Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactive texturing by polyhedron decomposition

For visualization in virtual reality, two topics are of major importance: real-time rendering and realism. To meet these requirements, modern graphics hardware has to be applied wherever possible. A commonly used method to improve realism without decreasing the rendering speed is texturing. Today, fast texture mapping algorithms are even integrated in low-cost hardware. However, high-resolving and non-distorting texturing is very difficult and sometimes even impossible for non-convex complex polyhedra. Nevertheless, the realism of many virtual reality applications could be improved by using non-distorted textures. Especially in surgical simulation, each anatomical detail has to be placed correctly on very complex models of human organs. For this, a new method has been developed, allowing the interactive placement of high-resolution bitmaps to any desired position on the model's surface. In addition, the visualization quality can be improved by using an antialiasing filter. This method, called arbitrary texture placement, utilizes polyhedron decomposition to split one object of complex shape into N triangles. Treating each triangle of the surface as independent object it is possible to assign them an unique part of the texture space where color information can be stored. If a bitmap is applied to the polyhedron's surface, the involved triangles are determined and the pieces of the bitmap inside the triangle are stored at the corresponding areas in the texture space. An example shows the appliance of the method to an anatomical model of the ventricular system in the human brain, used for simulating minimally invasive neurosurgery.
Spotting Fake Reviews using Positive-Unlabeled Learning

Fake review detection has been studied by researchers for several years. However, so far all re- ported studies are based on English reviews. This paper reports a study of detecting fake reviews in Chinese. Our review dataset is from the Chinese review hosting site Di- anping 1 , which has built a fake review detection system. They are confident that their algorithm has a very high precision, but they don't know the recall. This means that all fake reviews detected by the system are almost certainly fake but the remaining reviews may not be all genuine. This paper first reports a supervised learning study of two classes, fake and unknown. However, since the unknown set may contain many fake reviews, it is more appropriate to treat it as an unlabeled set. This calls for the model of learning from positive and unla- beled examples (or PU-learning). Experimental results show that PU learning not only outperforms supervised learning significantly, but also detects a large number of potentially fake reviews hidden in the unlabeled set that Dianping fails to detect.
Quantitative analysis of iris changes after physiologic and pharmacologic mydriasis in a rural Chinese population.

PURPOSE To estimate and compare the change in iris cross-sectional area (IA) and iris volume (IV) following physiologic and pharmacologic pupil dilation in primary angle closure suspects (PACS) and normal subjects. METHODS Anterior segment-optical coherence tomography (AS-OCT) measurements in light, dark, and following pharmacologic dilation were obtained on 186 PACS and 224 normal subjects examined during the 5-year follow-up of the Handan Eye Study. Iris cross-sectional area, IV, and other biometric parameters calculated using the Zhongshan angle assessment program in the right eyes of all subjects were analyzed. RESULTS The mean IA and IV decreased in dark compared with light and after pharmacologic dilation in both PACS and normal eyes. This change was statistically significant in normal eyes: light versus pharmacologic dilation for IA (P = 0.038) and for IV, both light versus dark (P = 0.031) and light versus pharmacologic dilation (P = 0.012). A longer axial length (P = 0.028) and a greater change in pupil diameter (PD) (P < 0.001) were associated with a larger decrease of IA for the light to dark comparison. A diagnosis of normal eyes (P = 0.011), larger PD in dark (P = 0.001), and a larger change in PD (P = 0.001) were associated with a larger decrease of IV from light to dark. CONCLUSIONS The differences in iris behavior between PACS and normal rural Chinese subjects following physiologic or pharmacologic pupillary dilation may help provide insights into the pathogenesis of angle closure.
Classical lifting processes and multiplicative vector fields

We extend the calculus of multiplicative vector fields and differential forms and their intrinsic derivatives from Lie groups to Lie groupoids; this generalization turns out to include also the classical process of complete lifting from arbitrary manifolds to tangent and cotangent bundles. Using this calculus we give a new description of the Lie bialgebroid structure associated with a Poisson groupoid.
Hyponatremia of exercise

