Miracle-dz/UniFAR-FTUs huggingface dataset:
Level set evolution without re-initialization: a new variational formulation

In this paper, we present a new variational formulation for geometric active contours that forces the level set function to be close to a signed distance function, and therefore completely eliminates the need of the costly re-initialization procedure. Our variational formulation consists of an internal energy term that penalizes the deviation of the level set function from a signed distance function, and an external energy term that drives the motion of the zero level set toward the desired image features, such as object boundaries. The resulting evolution of the level set function is the gradient flow that minimizes the overall energy functional. The proposed variational level set formulation has three main advantages over the traditional level set formulations. First, a significantly larger time step can be used for numerically solving the evolution partial differential equation, and therefore speeds up the curve evolution. Second, the level set function can be initialized with general functions that are more efficient to construct and easier to use in practice than the widely used signed distance function. Third, the level set evolution in our formulation can be easily implemented by simple finite difference scheme and is computationally more efficient. The proposed algorithm has been applied to both simulated and real images with promising results.
1.4T study of proton magnetic relaxation rates, iron concentrations, and plaque burden in Alzheimer's disease and control postmortem brain tissue

We measured proton magnetic longitudinal (R1) and transverse (R2) relaxation rates at 1.4T, iron concentrations, water contents, and amyloid plaque densities in postmortem brain tissue samples from three Alzheimer's disease (AD), two possible AD, and five control subjects. Iron concentrations and R1 were significantly higher in the temporal cortex region of our AD group compared to the controls. Frequency analyses showed that the observed trends of higher iron, R1, and R2 in AD gray matter regions were statistically significant. Simple regression models indicated that for AD and control gray matter the iron concentrations and water contents have significant linear correlations with R1 and R2. Multiple regression models based on iron concentrations and water contents were highly significant for all groups and tissue types and suggested that the effects of iron become more important in determining R1 and R2 in the AD samples. At 1.4T R1 and R2 are strongly affected by water content and to a lesser extent by variations in iron concentrations. The AD plaque density did not correlate with iron concentrations, water contents, R1, or R2, suggesting that increases in AD brain iron are not strongly related to the accumulation of amyloid plaques. Magn Reson Med, 2008. © 2008 Wiley‐Liss, Inc.
Hairy cell leukemia in three siblings: An apparent HLA‐linked disease

In a sibship of 11 adults the HLA haplotype A1, B7 occurred in four brothers, three of whom developed hairy cell leukemia (HCL) within a seven‐year period. While this haplotype does not appear to occur with increased frequency in random cases of HCL, the fact that three cases of this uncommon and unique disorder occurred within one family and affected siblings with a common haplotype strongly suggests a genetic linkage.
Quantification of Botrytis in Grape Juice Determined by a Monoclonal Antibody-based Immunoassay

Monoclonal antibodies to Botrytis //, raised in a previous study, were used to develop a plate—trapped antigen enzyme linked immunosorbent assay ( PTA-ELISA) to detect and quantify Botrytis antigens in juice from infected grapes. Using a dilution series of extracts from freezedried preparations of B. cinerea grown in liquid culture on grape juice and juice from artificially infected and healthy Cabernet Sauvignon and Semillon grapes, we have shown that BC-12.CA4, a genus-specific antibody, can be used in micro-titer PTA-ELISA tests to measure levels of infection from 0 to 5%. Forty-one samples of juice from 15 different cultivars from seven different wineries in the Central Valley region in California were tested along with juice from healthy-looking grapes of the same cultivars. No cross-reaction was found with any of the cultivars tested for juice from healthy-looking berries taken from loads with low levels of infection. Using BC-12.CA4 immunoassay levels of rot were generally higher than visual assessments of bunch rot particularly with machine-harvested grapes at the end of the season. However, in early season samples immunoassay estimates were, in some cases, lower than the visual assessments. It is strongly suspected that in the latter case fungi other than Botrytis were the main cause of bunch rot. Preliminary studies with another antibody, that recognizes both B. cinerea and Aspergillus niger , confirmed that the bunch rot in these cases was mostly due to fungi other than Botrytis.
Predictors of First Recurrence of Clostridium difficile Infection: Implications for Initial Management

