Miracle-dz/UniFAR-FTUs huggingface dataset:
Human cytomegalovirus upregulates NF-kappa B activity by transactivating the NF-kappa B p105/p50 and p65 promoters

During human cytomegalovirus (HCMV) infection, a series of regulated events take place following virus binding and entry into the cell, including the upregulation of cellular transcription factors, such as NF-kappa B, which play an essential role in the viral life cycle. We show here that NF-kappa B message is induced during HCMV infection and that the induction is biphasic, suggesting an initial induction at immediate-early (IE) times and a second round of induction at early times. This hypothesis is supported by experiments using cyclohexamide, which showed that the first tier of induction was drug insensitive, while the second tier was drug sensitive. We then show that virus binding alone is sufficient to stimulate NF-kappa DNA binding activity, supporting its role in the initial induction of NF-kappa B. To begin to elucidate the mechanism(s) for the second tier of NF-kappa B regulation, we examined promoter constructs from the NF-kappa B subunits (p105/p50 and p65) for responsiveness following HCMV infection. HCMV infection transactivated the p105/p50 and p65 promoters. The viral IE proteins (IE1-72, IE2-55, and IE2-86) are expressed during the time we see NF-kappa B induction, so we examined their role in NF-kappa B induction. The IE1-72, IE2-55, and IE2-86 proteins transactivated the p65 promoter, while only the IE2-55 protein transactivated the p105/p50 promoter. The p105/p50 promoter has NF-kappa B sites; therefore, upregulation could also be caused by an autoregulatory mechanism. The p65 promoter, however, has been demonstrated to contain only Sp1 sites. To investigate the potential role of SP1, we examined nuclear extracts from HCMV-infected cells. Here, we show that there is a biphasic increase in SP1 activity during viral infection and that there is apparently an absolute requirement for SP1 in the transactivation of the p65 promoter. In conclusion, we suggest a model in which the initial induction of NF-kappa B occurs through viral modulation of cellular factors and the sustained levels of NF-kappa B induction are regulated by a combination of cellular and viral factors.
A modular distributed simulation‐based architecture for intelligent transportation systems

Simulations have been used extensively for evaluating scenarios, which are very difficult, costly or impractical to implement in real systems. Testing in a synthetic, realistic environment provides a means to determine the viability of solutions. Simulations have proved to be very useful in the verification of algorithms and protocols, offering tools for testing them in different situations. The simulation of vehicular area networks pose additional challenges as realistic mobility models are crucial and must be incorporated in scenario elements while applications and communication protocols are tested. Several simulators and simulation frameworks have been designed that aim to synthetically reproduce communication and mobility of vehicles as realistically as possible. The majority of such simulators merge pre‐existing networking and mobility simulators, which add issues regarding compatibility and realism. Such simulators present limited run‐time 3D visualization tools, essential for providing immersive environments. Therefore, in this paper, we propose real‐time simulation and 3D visualization for vehicular networks of realistic scenarios. This proposed simulation system generates output in real time, making use of 3D‐modelled real‐world maps and effectively generating visualization as elements are updated in the simulation. Experiments have been conducted with simulation and visualization components to evaluate delays and performance of the proposed simulator. Copyright © 2016 John Wiley & Sons, Ltd.
Global Higher Education: Development and Implications

Global higher education is experiencing a myriad of challenges that impact the performance and application of education throughout the world. Globalization is a force that encompasses the virtual economy and how knowledge and information are shared and used. Higher education is seen as the primary vehicle for nations to improve the economic conditions for citizens in this new economy. Concurrently, technology has impacted the ability of higher education to respond the multiple difficulties of virtual learning, increased communication efficiency and how to respond to the anytime, anywhere learning demands. Global higher education continues to develop and evolve and global leaders should recognize the essential mission of global higher education to the creation, exchange and implementation of knowledge in a global marketplace.
In silico analysis of influence of the missense mutation P629S on the molecular interaction and 3D properties of PIK3R5

