Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulating an Actomyosin in Vitro Motility Assay: Toward the Rational Design of Actomyosin-Based Microtransporters

We present a simulation study of an actomyosin in vitro motility assay. In vitro motility assays have served as an essential element facilitating the application of actomyosin in nanotechnology; such applications include biosensors and biocomputation. Although actomyosin in vitro motility assays have been extensively investigated, some ambiguities remain, as a result of the limited spatio-temporal resolution and unavoidable uncertainties associated with the experimental process. These ambiguities hamper the rational design of nanodevices for practical applications. Here, with the aim of moving toward a rational design process, we developed a 3D computer simulation method of an actomyosin in vitro motility assay, based on a Brownian dynamics simulation. The simulation explicitly included the ATP hydrolysis cycle of myosin. The simulation was validated by the reproduction of previous experimental results. More importantly, the simulation provided new insights that are difficult to obtain experimentally, including data on the number of myosin motors actually binding to actin filaments, the mechanism responsible for the guiding of actin filaments by chemical edges, and the effect of the processivity of motor proteins on the guiding probabilities. The simulations presented here will be useful in interpreting experimental results, and also in designing future nanodevices integrated with myosin motors.
A Large-Scale Malleable Tsunami Simulation Realized on an Elastic MPI Infrastructure

Realization of resource awareness and elasticity in hardware and software is an answer to many problems and challenges we are facing in High Performance Computing (HPC) today. Resource utilization inefficiency is a real problem in current HPC systems due to the current static, inflexible resource assignment configuration. One way to resolve this problem is to change the static resource assignment setting---by introducing runtime resource elasticity, which requires both malleability in software implementation and support for runtime resource adaptation in the system infrastructure. In this paper, we show a successful implementation of a malleable tsunami simulation realized on an elastic MPI infrastructure we previously proposed. We also prove that introducing malleability to such a tightly coupled parallel application can be beneficial.
MIMO-OFDM Channel Estimation with Eigenbeamforming and User-Specific Reference Signals

MIMO-OFDM systems with channel reciprocity allow spatial multiplexing using Eigenbeamforming. However, Eigenbeamforming requires singular value decomposition, which is phase ambiguous and causes the precoded channel to become phase discontinuous in frequency domain. This changes statistical properties of channel components, which degrades the perfor- mance of channel estimation. In this paper we propose phase unifying method to improve channel statistics and consequently decrease the error in channel estimation. In addition, we investigate the 2D-Wiener channel estimation with respect to different channel frequency correla- tion functions. The performance is evaluated using LTE link simulator.
Calcium‐dependent responses in neurons of the isolated respiratory network of newborn rats.

1. Membrane potentials (Em) and currents (Im) were measured using whole‐cell patch clamp techniques in inspiratory (Insp, types I‐III), preinspiratory (Pre‐I) and tonic expiratory (Exp) neurons of the ventral respiratory group (VRG) in the isolated brainstem‐spinal cord preparation of 0‐ to 4‐day‐old rats. 2. After blocking on‐going synaptic activity with 0.2‐0.5 microM tetrodotoxin (TTX), Ca(2+)‐dependent responses were analysed using patch pipettes containing 120 mM Cs+ and 20 mM tetraethylammonium (TEA) to block K+ conductances. 3. In all cells studied, all‐or‐none high voltage‐activated (HVA) Ca2+ spikes with an activation threshold of ‐33 +/‐ 6.9 mV (n = 37) were evoked by depolarizing current pulses. 4. In less than 15% of Insp and Pre‐I cells and in 20% of Exp neurons, termination of hyperpolarizing pulses led to low voltage‐activated (LVA) Ca2+ spikes with a threshold potential of between ‐70 and ‐60 mV (n = 7). 5. In more than 50% of Insp III and Pre‐I neurons, depolarizing pulses evoked graded ‘plateau’ potentials with an amplitude of 5‐20 mV. Slow voltage ramp commands revealed that this type of Ca2+ response was due to an inward current with a mean activation threshold of ‐42 +/‐ 2.1 mV (n = 5). These intermediate voltage‐activated (IVA) plateau potentials persisted for several seconds after termination of depolarizing current pulses and decreased in amplitude at more negative holding potentials. 6. The HVA and LVA Ca2+ spikes as well as the IVA plateau potentials and the underlying inward current were potentiated after extracellular addition of 2 mM Ba2+ whereas 1‐2 mM Co2+ led to blockade of these responses. 7. Nifedipine (10 microM) selectively suppressed HVA Ca2+ potentials whereas 0.2‐0.4 microM omega‐agatoxin‐IVA reduced the IVA response without major effects on HVA Ca2+ spikes. omega‐Conotoxin‐GVIA (2 microM) led to a partial blockade of both IVA and HVA potentials. 8. After extracellular application of TTX, Ba2+ and/or TEA, HVA and LVA Ca2+ spikes as well as IVA plateau potentials were also revealed using patch pipettes containing K+ instead of Cs+ and TEA. 9. The results indicate that neonatal respiratory neurons have a complex set of Ca(2+)‐dependent membrane conductances. The relevance of these conductances for initiation and maintenance of respiratory bursts is discussed.
No Evidence for Bioenergetic Interaction between Digestion and Thermoregulation in Steller Sea Lions Eumetopias jubatus

