Miracle-dz/UniFAR-FTUs huggingface dataset:
Activated Function of the Pyruvate Dehydrogenase Phosphatase through Ca2+-facilitated Binding to the Inner Lipoyl Domain of the Dihydrolipoyl Acetyltransferase*

Micromolar Ca2+ facilitates ∼10-fold enhancement of pyruvate dehydrogenase phosphatase (PDP) activity by aiding the association of PDP with the dihydrolipoyl acetyltransferase (E2) component. Connected by linker regions, E2 consists of two lipoyl domains, the NH2-lipoyl domain (L1) and the interior lipoyl domain (L2), and a pyruvate dehydrogenase component binding domain surrounding a 60-mer inner core. Using recombinant constructs of L1 or L2, E2-enhanced PDP activity was markedly decreased by L2 but not by L1, effectively competing with intact E2 in Ca2+-dependent binding of PDP (half-maximal reduction at 2.0 μM L2 versus 6.7 μM E2 subunit). Using L2 fused to glutathione S-transferase resulted in direct Ca2+-dependent binding of PDP to L2 (Kd, ∼1.7 μM L2). Affinity-bound glutathione S-transferase-L2 was used to purify PDP to homogeneity by selective binding and elution by Ca2+ chelation. The large activity enhancement of PDP by E2 was eliminated by enzymatic removal of lipoates from E2 and restored by their enzymatic reintroduction. The critical role of the L2 lipoate is not in binding of PDP to E2, since PDP was still bound by delipoylated L2, and delipoylated L2 inhibited E2-enhanced PDP activity, although lipoylated L2 was more effective in each of these tests. Thus, pyruvate dehydrogenase complex activity is increased by enhanced availability of PDP to its E2-bound, phosphorylated pyruvate dehydrogenase substrate as a consequence of the Ca2+-facilitated interchange of PDP among the mobile L2 domains and an essential (undetermined) step engaging the L2 lipoate.
Fare System of Urban Public Transportation Services in Davao City, Philippines

A model of modal choice and destination choice was developed to simulate urban travel demand in Davao City, Philippines, and to evaluate fare-setting scenarios relevant to the possible introduction of a new public transportation (PT) system. This nested logit model, combining modal choice and destination choice, was estimated with local person trip survey data collected in 2015 that included data points on 3,531 households, 7,639 individuals, and 15,372 trips. Then, six fare scenarios were developed, incorporating four elements of the fare system, boarding charge, per-kilometer charge, charge distance, and transfer charge, based on the fare system in use in the Philippines. Five evaluation indexes were then applied: average individual benefit, new PT operator’s profit, social surplus, modal share of PT, and regional equity with respect to accessibility. The results demonstrated that (a) a lower fare increases an individual’s benefit from the trip, (b) a new PT operator’s profit assumes positive values in a wide range of fare scenarios, (c) a lower fare improves net social surplus, (d) a lower fare leads to higher modal share of PT, and (e) a higher fare tends to compromise the regional equity of accessibility. These results also suggest that from the viewpoint of enhancing social surplus, increasing the boarding charge is a preferable strategy at a higher fare level, whereas the mitigation of the per-kilometer charge is a preferable strategy at a lower fare level.
Evaluation of urinary bladder function after acute spinal cord injury: an experimental study.

OBJECTIVES The aim of this study was to evaluate the efficacy of early surgical decompression of acute spinal cord injury through the evaluation of urinary bladder function in rabbits. MATERIALS AND METHODS The study was done with 21 New Zealand male rabbits which were 9 to 12 months in age, and weighed an average of 2438 grams (range 2150 to 3550 g). The animals were assigned into four groups as follows: a control group (n=5), a laminectomy group (n=6), a 15-second compression group (n=5) and a 60-second compression group (n=5). A 60 gram compression force was applied on both compression groups with aneurysm clips. All rabbits were sacrificed seven days postoperatively. Urinary bladder tissues were dissected and in vitro relaxation and contraction tests were performed in organ baths. RESULTS At the beginning of each experiment, 80 mM KCl was added to the isolated organ bath with no significant difference among all four groups (p>0.05). Carbachol was then added to the organ bath and contraction responses were obtained. Carbachol contraction responses were calculated as the percentage of the 80 mM KCl contraction responses, with compression groups showing significant difference from control and sham-operated groups (p<0.05). Electrical field stimulation responses were obtained for all group preparations at 4, 8, 16, 32 Hz frequencies, and showed significant difference in the 15 and 60-second compression groups (p<0.05). The contractility was assessed using E-max and pD2 values. All groups exhibited same pD2 values. CONCLUSION The study demonstrated a slightly better outcome for bladder contractility with early decompression. However, there was no significant difference between early and delayed decompression groups.
Back to the Future: A 25-Year Retrospective on GTAP and the Shaping of a New Agenda