PIK3R5 is the regulatory subunit of Phosphoinositide 3-kinase γ (PI3Kγ) that is responsible for phosphory-lating membrane lipids to activate the AKT pathway. PIK3R5 binds Gβγ and facilitates the interaction with p110γ catalytic subunit (PIK3CG) during PI3Kγ activation. The identification of PIK3R5 P629S mutation in AOA2 patients indicated a potential defect in the AKT pathway resulting from impaired PIK3R5 interaction with Gβγ and PIK3CG, defective AKT pathway can result in cerebellar cell death causing neurological symptoms. Our in silico macromolecular docking of the wild type and mutant PIK3R5 protein models with ligand revealed an energy requirement to maintain the mutant complexes compared to no energy required to maintain the wild type complexes, in addition, the mutant structures were loose compared to rigid wild type structures, such structural changes may impair the molecular function of the PIK3R5 and hence affect the AKT pathway.
Marine nurseries and effective juvenile habitats: concepts and applications

Much recent attention has been focused on juvenile fish and invertebrate habitat use, particularly defining and identifying marine nurseries. The most significant advancement in this area has been the development of a standardized framework for assessing the relative importance of juvenile habitats and classifying the most productive as nurseries. Within this framework, a marine nursery is defined as a juvenile habitat for a particular species that contributes a greater than average number of individuals to the adult population on a per-unit-area basis, as compared to other habitats used by juveniles. While the nursery definition and framework provides a powerful approach to identifying habitats for conservation and restoration efforts, it can omit habitats that have a small per-unit-area contribution to adult populations, but may be essential for sustaining adult populations. Here we build on the nursery concept by developing a framework for evaluating juvenile habitats based on their overall contribution to adult populations, and introduce the concept of Effective Juvenile Habitat (EJH) to refer to habitats that make a greater than average overall contribution to adult populations.
Next-generation sequencing in precision oncology: challenges and opportunities

High throughput gene sequencing is transforming the utilization of genomics in patient care by providing physicians with a powerful tool to aid the diagnosis and management of disease, particularly in precision oncology. As next-generation sequencing (NGS)-based diagnostic assays are developed, significant hurdles such as assessing tumor heterogeneity, characterizing ‘driver’ and ‘passenger’ mutations, typing molecular signatures of individual cancers and determining limits of detection pose significant challenges for clinical laboratories and downstream bioinformatics analyses. Despite these challenges, NGS has the potential to affect all facets of cancer treatment, including early detection and diagnosis through cancer screening in at-risk populations and assessing therapeutic efficacy by detection of circulating tumor DNA via noninvasive blood draws. As the utilization of NGS in precision oncology matures, NGS-based laboratory tests could be used throughout the evolution of cancer in patients and allow for cancers to be monitored and managed as a chronic disease, rather than an acute condition.
First Time Application of IFRs and Its Impact on Financial Ratios: A Study on Turkish Listed Firms

As the world economy is getting globalized, the parties using accounting information have faced new problems. Those problems stem from different accounting practices of countries. Although many international organizations have carried out studies on the harmonization of different accounting practices, International Accounting Standards Board (IASB) (previously named as International Accounting Standards Committee (IASC)) has been universally accepted and officially recognized organization. Therefore the idea of harmonizing the international accounting has been realized by the implementation of standards (International Accounting Standards (IAS) and International Financial Reporting Standards (IFRS)) issued by IASC/IASB. In our study, we investigated the extent of differences between the results of financial ratios gath-ered from financial statements prepared as per IAS/IFRS in accordance with the provisions of Turkish Capital Markets Board’s communiqué Series XI, No.: 25 and the financial statements prepared as per the legislation before this communiqué within Istanbul Stock Exchange (ISE).
Metabolism of 7 beta-alkyl chenodeoxycholic acid analogs and their effect on cholesterol metabolism in hamsters.