ConclusionsThere is little doubt that proper hydration benefits physiologic function, performance, and health. There is also little doubt that excessive drinking can create a potentially lifethreatening situation. It appears that excessive fluid intake is the primary cause in most cases of hyponatremia in athletes. Hyponatremia can be prevented by educating athletes about proper hydration practices and adequate sodium intake.
Dynamical vs. Equilibrium Properties of the QCD Phase Transition

We employ an Einstein-Maxwell-Dilaton (EMD) holographic model, which is known to be in good agreement with lattice results for the QCD equation of state with $(2+1)$ flavors and physical quark masses, to investigate the temperature and baryon chemical potential dependence of the susceptibilities, conductivities, and diffusion coefficients associated with baryon, electric, and strangeness conserved charges. We also determine how the bulk and shear viscosities of the plasma vary with increasing baryon density. The diffusion of conserved charges and the hydrodynamic viscosities in a baryon rich quark-gluon plasma are found to be suppressed with respect to the zero net baryon case. The transition temperatures associated with equilibrium and non-equilibrium quantities are determined as a function of the baryon chemical potential for the first time. Because of the crossover nature of the QCD phase transition even at moderately large values of the chemical potential, we find that the transition temperatures associated with different quantities are spread in the interval between $130-200$ MeV and they all decrease with increasing baryon chemical potential.
Can endoscopy be avoided in the assessment of ulcerative colitis in clinical trials?

Background: There is no gold standard index in the measurement of ulcerative colitis (UC) disease activity in clinical trials. Mucosal healing has been described as an important clinical endpoint requiring endoscopic assessment, which is unpleasant for the patient and may hamper recruitment to trials. The aim of this study was to determine whether endoscopy is necessary in the assessment of UC disease activity and whether a noninvasive disease activity index (partial Mayo score) could be used to predict the Mayo score. Methods: In all, 149 subjects with moderate to severe UC enrolled in a clinical trial were assessed using total and partial Mayo scores. Histologic assessment of biopsies was performed. A regression model was constructed to predict total Mayo score from the partial Mayo score and histology score from the Mayo score. A Bland–Altman test of agreement was performed. Results: The partial Mayo score correlated closely with the total Mayo score at week 4 (rho = 0.97) and week 8 (rho = 0.98). The model to predict total from partial Mayo score showed excellent correlation (rho = 0.97) and good agreement with the total Mayo score at week 4 and the week 8 validation set (rho = 0.97) and accurately classified disease severity (kappa = 0.82). The model to predict histology score from the Mayo score correlated only moderately with the actual histology score at week 4 (rho = 0.59) and week 8 (rho = 0.36). Conclusions: The Mayo score can be accurately predicted from the partial Mayo score. A noninvasive index can replace the Mayo score in future clinical trials. (Inflamm Bowel Dis 2012;)
Evidence for an oscillatory signature in atmospheric neutrino oscillations.

Muon neutrino disappearance probability as a function of neutrino flight length L over neutrino energy E was studied. A dip in the L/E distribution was observed in the data, as predicted from the sinusoidal flavor transition probability of neutrino oscillation. The observed L/E distribution constrained nu(micro)<-->nu(tau) neutrino oscillation parameters; 1.9x10(-3)0.90 at 90% confidence level.
UvA-DARE ( Digital Academic Repository ) A State Change in the Missing Link Binary Pulsar System PSR J 1023 + 0038

We present radio and γ -ray observations, which, along with concurrent X-ray observations, reveal that the binary millisecond pulsar (MSP)/low-mass X-ray binary transition system PSR J1023+0038 has undergone a transformation in state. Whereas until recently the system harbored a bright millisecond radio pulsar, the radio pulsations at frequencies between 300 to 5000 MHz have now become undetectable. Concurrent with this radio disappearance, the γ -ray flux of the system has quintupled. We conclude that, though the radio pulsar is currently not detectable, the pulsar mechanism is still active and the pulsar wind, as well as a newly formed accretion disk, are together providing the necessary conditions to create the γ -ray increase. This system is the first example of a compact, low-mass binary which has shown significant state changes accompanied by large changes in γ -ray flux; it will continue to provide an exceptional test bed for better understanding the formation of MSPs as well as accretion onto neutron stars in general.
A case study on regression test suite maintenance in system evolution

