of determining the throughput capacity of a wireless network. We propose a scheduling algorithm to achieve this capacity within an approximation factor. Our analysis is performed in the physical interference model, where nodes are arbitrarily distributed in Euclidean space. We consider the problem separately from the routing problem and the power control problem, i.e., all requests are single-hop, and all nodes transmit at a fixed power level. The existing solutions to this problem have either concentrated on special-case topologies, or presented optimality guarantees which become arbitrarily bad (linear in the number of nodes) depending on the network's topology. We propose the first scheduling algorithm with approximation guarantee independent of the topology of the network. The algorithm has a constant approximation guarantee for the problem of maximizing the number of links scheduled in one time-slot. Furthermore, we obtain a O(log n) approximation for the problem of minimizing the number of time slots needed to schedule a given set of requests. Simulation results indicate that our algorithm does not only have an exponentially better approximation ratio in theory, but also achieves superior performance in various practical network scenarios. Furthermore, we prove that the analysis of the algorithm is extendable to higher-dimensional Euclidean spaces, and to more realistic bounded-distortion spaces, induced by non-isotropic signal distortions. Finally, we show that it is NP-hard to approximate the scheduling problem to within n 1-epsiv factor, for any constant epsiv > 0, in the non-geometric SINR model, in which path-loss is independent of the Euclidean coordinates of the nodes.
Deregulated NFATc1 activity transforms murine fibroblasts via an autocrine growth factor‐mediated Stat3‐dependent pathway

The nuclear factor of activated T cells (NFAT) family of transcription factors has recently been implicated with a role in tumorigenesis. Forced expression of a constitutively active NFATc1 mutant (caNFATc1) has been shown to transform immortalized murine fibroblasts in vitro, while constitutive activation of the NFAT‐signaling pathway has been found in a number of human cancers, where it has been shown to contribute towards various aspects of the tumor phenotype. Here we have investigated the molecular mechanisms underlying the oncogenic potential of deregulated NFAT activity. We now show that ectopic expression of caNFATc1 in murine 3T3‐L1 fibroblasts induces the secretion of an autocrine factor(s) that is sufficient to promote the transformed phenotype. We further demonstrate that this NFATc1‐induced autocrine factor(s) specifically induces the tyrosine phosphorylation of the Stat3 transcription factor via a JAK kinase‐dependent pathway. Interestingly, this effect of sustained NFAT signaling on the autocrine growth factor‐mediated activation of Stat3 is not restricted to murine fibroblasts, but is also observed in the PANC‐1 and MCF10A human cell lines. Most importantly, we find that the shRNA‐mediated depletion of endogenous Stat3 significantly attenuates the ability of caNFATc1 to transform 3T3‐L1 fibroblasts. Taken together, our results afford significant new insights into the molecular mechanisms underlying the oncogenic potential of deregulated NFATc1 activity by demonstrating that constitutive NFATc1 activity transforms cells via an autocrine factor‐mediated pathway that is critically dependent upon the activity of the Stat3 transcription factor. J. Cell. Biochem. 108: 237–248, 2009. © 2009 Wiley‐Liss, Inc.
Central Control of Brown Adipose Tissue Thermogenesis

Thermogenesis, the production of heat energy, is an essential component of the homeostatic repertoire to maintain body temperature during the challenge of low environmental temperature and plays a key role in elevating body temperature during the febrile response to infection. Mitochondrial oxidation in brown adipose tissue (BAT) is a significant source of neurally regulated metabolic heat production in many species from mouse to man. BAT thermogenesis is regulated by neural networks in the central nervous system which responds to feedforward afferent signals from cutaneous and core body thermoreceptors and to feedback signals from brain thermosensitive neurons to activate BAT sympathetic nerve activity. This review summarizes the research leading to a model of the feedforward reflex pathway through which environmental cold stimulates BAT thermogenesis and includes the influence on this thermoregulatory network of the pyrogenic mediator, prostaglandin E2, to increase body temperature during fever. The cold thermal afferent circuit from cutaneous thermal receptors, through second-order thermosensory neurons in the dorsal horn of the spinal cord ascends to activate neurons in the lateral parabrachial nucleus which drive GABAergic interneurons in the preoptic area (POA) to inhibit warm-sensitive, inhibitory output neurons of the POA. The resulting disinhibition of BAT thermogenesis-promoting neurons in the dorsomedial hypothalamus activates BAT sympathetic premotor neurons in the rostral ventromedial medulla, including the rostral raphe pallidus, which provide excitatory, and possibly disinhibitory, inputs to spinal sympathetic circuits to drive BAT thermogenesis. Other recently recognized central sites influencing BAT thermogenesis and energy expenditure are also described.
Fatty acids linked to cardiovascular mortality are associated with risk factors