The metabolism of 7-ethyl- and 7-propyl-chenodeoxycholic acids was studied in hamsters. Both bile acid analogs were absorbed efficiently by the intestine and secreted into the bile at rates similar to those of chenodeoxycholic acid. After intraduodenal administration into bile fistula hamsters, the 7-alkyl analogs were present in bile as the glycine and taurine conjugates. The glycine/taurine ratios were: chenodeoxycholic acid, 1.9; 7-ethyl analog, 0.3; and 7-propyl analog, 0.2. After oral administration, during a 21-day feeding experiment, the 14C-labeled analogs were recovered quantitatively in the feces. Chenodeoxycholic acid was largely 7-dehydroxylated to lithocholic acid in the intestinal tract. In contrast, the 7 alpha-hydroxy group of the 7-alkyl bile acids was completely resistant to bacterial action. 7-Ethyl-chenodeoxycholic acid was transformed in part to a compound tentatively identified as 7 alpha-hydroxy-3-oxo- 7 beta-ethyl-5 beta-cholanoic acid while 7-propyl-chenodeoxycholic acid was excreted unchanged. In the hamsters used, the 7-alkyl bile acid analogs did not inhibit the bacterial dehydroxylation of chenodeoxycholic acid. At the end of the 21-day feeding period, analysis of the gallbladder bile showed that 7-methyl-, 7-ethyl-, and 7-propyl-chenodeoxycholic acids accounted for 38, 31, and 12% of total bile acids, respectively. The 7-alkyl bile acids decreased cholesterol absorption; the 7-propyl analog caused significant decrease in serum and liver cholesterol concentration. These experiments demonstrate that the 7-ethyl- and 7-propyl chenodeoxycholic acids, just like the 7-methyl-analog, are absorbed by the intestine and participate in the enterohepatic circulation. (ABSTRACT TRUNCATED AT 250 WORDS)
Motion capture system using Wiimote motion sensors

The purpose of this study is to examine the Wiimote MotionPlus system as a method to capture angular kinematic data of the knee, hip and back of a participant performing a lifting task. Twenty one subjects were recruited and asked to perform a lifting task while having four Wiimotes strapped to the lower leg, upper leg, and back at the hip and below the shoulder blades. The raw signals from the four Wiimotes were filtered and normalized before being combined to obtain the proper change in angular data. The results of the study demonstrate that it is feasible to combine the data from multiple Wiimotes to obtain kinematic data which may be used in ergonomic analysis.
An E-band slotted waveguide monopulse array antenna with corporate-feed using diffusion bonding of laminated plates

In this paper, we demonstrate an E-band plate-laminated 16 × 16-element slotted waveguide monopulse array antenna with corporate-feed using the diffusion bonding technology. The proposed antenna architecture combines radiating elements, a corporate-feed circuit and a comparator, which are vertically interconnected to achieve a compact size and a reduced loss. The design, characterization, and experimental results are presented.
Stress injury of the lunate in tennis players: a case series and related biomechanical considerations

Objective: To investigate clinical and imaging differential diagnosis and tennis stroke biomechanics potentially involved in lunate stress injury pathogenesis. Methods: The present report describes five competitive tennis players with overuse-related dorsal wrist pain assessed by magnetic resonance imaging. Results: Magnetic resonance imaging revealed the presence of lunate stress injury. All players were treated conservatively, with symptom resolution and complete functional recovery achieved at 14 weeks. Conclusions: Lunate stress injuries should be considered in the differential diagnosis of overuse-related dorsal wrist pain in tennis players.
Proton Transverse Nuclear Magnetic Relaxation in Oxidized Blood: a Numerical Approach

When red blood cells are deoxygenated, hemoglobin, which is then transformed into deoxyhemoglobin or methemoglobin, becomes paramagnetic. The transverse nuclear magnetic relaxation rate of water protons is considerably enhanced by this chemical transformation. A general agreement exists about the origin of the phenomenon—local field inhomogene‐ities induced by paramagnetic centers randomly distributed within the cell—but the localization of the region that dominates the relaxation is unclear. We addressed this problem with a computer simulation devoted to the determination of transverse magnetic relaxation of water protons in the presence of superparamagnetic MRI contrast agent candidates. The simulation confirms an earlier experimental result that shares equitably the responsibility for the observed relaxation between intracellular and extracellular water.
Post-operative telephone review is cost-effective and acceptable to patients