Symptomatic recurrence of Clostridium difficile infection (CDI) occurs in approximately 20% of patients and is challenging to treat. Identifying those at high risk could allow targeted initial management and improve outcomes. Adult toxin enzyme immunoassay–positive CDI cases in a population of approximately 600 000 persons from September 2006 through December 2010 were combined with epidemiological/clinical data. The cumulative incidence of recurrence ≥14 days after the diagnosis and/or onset of first-ever CDI was estimated, treating death without recurrence as a competing risk, and predictors were identified from cause-specific proportional hazards regression models. A total of 1678 adults alive 14 days after their first CDI were included; median age was 77 years, and 1191 (78%) were inpatients. Of these, 363 (22%) experienced a recurrence ≥14 days after their first CDI, and 594 (35%) died without recurrence through March 2011. Recurrence risk was independently and significantly higher among patients admitted as emergencies, with previous gastrointestinal ward admission(s), last discharged 4–12 weeks before first diagnosis, and with CDI diagnosed at admission. Recurrence risk also increased with increasing age, previous total hours admitted, and C-reactive protein level at first CDI (all P < .05). The 4-month recurrence risk increased by approximately 5% (absolute) for every 1-point increase in a risk score based on these factors. Risk factors, including increasing age, initial disease severity, and hospital exposure, predict CDI recurrence and identify patients likely to benefit from enhanced initial CDI treatment.
Association between Self-Reported Health Status and Frailty in Community-Dwelling Elderly.

BACKGROUND The phenotype of frailty proposed by Fried et al. has been related with increased vulnerability for the development of adverse health-related outcomes. However, this phenotype is not often used in daily clinical practice. On the other hand, poor self-reported health status (SRHS) has been associated with similar adverse health-related outcomes. OBJECTIVES To determine the association between poor SRHS and frailty. DESIGN, SETTING AND PARTICIPANTS Cross-sectional study of 927 community-dwelling elderly aged 70 and older, participating in the Mexican Study of Nutritional and Psychosocial Markers of Frailty. MEASUREMENTS SRHS was established by the question "How do you rate your health status in general? " Frailty was defined according to the phenotype proposed by Fried et al. The association between SRHS and frailty was determined through the construction of multinomial logistic regression models. Final analyses were adjusted by socio-demographic and health covariates, including depressive symptoms. Also, agreement between SRHS and the phenotype of frailty was explored. RESULTS Prevalence of frailty was 14.1%, and 4.4% of participants rated their health status as "poor". The unadjusted regression analyses demonstrated that fair and poor SRHS were significantly associated with prefrail and frail status. After adjustment for multiple covariates, the association remained statistically significant. However, in the final adjustment for depressive symptoms, only the association between poor SRHS and frail status continued to be statistically significant. Fair agreement between poor SRHS and frail status was also found. CONCLUSION Poor SRHS shares common correlates as well as health-related adverse outcomes with frailty syndrome, and remains associated with it even when possible confounders are taken into account. Therefore, poor SRHS could be further explored as an option for frailty syndrome screening.
Eurographics Symposium on Point-based Graphics (2006) Octree-based Point-cloud Compression

In this paper we present a progressive compression method for point sampled models that is specifically apt at dealing with densely sampled surface geometry. The compression is lossless and therefore is also suitable for storing the unfiltered, raw scan data. Our method is based on an octree decomposition of space. The point-cloud is encoded in terms of occupied octree-cells. To compress the octree we employ novel prediction techniques that were specifically designed for point sampled geometry and are based on local surface approximations to achieve high compression rates that outperform previous progressive coders for point-sampled geometry. Moreover we demonstrate that additional point attributes, such as color, which are of great importance for point-sampled geometry, can be well integrated and efficiently encoded in this framework.
Formulation, in-vitro characterization and clinical evaluation of curcumin in-situ gel for treatment of periodontitis