Background Although saturated fatty acids (FAs) have been linked to cardiovascular mortality, it is not clear whether this outcome is attributable solely to their effects on low-density lipoprotein cholesterol (LDL-C) or whether other risk factors are also associated with FAs. The Western Alaskan Native population, with its rapidly changing lifestyles, shift in diet from unsaturated to saturated fatty acids and dramatic increase in cardiovascular disease (CVD), presents an opportunity to elucidate any associations between specific FAs and known CVD risk factors. Objective We tested the hypothesis that the specific FAs previously identified as related to CVD mortality are also associated with individual CVD risk factors. Methods In this community-based, cross-sectional study, relative proportions of FAs in plasma and red blood cell membranes were compared with CVD risk factors in a sample of 758 men and women aged ≥35 years. Linear regression analyses were used to analyze relations between specific FAs and CVD risk factors (LDL-C, high-density lipoprotein cholesterol, triglycerides, C-reactive protein, systolic blood pressure, diastolic blood pressure, heart rate, body mass index, fasting glucose and fasting insulin, 2-hour glucose and 2-hour insulin). Results The specific saturated FAs previously identified as related to CVD mortality, the palmitic and myristic acids, were adversely associated with most CVD risk factors, whereas unsaturated linoleic acid (18:2n-6) and the marine n-3 FAs were not associated or were beneficially associated with CVD risk factors. Conclusions The results suggest that CVD risk factors are more extensively affected by individual FAs than hitherto recognized, and that risk for CVD, MI and stroke can be reduced by reducing the intake of palmitate, myristic acid and simple carbohydrates and improved by greater intake of linoleic acid and marine n-3 FAs.
D-Map: Visual analysis of ego-centric information diffusion patterns in social media

Popular social media platforms could rapidly propagate vital information over social networks among a significant number of people. In this work we present D-Map (Diffusion Map), a novel visualization method to support exploration and analysis of social behaviors during such information diffusion and propagation on typical social media through a map metaphor. In D-Map, users who participated in reposting (i.e., resending a message initially posted by others) one central user's posts (i.e., a series of original tweets) are collected and mapped to a hexagonal grid based on their behavior similarities and in chronological order of the repostings. With additional interaction and linking, D-Map is capable of providing visual portraits of the influential users and describing their social behaviors. A comprehensive visual analysis system is developed to support interactive exploration with D-Map. We evaluate our work with real world social media data and find interesting patterns among users. Key players, important information diffusion paths, and interactions among social communities can be identified.
Pre-dilution on-line haemofiltration vs low-flux haemodialysis: a randomized prospective study.

BACKGROUND Accumulation of larger molecular weight uraemic toxins molecules may have a negative effect on the cardiovascular and nutritional state of dialysis patients and influence uraemic symptomatology. Their clearance can be enhanced by the use of haemofiltration (HF). METHODS The effects of low-flux haemodialysis (HD) (ultrapure dialysate; polyamide membranes) and pre-dilution on-line HF (1:1 blood/substitution ratio; target filtration volume: 1.2 times body weight) on cardiovascular and nutritional parameters, interdialytic levels of uraemic toxins and quality of life (QOL; Laupacis questionnaire) were assessed during 1 year follow-up. Forty patients were randomized. RESULTS After 1 year, 27 patients were eligible for analysis (HF: 13 patients; HD: 14 patients). Left ventricular mass index did not change in the HF patients (127+/-33 --> 131+/-36 g/m(2) after 12 months) or in the HD group (135+/-34 --> 138+/-32 g/m(2)). Also, there were no changes in pulse wave velocity, and 48 h systolic and diastolic blood pressures. Lean body mass, assessed by dual-energy X-ray absorptiometry, increased in the HF group (44.8+/-8.9 --> 46.2+/-9.6 kg; P<0.05), but not in the HD group (49.4+/-9.2 --> 50.6+/-8.8 kg), although differences between groups were not significant. Insulin-like growth factor-1 levels remained stable in the HF patients, but decreased in the HD group (P<0.05 between groups). QOL for physical symptoms improved in the HF group (4.2+/-1.2 --> 5.0+/-1.1; P<0.05 within the HF group and P = 0.06 between groups), but not in the HD group (4.0+/-1.0 --> 4.4+/-1.4). beta2-microglobulin, complement factor D and homocysteine decreased significantly in the HF but not in the HD group, whereas l-ADMA, leptin and advanced glycation end-products-related fluorescence did not change. CONCLUSIONS No changes in cardiovascular parameters were observed during pre-dilution on-line HF compared with low-flux HD. Treatment with on-line HF resulted in marked changes in the uraemic toxicity profile, an improvement in physical well-being and a small improvement in nutritional state.
Anatomical labeling of brain CT scan anomalies using multi-context nearest neighbor relation networks

This work is an endeavor to develop a deep learning methodology for automated anatomical labeling of a given region of interest (ROI) in brain computed tomography (CT) scans. We combine both local and global context to obtain a representation of the ROI. We then use Relation Networks (RNs) to predict the corresponding anatomy of the ROI based on its relationship score for each class. Further, we propose a novel strategy employing nearest neighbors approach for training RNs. We train RNs to learn the relationship of the target ROI with the joint representation of its nearest neighbors in each class instead of all data-points in each class. The proposed strategy leads to better training of RNs along with increased performance as compared to training baseline RN network.