When a system is maintained, its automated test suites must also be maintained to keep the tests up to date. Even though practice indicates that test suite maintenance can be very costly we have seen few studies considering the actual efforts for maintenance of test-ware. We conducted a case study on an evolving system with three updated versions, changed with three different change strategies. Test suites for automated unit and functional tests were used for regression testing the extended applications. With one change strategy more changes were made in the tests code than in the system that was tested, and with another strategy no changes were needed for the unit tests to work.
Evidence for gene‐environment interaction in a genome wide study of nonsyndromic cleft palate

Nonsyndromic cleft palate (CP) is a common birth defect with a complex and heterogeneous etiology involving both genetic and environmental risk factors. We conducted a genome‐wide association study (GWAS) using 550 case‐parent trios, ascertained through a CP case collected in an international consortium. Family‐based association tests of single nucleotide polymorphisms (SNP) and three common maternal exposures (maternal smoking, alcohol consumption, and multivitamin supplementation) were used in a combined 2 df test for gene (G) and gene‐environment (G × E) interaction simultaneously, plus a separate 1 df test for G × E interaction alone. Conditional logistic regression models were used to estimate effects on risk to exposed and unexposed children. While no SNP achieved genome‐wide significance when considered alone, markers in several genes attained or approached genome‐wide significance when G × E interaction was included. Among these, MLLT3 and SMC2 on chromosome 9 showed multiple SNPs resulting in an increased risk if the mother consumed alcohol during the peri‐conceptual period (3 months prior to conception through the first trimester). TBK1 on chr. 12 and ZNF236 on chr. 18 showed multiple SNPs associated with higher risk of CP in the presence of maternal smoking. Additional evidence of reduced risk due to G × E interaction in the presence of multivitamin supplementation was observed for SNPs in BAALC on chr. 8. These results emphasize the need to consider G × E interaction when searching for genes influencing risk to complex and heterogeneous disorders, such as nonsyndromic CP. Genet. Epidemiol. 2011. © 2011 Wiley‐Liss, Inc. 35: 469‐478, 2011
Traffic Measurement and Route Recommendation System for Mass Rapid Transit (MRT)

Understanding how people use public transport is important for the operation and future planning of the underlying transport networks. We have therefore developed and deployed a traffic measurement system for a key player in the transportation industry to gain insights into crowd behavior for planning purposes. The system has been in operation for several months and reports, at hourly intervals, (1) the crowdedness of subway stations, (2) the flows of people inside interchange stations, and (3) the expected travel time for each possible route in the subway network of Singapore. The core of our system is an efficient algorithm which detects individual subway trips from anonymized real-time data generated by the location based system of Singtel, the country's largest telecommunications company. To assess the accuracy of our system, we engaged an independent market research company to conduct a field study--a manual count of the number of passengers boarding and disembarking at a selected station on three separate days. A strong correlation between the calculations of our algorithm and the manual counts was found. One of our key findings is that travelers do not always choose the route with the shortest travel time in the subway network of Singapore. We have therefore also been developing a mobile app which allows users to plan their trips based on the average travel time between stations.
Volumetric image-guidance: Does routine usage prompt adaptive re-planning? An institutional review