This article looks back at 25 years of achievements of the Global Trade Analysis Project (GTAP) from different angles. It covers the design features of the project and the collaboration in a global research network, the contributions GTAP has made to better informed trade policy making, its contributions in the area of environment and climate change and its capacity to absorb theoretical developments in applied modeling. The paper also makes some suggestions about future directions.
Polymorphism in CD33 and CD34 genes: a source of minor histocompatibility antigens on haemopoietic progenitor cells?

Following bone marrow stem cell transplantation allo‐responses against haemopoietic progenitor cells (HPC), causing graft rejection and graft‐versus‐leukaemia effects, can be induced by donor T cells recognizing peptides derived from polymorphic endogenous proteins present in HPC. Since CD33 and CD34 are both expressed on HPC, we looked for genetic polymorphisms that might be the source of minor histocompatibility antigens (mHA) on such cells. Bone marrow from 14 donors and their HLA‐identical recipients undergoing BMT for haematological malignancies were studied. Using non‐radioactive single‐strand conformation polymorphism analysis (cold SSCP) of complementary DNA encoding CD33 and CD34, three DNA polymorphisms, two in CD33 and one in CD34 were found and sequenced. Two were in non‐coding regions, but in CD33, ATA or ATG at codon 183 resulted in an Ile or Met in the protein sequence. Nonapeptides derived from both alleles were predicted to bind to HLA A68.1. Thus two alleles of CD33 protein exist that could be mHA. With an alternate allele frequency of < 10%, allo‐responses against CD33 would be uncommon after marrow transplantation. However, donors homozygous for this allele could be used to generate cytotoxic T cells against the frequent CD33 allele, for adoptive therapy of leukaemia.
Retroperitoneal laparoscopic versus open dismembered pyeloplasty for ureteropelvic junction obstruction.

OBJECTIVE To compare classical open pyeloplasty with retroperitoneal laparoscopic pyeloplasty in effectiveness, potential advantages and complications. MATERIALS AND METHODS Between March 2006 and April 2010, 113 patients with ureteropelvic junction obstruction underwent retroperitoneal laparoscopic dismembered pyeloplasty were retrospectively compared with those of 59 patients who underwent open dismemberse pyeloplasty through a retroperitoneal flank approach. The Chi-square test was used for statistical analysis of qualitative data and the Student t-test for analysis of quantitative data. P < 0.05 was considered significant. RESULTS Operative time was shorter in the retroperitoneal laparoscopic group (mean 125 min) compared to the open pyeloplasty group (mean 142 min, P < 0.05). Mean hospital stay was shorter in the retroperitoneal laparoscopic group (mean 6 days, compared to 9 days, open). Complication rates, including anastomotic urinary leakage, stenosis and infection, were 4.42% in retroperitoneoscopic compared to 6.78% open surgery. Anastomotic leakage was 3 cases in the retroperitoneoscopic group versus 1 case in the open group. Success, defined as improved ultrasonic or renographic parameters, with resolution of symptoms where discernable, was noted in 98.0% of the open group and 98.1% of the retroperitoneoscopic group with a mean follow up of 38.4 and 32.7 months, respectively. CONCLUSIONS Retroperitoneal laparoscopic dismembered pyeloplasty in treatment of ureteropelvic junction obstruction is a minimally invasive, safe and effective therapy with short procedure time, less complications, and shorter convalescence.
Automated malicious advertisement detection using VirusTotal, URLVoid, and TrendMicro