The increase in metabolism during digestion—the heat increment of feeding—is often regarded as an energetic waste product. However, it has been suggested that this energy could offset thermoregulatory costs in cold environments. We investigated this possibility by measuring the rate of oxygen consumption of four juvenile Steller sea lions (Eumetopias jubatus) before and after they ingested a meal in water temperatures of 2°–8°C. Rates of oxygen consumption of fasted and fed animals increased in parallel with decreasing water temperature, such that the apparent heat increment of feeding did not change with water temperature. These results suggest that Steller sea lions did not use the heat released during digestion to offset thermoregulatory costs.
Results of conservative management of clinically localized prostate cancer.

BACKGROUND The selection of treatment for patients with localized prostate cancer requires reliable information about the outcome of conservative management. Previous studies of this question are generally considered unreliable because they were uncontrolled and nonrandomized. METHODS We performed a pooled analysis of 828 case records from six nonrandomized studies, published since 1985, of men treated conservatively (with observation and delayed hormone therapy but no radical surgery or irradiation) for clinically localized prostate cancer. A Cox regression analysis was performed to determine which factors influenced survival among patients who did not die of causes other than prostate cancer (disease-specific survival). Kaplan-Meier curves for overall and metastasis-free survival among such patients were compared with use of the log-rank method and the Mantel-Haenszel test. RESULTS Factors that had a significant effect on disease-specific survival were grade 3 tumors (risk ratio, 10.04), residence in Israel (risk ratio, 2.48) or New York (risk ratio, 0.37), and age under 61 years (risk ratio, 0.32). Ten years after diagnosis, disease-specific survival (with data on men who died from causes other than prostate cancer censored) was 87 percent for men with grade 1 or 2 tumors and 34 percent for those with grade 3 tumors; metastasis-free survival among men who had not died of other causes was 81 percent for grade 1, 58 percent for grade 2, and 26 percent for grade 3 disease. These findings were not affected by the inclusion of men who had early-stage cancer, were older, had worse-than-average health, or underwent delayed radiation therapy or radical prostatectomy. CONCLUSIONS The strategy of initial conservative management and delayed hormone therapy is a reasonable choice for some men with grade 1 or 2 clinically localized prostate cancer, particularly for those who have an average life expectancy of 10 years or less. New treatment strategies are needed for men with grade 3 prostate cancer.
Alleviation of toxic hexavalent chromium using indigenous aerobic bacteria isolated from contaminated tannery industry sites