Introduction Patients undergoing selective minor emergency and elective procedures are followed up by a nurse-led structured telephone review six weeks post-operatively in our hospital. Our study objectives were to review patients' satisfaction, assess cost-effectiveness and compare our practice with other surgical units in Northern Ireland (NI). Patients and Methods Completed telephone follow-up forms were reviewed retrospectively for a three-year period and cost savings calculated. Fifty patients were contacted prospectively by telephone using a questionnaire to assess satisfaction of this follow-up. A postal questionnaire was sent to 68 general and vascular surgeons in NI, assessing individual preferences for patient follow-up. Results A total of 1378 patients received a telephone review from September 2005 to September 2008. One thousand one hundred and seventy-seven (85.4%) were successfully contacted, while 201 (14.6%) did not respond despite multiple attempts. One hundred and forty-seven respondents (10.7%) required further outpatient follow-up, thereby saving 1231 outpatient reviews, equivalent to £41,509 per annum. Thirty-nine (78%) patients expected post-operative follow-up, with 29 (58%) expecting this in the outpatient department. However, all patients were satisfied with the nurse-led telephone review. Fifty-three (78%) consultants responded. Those who always, or occasionally, review patients post-operatively varies according to the operation performed, ranging from 2.2% appendicectomy patients to 40.0% for varicose vein surgery. Conclusion Current practice in NI varies, but a significant proportion of patients are not routinely reviewed. This study confirmed that patients expect post-operative follow-up. A nurse-led telephone review service is acceptable to patients, cost-effective and reduces the number of unnecessary outpatient reviews.
Regulation of cytosolic calcium by collagen in single human platelets

1 There is controversy in the literature as to whether collagen is able to induce directly a rise in cytosolic calcium concentration ([Ca2+]i) in human platelets. We have addressed this question by observing the cytosolic calcium response of single fura‐2‐loaded human platelets settling onto a collagen‐coated surface using dynamic fluorescence ratio imaging. 2 Following a short lag phase after adherence to collagen fibres, platelets underwent a rapid rise in cytosolic calcium from basal values of 80 ± 13 nM (n = 24) to a peak of 475 ± 42 nM (n = 24) which was sustained for the remaining period of the experiment. 3 The tyrphostin protein tyrosine kinase inhibitor, ST271, reduced substantially the proportion of platelets which exhibited a rise in [Ca2+]i on adherence to collagen and transformed the response in remaining cells to one of oscillations. 4 In contrast, and as a control for collagen, laminin‐coated surfaces induced adherence of human platelets without elevating intracellular [Ca2+]; the cells however remained responsive to ADP. 5 We conclude that collagen directly induces a rise in cytosolic calcium in single human platelets through a tyrosine kinase‐mediated pathway.
Screening for Carotid Artery Stenosis and Renal Artery Stenosis in Patients Undergoing Tunneled Cuffed Hemodialysis Catheter Placement

In this study, we noted the common risk factors with atherosclerosis and chronic renal disease. We, therefore, hypothesized that the placement of a dialysis catheter would be a useful marker in identifying populations at increased risk of vascular disease (carotid, renal, and aortic). To further explore this issue, we examined the results of duplex scanning of the carotid arteries and aortorenal arteries in patients undergoing dialysis catheter placement. Over 49 months, each of the 123 patients who underwent permanent tunneled dialysis catheter placement received a carotid duplex study. Twelve patients (9.8%) had ≥ 60% stenosis and 8 patients (6.5%) had 70% to 99% stenosis. Furthermore, 109 patients who underwent a aortorenal artery duplex study were also analyzed. The study population demonstrated a prevalence rate of 3.7% for abdominal aorta aneurysm (AAA) and 4.6% for renal artery stenosis (RAS). Based upon these data, we suggest performing routine carotid duplex scans in patients who will also receive dialysis catheter placement. However, the data did not support routine screening of AAA or RAS.
Dynamic Optical Fiber Sensing With Brillouin Optical Time Domain Reflectometry: Application to Pipeline Vibration Monitoring