The Internet economy is based on free access to content in exchange of viewing advertisements that might lead to online purchases. Advertisements represent an important source of revenue to Advertising companies. Those companies employ every possible technique and trick to maximize clicks and visits to advertisers' websites. Modern websites exchange advertisement contents from ads' providers (such as Google AdSense), which means they do not control the contents of those advertisements. Although large providers such as Google and Yahoo! are supposed to be trustworthy, ad arbitration allows them to auction of those ad slots to other providers. Therefore, web administrators cannot guarantee the source of the ads on their delegated website areas. Those advertisements contain Javascript and may redirect to malicious websites which might lead to malicious code being executed or malware being installed. This paper proposes and implements a system for automatically detecting malicious advertisements. It employs three different online malware domain detections systems (VirusTotal, URLVoid, and TrendMicro) for malicious advertisements detection purposes and reports the number of detected malicious advertisements using each system. In addition, we study the efficiency of each system by calculating the confusion matrix and accuracy. We find that URLVoid is the best in terms of accuracy (73%) because it uses a combination of well known website scanners and domain blacklists.
A boundary representation technique for three-dimensional objects

The marching cubes algorithm of W.E. Lorensen and H.E. Cline (1987) is a method that is used frequently in 3D object visualisation. The underlying concept of the technique is to form piecewise planar approximations to surfaces, for which pre-determined normals are used for shading purposes. It should be noted that these approximations are precisely as accurate as the data given; there is no loss in quality or error introduced. The approach of using these cubes to represent data can also be used to fully describe the piecewise planar approximation to the surface. Problems arise however, in terms of the storage space required for the representation of large objects, and it is this issue that is addressed in this paper. We present an algorithm that transforms pixel-wise data into a boundary representation that has potential for large reductions in storage. The algorithm does not involve any further approximation of the surface of the object than that given as input. The algorithm also provides a structure that makes surface analysis and matching very simple.
Field Sampling Rate of BG-Sentinel Traps for Aedes aegypti (Diptera: Culicidae) in Suburban Cairns, Australia

ABSTRACT Mini-mark-release-recapture experiments were conducted in suburban Cairns, Australia to establish the sampling rate of the Biogents-Sentinel (BGS) trap for adult Aedes aegypti (L.). Small cohorts of marked mosquitoes (30 females and 15 males) were released at typical Cairns residences, and the number of marked mosquitoes recaptured in the BGS trap after 24 h was recorded. The sampling rate was compared between two seasons and two common housing styles (high-set ‘Queenslander-style’ timber and low-set brick houses), between old gravid and young nulliparous females, and between mosquitoes released in different areas of a house. Overall, the BGS traps recaptured a mean (±SEM) of 24.6% (±1.9) of the released marked female mosquitoes in 24 h. The mean recapture rate for females was significantly higher in the dry season (30.4% ± 2.8) compared with the wet (18.8% ± 2.2). The overall recapture rates did not differ significantly between the two house types, but variability between the individual premises was high. An overall mean of 18.2% (±1.7) of males was collected. Recapture rates of young nullipars and older gravid females were similar. These recapture rates can be used to estimate the population density of Ae. aegypti females in north Queensland, although it will provide an underestimate as trap sample was largely representative of mosquitoes present in the same area as the trap, and not from other areas of the house.
Short Communication FE65 in Alzheimer’s Disease Neuronal Distribution and Association with Neurofibrillary Tangles

FE65, a protein expressed in the nervous system, has the ability to bind the C-terminal domain of the amyloid precursor protein. This suggests a role for FE65 in the pathogenesis of Alzheimer’s disease (AD). The present study was conducted to find out if the distribution of FE65 immunoreactivity was affected during the course of AD, and to determine the degree of co-localization of FE65 with other proteins known to be involved in AD. Single immunoperoxidase-labeling experiments, conducted on six sporadic AD patients and six nondemented age-matched controls, showed that the proportion of volume occupied by FE65 immunoreactivity was not modified in the isocortex of AD patients. However, in hippocampal area CA4, increased FE65 immunoreactivity seemed to be associated with the severity of the disease. Double-immunofluorescent labeling did not show any clear co-localization of FE65 with the amyloid precursor protein. FE65 immunoreactivity was also absent from focal and diffuse deposits of the (cid:2) -amyloid peptide. Unexpectedly double labeling experiments showed a co-localization of FE65 and tau proteins in intracellular tangles. Ultrastructural observations confirmed that FE65 was associated with paired helical filaments. (Am J Pathol 2001, 158:1585–1591) Alzheimer’s
Inference of past population expansion from the timing of coalescence events in a gene genealogy.