ABSTRACT In the last decade, much attention has been paid to bioremediation of Cr(VI) using various bacterial species. Cr(VI) remediation by indegeneous bacteria isolated from contaminated sites of a tannery industry located in Tamil Nadu, India, was investigated in this study. Three Cr(VI) resistant bacterial strains (TES-1, TEf-1, and TES-2) were isolated and selected based on their Cr(VI) reduction ability in minimal salt medium. Among these three bacterial strains, TES-1 was found to be most efficient in bioreduction, while TES-2 was only found to be Cr(VI) resistant and showed negligible bioreduction, whereas TEf-1 was observed to be most Cr(VI) tolerant. Potential for bioremediation of TES-1 and TEf-1 was further investigated at different concentrations of Cr(VI) in the range of 50 to 350 mg L−1. TEf-1 showed prominent synchronous growth throughout the experiment, whereas TES-1 took a longer acclimatization time. Minimum inhibitory concentrations (MIC) of Cr(VI) for TES-1 and TEf-1 were approximated as 600 mg L−1 and 750 mg L−1, respectively. The kinetic behavior of Cr(VI) reduction by TES-1 and TEf-1 exhibited zero- and first-order removal kinetics for Cr(VI), respectively. The most efficient strain TES-1 was identified as Streptomyces sp. by gene sequencing of 16S rRNA.
A MicroPirani Pressure Sensor Based on the Tungsten Microhotplate in a Standard CMOS Process

This paper reports a tungsten microhotplate fabricated in a standard CMOS process and the implementation of a MicroPirani pressure sensor with it. A monolithic constant-current circuit including an operational amplifier is used to bias the tungsten microhotplate to measure the gas pressure. The sensor shows a linear response to the gas pressure in the range of 1-100 Pa when driven by a constant current of 7 mA. In this regime, the sensitivity of the sensor is 0.23 mV/Pa, the linearity is 4.95%, and the hysteresis is 8.69%. The MicroPirani pressure sensor in this paper can be used in a medium-vacuum measurement. Because tungsten in a standard CMOS process has a large temperature coefficient regardless of the different manufacturing processes, the design of the tungsten microhotplate can be applied to other thermal-based sensors, even in different standard CMOS processes.
Evaluation of Patients With Symptoms Suggestive of Chronic Polyneuropathy

Objectives The aim of this study was to determine the diagnostic yield and to describe the spectrum of diagnosis encountered by evaluation of patients with symptoms suggestive of chronic polyneuropathy. Methods We prospectively evaluated 198 patients referred to a department of neurology with symptoms suggestive of polyneuropathy. The evaluation included nerve conduction studies with near-nerve technique, quantitative examination of temperature sensation, blood tests, chest x-rays, and skin biopsies as well as diagnostic tests for differential diagnoses. Results Polyneuropathy was found in 147 patients, alternative diagnoses in 25, and 26 remained undiagnosed. The etiology of polyneuropathy could not be identified in 25% of the patients with polyneuropathy. In the remaining 75%, the cause of neuropathy was diabetes and/or alcohol abuse (41%), monoclonal gammopathy of undetermined significance (5%), drugs (5%), connective tissue disease (3%), and a number of less frequent conditions. A previously undiagnosed condition was found in 30% of the patients with polyneuropathy. Conclusion Evaluation of patients with symptoms suggestive of polyneuropathy reveals a high fraction of patients with previously undiagnosed conditions both in patients ending up with a polyneuropathy diagnosis and those without this diagnosis.
Absence of ocular effects after either single or repeated exposure to 10 mW/cm(2) from a 60 GHz CW source.

This study was designed to examine ocular effects associated with exposure to millimeter waves (60 GHz). Rabbits served as the primary experimental subjects. To confirm the results of the rabbit experiments in a higher species, the second phase of the study used nonhuman primates (Macaca mulatta). First, this study used time-resolved infrared radiometry to assess the field distribution patterns produced by different antennas operating at 60 GHz. These results allowed us to select an antenna that produced a uniform energy distribution and the best distance at which to expose our experimental subjects. The study then examined ocular changes after exposure at an incident power density of 10 mW/cm(2). Acute exposure of both rabbits and nonhuman primates consisted of a single 8 h exposure, and the repeated exposure protocol consisted of five separate 4 h exposures on consecutive days. One eye in each animal was exposed and the contralateral eye served as the sham-exposed control. After postexposure diagnostic examinations, animals were euthanized and the eyes were removed. Ocular tissue was examined by both light and transmission electron microscopy. Neither microscopic examinations nor the diagnostic procedures performed on the eyes of acute and repeatedly exposed rabbits found any ocular changes that could be attributed to millimeter-wave exposure at 10 mW/cm(2). Examination of the primates after comparable exposures also failed to detect any ocular changes due to exposure. On the basis of our results, we conclude that single or repeated exposure to 60 GHz CW radiation at 10 mW/cm(2) does not result in any detectable ocular damage.
Dealing with existential anxiety in exercise-based cardiac rehabilitation: a phenomenological-hermeneutic study of patients' lived experiences.