Purpose. To investigate how the use of volumetric image-guidance using an on-board cone-beam computed tomography (CBCT) system impacts on the frequency of adaptive re-planning. Material and methods. Treatment courses of 146 patients who have undergone a course of external beam radiation therapy (EBRT) using volumetric CBCT image-guidance were analyzed. Target locations included the brain, head and neck, chest, abdomen, as well as prostate and non-prostate pelvis. The majority of patients (57.5%) were treated with hypo-fractionated treatment regimens (three to 15 fraction courses). The frequency of image-guidance ranged from daily (87.7%) to weekly or twice weekly. The underlying medical necessity for adaptive re-planning as well as frequency and consequences of plan adaptation to dose-volume parameters was assessed. Results. Radiation plans of 34 patients (23.3%) were adapted at least once (up to six time) during their course of EBRT as a result of image-guidance CBCT review. Most common causes for adaptive planning were: tumor change (mostly shrinkage: 10 patients; four patients more than one re-plan), change in abdominal girth (systematic change in hollow organ filling; n=7, two patients more than one re-plan), weight loss (n=5), and systematic target setup deviation from simulation (n=5). Adaptive re-plan was required mostly for conventionally fractionated courses; only 5 patient plans undergoing hypo-fractionated treatment were adjusted. In over 91% of adapted plans, the dose-volume parameters did deviate from the prescribed plan parameters by more than 5% for at least 10% of the target volume, or organs-at-risk in close proximity to the target volume. Discussion. Routine use of volumetric image-guidance has in our practice increased the demand for adaptive re-planning. Volumetric CBCT image-guidance provides sufficient imaging information to reliably predict the need for dose adjustment. In the vast majority of cases evaluated, the initial and adapted dose-volume parameters differed to a degree that was considered clinically significant.
The effect of weighted body armor on close combat reaction time and core muscle activation

The purpose of this study was to measure the choice reaction time and myoelectric activity of the right and left rectus abdominus, and right and left external obliques required to initiate movement in response to a visual stimulus that signaled performance of four different closecombat movements (left or right cross and left or right dodge). Reaction time and myoelectric activity were then compared with performing the movements in response to the visual stimulus while wearing a weighted vest that simulated wearing tactical body armor. Myoelectric activity was measured as the average root mean square (RMS) of the surface electromyography (sEMG) values. The hypotheses were that average time to react to the visual stimulus for each movement and average myoelectric activity to initiate the movement would be greater under the weighted vest condition. The participants were 10 active martial arts/boxing performers from different disciplines with a minimum one year experience in their discipline. During two separate sessions, the participants completed eight warm-up trials and 24 measured trials, with the first four trials deleted. The stimuli were activated in a random order with foreperiods ranging from 10 to 20 seconds between trials. The sessions were randomly chosen to be either loaded or unloaded conditions. Surface EMG electrodes detected the myoelectric activity of the right and left rectus abdominus, and right and left external oblique muscles. The electrodes pre-amplified the myoelectric signals by a factor of 35. The sEMG signals of the four muscles were treated with a 20 Hz low cut/high pass filter, amplified by a factor of 20,000, and the RMS of the filtered signals were derived using an 11.75 ms time window. The analog RMS sEMG was sampled at 1020 Hz and converted to digital form. The reaction time for each movement was determined from the initiation of the stimulus to the point at which myoelectric activity
Effect of conjugated linoleic acid and acetate on milk fat synthesis and adipose lipogenesis in lactating dairy cows.

During biohydrogenation-induced milk fat depression (MFD), nutrients are spared from milk fat synthesis and are available for other metabolic uses. Acetate is the major carbon source spared and it may increase lipid synthesis in adipose tissue during MFD. The objective of this study was to compare the effect of trans-10,cis-12 conjugated linoleic acid (CLA) and the amount of acetate spared during CLA-induced MFD on adipose tissue lipogenesis. Nine multiparous, lactating, ruminally cannulated Holstein cows (244 ± 107 d in milk; 25 ± 8.4 kg of milk/d; mean ± standard deviation) were randomly assigned to treatments in a 3 × 3 Latin square design. Experimental periods were 4 d followed by a 10-d washout. Treatments were control (CON), ruminal infusion of acetate (AC; continuous infusion of 7 mol/d adjusted to pH 6.1 with sodium hydroxide), or abomasal infusion of CLA (10 g/d of both trans-10,cis-12 CLA and cis-9,trans-11 CLA). Dry matter intake, milk yield, and milk protein yield and percentage were not affected by treatments. Compared with CON, milk fat yield decreased 23% and fat percent decreased 28% in CLA, and milk fat yield increased 20% in AC. Concentration and yield of milk de novo synthesized fatty acids (C16) was increased by CLA, compared with CON. Yield of de novo synthesized fatty acids and palmitic acid was increased by AC, compared with CON. Lipogenesis capacity of adipose tissue explants was decreased 72% by CLA, but was not affected by AC. Acetate oxidation by adipose explants was not affected by treatments. Treatments had no effect on expression of key lipogenic factors, lipogenic enzymes, and leptin; however, expression of fatty acid binding protein 4 was reduced in CLA compared with CON. Additionally, hormone-sensitive lipase and perilipin 1 were decreased by CLA and acetate. Plasma glucose and glucagon concentrations were not affected by treatments; however, CLA increased nonesterified fatty acids 17.7%, β-hydroxybutyrate 16.1%, and insulin 27.8% compared with CON, and AC increased plasma β-hydroxybutyrate 18%. In conclusion, during CLA-induced MFD in low-producing cow adipose tissue was sensitive to the anti-lipogenic effects of CLA, while spared acetate did not stimulate adipose lipogenesis. However, acetate may play an important role in stimulating lipogenesis and improving energy status in the mammary gland under normal conditions.
Re-Sequencing of the APOL1-APOL4 and MYH9 Gene Regions in African Americans Does Not Identify Additional Risks for CKD Progression