We investigate the expected coalescent in populations growing exponentially. The distribution of expected times to coalescence events may show a linear relationship with a number of ancestral lineages, when the latter is subjected to the "epidemic transformation". However, in a number of viral populations, upward curves are created when the epidemically transformed number of ancestral lineages is plotted against time. We consider possible causes of such upward curves. These include the possibility that a curved line is created through a transformation failure due to a sample size that is too large. We suggest a new formula for predicting such failure. The second cause is a population size increasing at an accelerating rate. However, the combination of recent coalescent events and an upward curve is created by an accelerating population increase only under restricted conditions. Specifically, such a pattern is expected only when, were population growth not to have accelerated, the transformation would have failed anyway. The third cause of nonlinearity arises in the estimated coalescent, as distinct from the real coalescent, if the mutation rate is small. However, coalescence times estimated from data typically give a straight line following epidemic transformation, but the rate of exponential increase, or r value, will be underestimated.
Improved detection of rough defects for ultrasonic nondestructive evaluation inspections based on finite element modeling of elastic wave scattering

Defects which possess rough surfaces greatly affect ultrasonic wave scattering behavior, usually reducing the magnitude of reflected signals. Understanding and accurately predicting the influence of roughness on signal amplitudes is crucial, especially in nondestructive evaluation (NDE) for the inspection of safety-critical components. An extension of Kirchhoff theory has formed the basis for many practical applications; however, it is widely recognized that these predictions are pessimistic because of analytical approximations. A numerical full-field modeling approach does not fall victim to such limitations. Here, a finite element (FE) modeling approach is used to develop a realistic methodology for the prediction of expected backscattering from rough defects. The ultrasonic backscatter from multiple rough surfaces defined by the same statistical class is calculated for normal and oblique incidence. Results from FE models are compared with Kirchhoff theory predictions and experimental measurements to establish confidence in the new approach. At lower levels of roughness, excellent agreement is observed between Kirchhoff theory, FE, and experimental data, whereas at higher values, the pessimism of Kirchhoff theory is confirmed. An important distinction is made between the total, coherent, and diffuse signals and it is observed, significantly, that the total signal amplitude is representative of the information obtained during an inspection. This analysis provides a robust basis for a less sensitive, yet safe, threshold for inspection of rough defects.
The Return to Work Experiences of Colorectal Cancer Survivors

Abstract: During the past 15 years, the number of colorectal cancer survivors has risen dramatically. While it is unclear how many colorectal cancer survivors were employed at the time of diagnosis, it is reasonable to expect a significant proportion of these survivors were temporarily displaced from the work force. This article describes the return to work experiences of 250 colorectal cancer survivors. The majority (80%) of the survivors were employed at diagnosis and 89% returned to work. Of those who returned to work, 81% sustained employment 5 years postdiagnosis. Results indicate survivors were successful in their attempt to return to work and sustain employment. However, 34% of survivors delayed their return beyond 2 months postdiagnosis. After controlling for ethnicity, education, and disease severity, the reason for delay was related to chemotherapy treatment Prospective studies of colorectal cancer survivors to document barriers to work return can guide interventions and occupational services to keep survivors healthy and in the workplace.
Comparison of characteristics between nonobese and overweight/obese subjects with nonalcoholic fatty liver disease in a South Indian population.