AIMS AND OBJECTIVES To investigate patients' lived experiences of exercise-based cardiac rehabilitation. BACKGROUND Exercise-based cardiac rehabilitation is used to enable patients with cardiac problems to move forward to lead satisfying lives. However, knowledge of patients' concerns while they follow the current programmes is sparse. DESIGN This study, which included nine men and two women with unstable angina pectoris and non-ST-elevation myocardial infarction, used a phenomenological-hermeneutic approach. METHODS The patients were followed by field observations during exercise-based cardiac rehabilitation. Focus group interviews were conducted at the programme end, and individual interviews were performed one to two months later. The interpretation comprised three methodological steps: naïve reading, structural analysis, and comprehensive interpretation and discussion. FINDINGS Although both physically and psychologically challenged, the patients were encouraged to maintain an active lifestyle. Three themes were identified: anxiety regarding exercise, whereby the patients are initially insecure about how to behave with their diseased hearts; encouragement from training together, whereby the patients support each other in exercising; and growing confidence in the heart, whereby the patients enjoy being physically active. CONCLUSIONS In exercise-based cardiac rehabilitation, patients' insecurity with respect to their heart disease is revealed as an existential anxiety. Through peer support and a positive physical perception, the patients gain renewed self-efficacy, helping them to continue their lives in an active and satisfying way. RELEVANCE TO CLINICAL PRACTICE Knowing that patients are confronted with an existential anxiety during exercise-based cardiac rehabilitation is important because it requires specific care. Recognising this anxiety also highlights how participating in the programme can be very demanding, which can help us understand aspects of adherence problems. Of greatest importance is that exercise-based cardiac rehabilitation enables patients to find a new foothold, which comprises enjoying being physically active.
Relationship between vitamin D deficiency and chronic low back pain in postmenopausal women.

OBJECTIVE To examine whether vitamin D deficiency is a determinant risk factor of chronic low back pain (LBP) in Moroccan postmenopausal women. METHODS A biochemical assay of serum calcium, phosphate, 25(OH)D, and parathormone (PTH) was performed for 105 patients complaining from a chronic LBP with no obvious causes and compared to those of 45 healthy patients. All participants were postmenopausal. Patients were matched with controls for age and body mass index (BMI). Vitamin D deficiency was defined as a circulating level of 25(OH)D below 20 ng/ml. RESULTS Vitamin D deficiency was significantly more common in patients suffering from chronic LBP than in controls (79 % vs 61.4 %; P= 0.02). Falls antecedent was also associated with chronic LBP (37.1 % in patients vs 20.5% in controls; P< 0.01). There was no significant association between chronic LBP and age, BMI, smoking status, nor with number of pregnancies. In multiple logistic regression, after adjusting for potential confounders factors potentially influencing chronic LBP (age, BMI, smoking status, number of pregnancies), the main determinants of chronic LBP were vitamin D deficiency [OR 2.5 (95% IC, 1.1-5.8; P = 0.04)] and falls antecedent [OR 3 (95% IC, 1.2-7.2; P = 0.01)]. CONCLUSION Our study shows a significant association between vitamin D deficiency and chronic LBP in Moroccan postmenopausal women. Further studies are clearly warranted to determine the effectiveness and the mechanism(s) of this links between vitamin D deficiency and chronic LBP.
A Dual Frequency Ka-Band Printed Fresnel Reflector for Ground Terminal Applications

Satellite-based telecommunication systems operating in Ka-band require high gain ground terminal antennas. A promising architecture based on dual frequency printed Fresnel reflectors is presented in this paper. The complete development of this antenna including its design methodology, manufacturing, and testing is described. In order to scan its beam, the proposed antenna system can either be combined with electric motors or be transformed into a reconfigurable reflectarray system by replacing the passive reflecting cells by reconfigurable ones. A possible way of implementing such electronically reconfigurable reflecting cells is also presented.
Effect of Antioxidants on Atherosclerotic Plaque Formation in Balloon-Denuded and Irradiated Hypercholesterolemic Rabbits