Background: In African Americans (AAs), APOL1 G1 and G2 nephropathy risk variants are associated with non-diabetic end-stage kidney disease (ESKD) in an autosomal recessive pattern. Additional risk and protective genetic variants may be present near the APOL1 loci, since earlier age ESKD is observed in some AAs with one APOL1 renal-risk variant, and because the adjacent gene MYH9 is associated with nephropathy in populations lacking G1 and G2 variants. Methods: Re-sequencing was performed across a ∼275 kb region encompassing the APOL1-APOL4 and MYH9 genes in 154 AA cases with non-diabetic ESKD and 38 controls without nephropathy who were heterozygous for a single APOL1 G1 or G2 risk variant. Results: Sequencing identified 3,246 non-coding single nucleotide polymorphisms (SNPs), 55 coding SNPs, and 246 insertion/deletions. No new coding variations were identified. Eleven variants, including a rare APOL3 Gln58Ter null variant (rs11089781), were genotyped in a replication panel of 1,571 AA ESKD cases and 1,334 controls. After adjusting for APOL1 G1 and G2 risk effects, these variations were not significantly associated with ESKD. In subjects with <2 APOL1 G1 and/or G2 alleles (849 cases; 1,139 controls), the APOL3 null variant was nominally associated with ESKD (recessive model, OR 1.81; p = 0.026); however, analysis in 807 AA cases and 634 controls from the Family Investigation of Nephropathy and Diabetes did not replicate this association. Conclusion: Additional common variants in the APOL1-APOL4-MYH9 region do not contribute significantly to ESKD risk beyond the APOL1 G1 and G2 alleles.
Different transport routes for high density lipoprotein and its associated free sterol in polarized hepatic cellss⃞s⃞ The online version of this article (available at http://www.jlr.org) contains an additional two figures. Published, JLR Papers in Press, December 16, 2003. DOI 10.1194/jlr.M300440-JL

We analyzed the intracellular transport of HDL and its associated free sterol in polarized human hepatoma HepG2 cells. Using pulse-chase protocols, we demonstrated that HDL labeled with Alexa 488 at the apolipoprotein (Alexa 488-HDL) was internalized by a scavenger receptor class B type I (SR-BI)-dependent process at the basolateral membrane and became enriched in a subapical/apical recycling compartment. Most Alexa 488-HDL was rapidly recycled to the basolateral cell surface and released from cells. Within 30 min of chase at 37°C, ∼3% of the initial cell-associated Alexa 488-HDL accumulated in the biliary canaliculus (BC) formed at the apical pole of polarized HepG2 cells. Even less Alexa 488-HDL was transported to late endosomes or lysosomes. The fluorescent cholesterol analog dehydroergosterol (DHE) incorporated into Alexa 488-HDL was delivered to the BC within a few minutes, independent of the labeled apolipoprotein. This transport did not require metabolic energy and could be blocked by antibodies against SR-BI. The fraction of cell-associated DHE transported to the BC was comparable when cells were incubated with either Alexa 488-HDL containing DHE or with DHE bound to methyl-β-cyclodextrin. We conclude that rapid, nonvesicular transport of sterol to the BC and efficient recycling of HDL particles underlies the selective sorting of sterol from HDLs in hepatocytes.