AIMS This study was designed to compare the characteristics of nonobese and overweight/obese subjects with nonalcoholic fatty liver disease (NAFLD) in an urban South Indian population. SUBJECTS AND METHODS The study group comprises 541 subjects drawn from the Chennai Urban Rural Epidemiology Study (CURES), which was carried out on a representative sample of Chennai city in southern India. NAFLD was diagnosed by ultrasonography. Subjects with NAFLD were classified as nonobese (body mass index of ≤22.9 kg/m(2)) and overweight/obese (body mass index of ≥23 kg/m(2)) based on World Health Organization Asia Pacific guidelines. Coronary artery disease (CAD) was assessed by a resting 12-lead electrocardiogram that was Minnesota-coded. Insulin resistance was assessed by using the homeostasis assessment model (HOMA-IR) using the following formula: fasting insulin (μIU/mL)×fasting glucose (mmol/L)/22.5. RESULTS In total, 173 of 541 (32%) subjects had NAFLD, of whom 48 (27.7%) had nonobese NAFLD and 125 (72.3%) had overweight/obese NAFLD. Compared with overweight/obese NAFLD patients, fasting blood glucose (104±29 vs. 119±45 mg/dL; P<0.05) and HOMA-IR (2.1±1.8 vs. 2.9±1.8; P<0.001) were lower and high-density lipoprotein cholesterol (43±9 vs. 39±8 mg/dL; P<0.001) was higher among nonobese NAFLD subjects. Multiple logistic regression analysis showed a significant association between nonobese NAFLD and CAD (P=0.013) even after adjusting for age, diabetes, hypercholesterolemia, HOMA-IR, and hypertension. CONCLUSIONS This study suggests that even nonobese NAFLD subjects have an association with CAD.
FAN (factor associated with neutral sphingomyelinase activation), a moonlighting protein in TNF‐R1 signaling

TNF‐α is a pleiotropic cytokine involved in the regulation of various biological effects, including cell survival and proliferation, cell differentiation, and cell death. Moreover, TNF‐α triggers proinflammatory responses, essentially through its ability to promote the expression of various proinflammatory genes. Most of the biological effects initiated by TNF‐α rely on its ability to bind to and activate TNF‐R1. As a consequence, molecular complexes are being formed, resulting from the recruitment of multiple adaptor proteins to the intracellular TNF‐R1 DD. The adaptor protein FAN constitutively binds to a proximal membrane domain of TNF‐R1 called NSD. Herein, the role of FAN in TNF‐α‐induced cell signaling and biological responses is discussed.
Apolipoprotein epsilon4 allele and problems with orientation are associated with a persistent decline in cognition in community-dwelling elderly persons.

BACKGROUND A decline in cognitive test scores in elderly persons can signal the beginning of a descent into dementia or may indicate only a short-term cognitive disturbance. It would be clinically useful to distinguish between the two outcomes and to identify characteristics of each. METHODS Four hundred thirty-seven community-dwelling elderly persons were given the Mini-Mental State Examination (MMSE) annually for an average of 7 years. A low score between baseline and final MMSE was identified. A low score 3 or more points lower than baseline score indicated cognitive decline. This decline was called persistent if the final MMSE score was also at least 3 points lower than baseline MMSE score; otherwise, the decline was considered transient. RESULTS Twenty participants (4.6%) experienced a persistent cognitive decline, 67 participants (15.3%) experienced a transient cognitive decline. Presence of the apolipoprotein epsilon4 allele was significantly associated with persistent cognitive decline (age-adjusted odd ratio [OR] = 11.46, p < .0001) but not with transient cognitive decline (age-adjusted OR = 1.53, p = .219). Incorrect answers on the orientation part of the MMSE at the time of cognitive decline was associated with persistent decline compared to transient decline (age-adjusted OR = 3.58, p = .058). CONCLUSIONS Persistent cognitive decline is an infrequent occurrence in community-dwelling elderly persons. Presence of the epsilon4 allele and errors made by the subject on questions of orientation may be useful in determining whether a cognitive decline is likely to be persistent.
Predicting whether songs will be hit using Logistic Regression

This paper predicts whether a song will be super hit and will it reach it to chart buster based on several music features. It is crucial to predicting the popularity of a song, especially in a business competitive world. We will use Logistic Regression in our model to predict the probability of reaching Top 10 songs in the popularity.