Brillouin distributed optical fiber strain sensors are often limited to static events because of necessary long acquisition time due to the frequency sweep technique. Dynamic distributed strain monitoring is necessary to ensure the integrity of linear structures submitted to fatigue loading or vibrations, such as subsea risers or flowlines, overhead pipelines, long bridges, railways, or high-rise towers. In this paper, a novel dynamic Brillouin optical time domain reflectometer for single ended truly distributed strain measurement based on the slope-assisted method is presented. The optical local oscillator frequency is adjusted to measure Brillouin backscattered power at the maximum slope of the Brillouin gain spectrum along the fiber length. Any strain variation inducing Brillouin frequency shift will be detected by amplitude variation. To demonstrate the performance of our acquisition system, three optical fibers have been implemented along a 10 m steel pipe submitted to vibration. Through this mockup testing, we were able to measure the oscillation damping time and the geometrical displacement of the pipe in real time. A 7.6 Hz acquisition rate was achieved with a strain error of ± 40 μ strain and with a spatial resolution of 1 m. From integration of longitudinal strains, pipe displacement is calculated with an error of ± 12 mm. A performance comparison between frequency sweep and slope assisted method is made with a 2 km fiber sensor.
Randomly Perturbed Radial Trajectories for Compressed Sensing MRI

Introduction: The recently introduced Compressed Sensing (CS) theory illustrates that a small number of random linear measurements can be sufficient to reconstruct sparse or compressible signals [1,2,3]. Since the number of measurements necessary for perfect reconstruction using the CS theory can be drastically smaller than the number of measurements required by the Nyquist sampling theory, CS has the potential to significantly accelerate data acquisition in MRI [4-10]. Although the initial CS theory was based on completely random sampling, it was later suggested that such random sampling may not always be necessary [11]. More specifically, recent results indicate that CS methods can yield exact recovery if the sparsity basis and the measurement basis obey the uniform uncertainty principle and are incoherent [11]. This pertains to MRI since complete random sampling is difficult to achieve with existing hardware. Earlier work in CS for MRI explored strategies for randomizing measurements for spirals [4] and 3DFT trajectories [5]. Recently, reconstructions from CS MRI data acquired on regular radial trajectories were demonstrated [7-10]. While the CS reconstruction of undersampled regular radial data resulted in significant reduction of streaking artifacts, compared to filtered backprojection or regridding, we demonstrate here that further improvements are possible by randomly perturbing the radial trajectories.
Cytotoxicity of a replication-defective mutant of herpes simplex virus type 1

Replication-defective mutants of herpes simplex virus type 1 (HSV-1) may prove useful as vectors for gene transfer, particularly to nondividing cells. Cgal delta 3 is an immediate-early gene 3 (IE 3) deletion mutant of HSV-1 that expresses the lacZ gene of Escherichia coli from the human cytomegalovirus immediate-early control region but does not express viral early or late genes. This vector was able to efficiently infect and express lacZ in cells refractory to traditional methods of gene transfer. However, 1 to 3 days postinfection, Cgal delta 3 induced cytopathic effects (CPE) in many cell types, including neurons. In human primary fibroblasts Cgal delta 3 induced chromosomal aberrations and host cell DNA fragmentation. Other HSV-1 strains that caused CPE, tested under conditions of viral replication-inhibition, included mutants of the early gene UL42, the virion host shutoff function, single mutants of IE 1, IE 2, and IE 3, and double mutants of IE 3 and 4 and IE 3 and 5. Inhibition of viral gene expression by UV irradiation of virus stocks or by preexposure of cells to interferon markedly reduced the CPE. We conclude from these studies that HSV-1 IE gene expression is sufficient for the induction of CPE, although none of the five IE gene products appear to be solely responsible. After infection of human fibroblasts with Cgal delta 3 at a low multiplicity of infection, we were able to recover up to 6% of the input virus 2 weeks later by a superinfection-rescue procedure, even though the virally transduced human cytomegalovirus-lacZ transgene was not expressed at this time. It is therefore likely that inhibition or inactivation of viral IE gene expression, either for establishing latency or for the long-term transduction of foreign genes by HSV-1 vectors, is essential to avoid the death of infected cells.