The oxidative modification of low-density lipoprotein (LDL) hypothesis implies that antioxidants should be effective in suppressing atherosclerosis. This study is designed to test the potential of antioxidants to inhibit atherosclerotic plaque progression in balloon-denuded and irradiated hypercholesterolemic rabbits. Rabbits were fed with a 1% cholesterol diet supplemented with or without a mixture of antioxidants (vitamin E, vitamin C, selenium, zinc, copper, manganese, N-acetylcysteine, glutamine). At 7 days both iliac arteries were balloon denuded, and 4 weeks later, 1 iliac artery underwent endovascular irradiation (n = 12), while the contralateral was sham treated (n = 12). Four weeks after irradiation, animals were euthanized, and arteries were fixed and processed for histo- or immunohistochemistry for determining the plaque area, macrophage count, and oxidized LDL-positive areas. Plasma antioxidant levels were significantly higher in the animals fed with antioxidant diet. Plasma (thiobarbituric acid-reactive substances) and arterial tissue oxidized LDL (immunoreactive to specific oxidized LDL antibody) levels were significantly higher in the irradiated as compared with nonirradiated animals (0.69 ± 0.09 and 31.05 ± 4.21 versus 0.24 ± 0.04 and 18.42 ± 4.62, P < 0.001 and 0.05), and antioxidants partially lowered the oxidized LDL levels (0.35 ± 0.14 and 25.41 ± 4.82, P < 0.001 and 0.01). Plaque area in the irradiated animals was 175% greater than in nonirradiated animals (P < 0.05). Antioxidant supplementation resulted in a 50% decrease in plaque area of both control and irradiated animals. Antioxidants reduced both the cholesterol-induced and radiation-enhanced circulating and tissue oxidized LDL levels, resulting in reduced plaque.
Care seeking for orofacial pain.

AIMS To determine the contribution of a wide range of factors to care-seeking behavior in orofacial pain patients, expressed as (A) decision to seek care and (B) number of health care practitioners visited. METHODS Subjects with orofacial pain complaints were recruited in seven TMD clinics and from a nonclinical population sample. They received a questionnaire including a wide range of possible predictors. To study which predictive variables were associated with the decision to seek care and with the number of health care practitioners visited, multiple regression models were built. RESULTS Two hundred three persons with orofacial pain participated in the study. Of these participants, 169 (140 females) had visited at least one health care practitioner (care seekers), while the other 34 persons (25 females) did not (non-care seekers). The decision to seek care was not only associated with the pain intensity (P < .05), but, in women, also with fear of jaw movements (P < .01): Women with more fear of jaw movements were more likely to seek care. Pain intensity and disability were not associated with the number of health care practitioners visited. Instead, the main predictors were catastrophizing (P = .004) and the use of painkillers (P = .008). CONCLUSIONS Pain intensity and fear of jaw movements play an important role in the decision to seek care for orofacial pain. The continuous search for help is associated with catastrophizing and the use of painkillers.
Linking differences in membrane tension with the requirement for a contractile actomyosin scaffold during exocytosis in salivary glands

In all the major secretory organs regulated exocytosis is a fundamental process that is used for releasing molecules in the extracellular space. Molecules destined for secretion are packaged into secretory vesicles that fuse with the plasma membrane upon the appropriate stimulus. In exocrine glands, large secretory vesicles fuse with specialized domains of the plasma membrane, which form ductal structures that are in direct continuity with the external environment and exhibit various architectures and diameters. In a recent study, we used intravital microscopy to analyze in detail the dynamics of exocytic events in the salivary glands of live rodents under conditions that cannot be reproduced in in vitro or ex vivo model systems. We found that after the opening of the fusion pore large secretory vesicles gradually collapse with their limiting membranes being completely absorbed into the apical plasma membrane canaliculi within 40–60 sec. Moreover, we observed that this controlled collapse requires the contractile activity of actin and its motor myosin II, which are recruited onto the large secretory vesicles immediately after their fusion with the plasma membrane. Here we suggest that the actomyosin complex may be required to facilitate exocytosis in those systems, such as the salivary glands, in which the full collapse of the vesicles is not energetically favorable due to a difference in membrane tension between the large secretory vesicles and the canaliculi.