Abstract This study aimed to develop syringeable in-situ curcumin (cur) gel for the treatment of periodontal pockets as well as to evaluate the clinical efficacy of Cur in-situ gel formulation. Different in-situ gel formulations of Cur were prepared using 30% of pluronic F127, and 1% of carbopol P934. The formulations were evaluated regarding gelation temperature, pH, viscosity, syringeability study, in-vitro release and chemical stability of cur. The effect of aging of gel formulations for 3months in refrigerator was investigated. The selected formulation was clinically evaluated through the determination of probing depth, plaque index, and bleeding index at baseline and 1 month after application. The formulations showed accepted gelation temperature ranging from 28 to 34 °C and all had pH value of 4. The viscosity of the formulations at 4 °C ranged from 19 000 to 37 000 cP. All formulations were easily syringeable through 21 gauge needle at cold temperature. Curcumin stability during the release study was maintained. Aging showed no significant effect on release profile, drug content, or the pH after 3 months, while it showed a slight increase in viscosity with concomitant decrease in gelation temperature. Selected formulations delivered into periodontal pocket evaluated clinically showed to be effective. The treated group revealed that the adjunctive use of intracrevicular 2% curcumin in-situ gel adjunct to mechanical treatment in patients with adult periodontitis could aid in significant clinical reduction of probing depth, bleeding index, and to less extent of plaque. This indicates that curcumin in this novel drug delivery system is an excellent candidate for periodontal disease treatment.
Characterizing and Discovering Spatiotemporal Social Contact Patterns for Healthcare

During an epidemic, the spatial, temporal and demographic patterns of disease transmission are determined by multiple factors. In addition to the physiological properties of the pathogens and hosts, the social contact of the host population, which characterizes the reciprocal exposures of individuals to infection according to their demographic structure and various social activities, are also pivotal to understanding and predicting the prevalence of infectious diseases. How social contact is measured will affect the extent to which we can forecast the dynamics of infections in the real world. Most current work focuses on modeling the spatial patterns of static social contact. In this work, we use a novel perspective to address the problem of how to characterize and measure dynamic social contact during an epidemic. We propose an epidemic-model-based tensor deconvolution framework in which the spatiotemporal patterns of social contact are represented by the factors of the tensors. These factors can be discovered using a tensor deconvolution procedure with the integration of epidemic models based on rich types of data, mainly heterogeneous outbreak surveillance data, socio-demographic census data and physiological data from medical reports. Using reproduction models that include SIR/SIS/SEIR/SEIS models as case studies, the efficacy and applications of the proposed framework are theoretically analyzed, empirically validated and demonstrated through a set of rigorous experiments using both synthetic and real-world data.
On the asymptotic properties of the group lasso estimator for linear models

We establish estimation and model selection consistency, pre- diction and estimation boundsand persistencefor the group-lassoestimator and model selectorproposed by Yuan and Lin (2006) for least squares prob- lems when the covariates have a natural grouping structure. We consider the case of a fixed-dimensionalparameter space with increasing sample size and the double asymptotic scenario where the model complexity changes with the sample size.
Integrated Postprandial Responses of the Diamondback Water Snake, Nerodia rhombifer

Among snakes, the magnitude to which intestinal performance is regulated with feeding and fasting is adaptively linked to their natural feeding frequency. For infrequently feeding boas and pythons, gastrointestinal form and function are widely regulated with each feeding bout. In contrast, snakes that naturally feed more frequently modestly regulate intestinal function with each meal. To further explore the postprandial responses of a frequently feeding snake and assess whether such responses are matched in magnitude, we examined the postprandial metabolic, morphologic, and functional responses of the diamondback water snake (Nerodia rhombifer) following the consumption of catfish meals equaling 25% of their body mass. After feeding, N. rhombifer experienced 5.4‐fold increases in metabolic rate and a specific dynamic action of 101 kJ that equaled 25.3% of the ingested energy. Nerodia rhombifer that were fed did not undergo any change in stomach tissue mass but did experience a rapid drop in gastric pH and a decline in tissue stores of pepsinogen. Feeding triggered an increase in pancreatic mass and a temporary loss of trypsin activity. The small intestine of N. rhombifer responded to feeding with a 70% increase in mass and a 27% increase in enterocyte length but no change in microvillus length. Intestinal nutrient uptake rates did not increase with feeding, whereas intestinal aminopeptidase‐N activity increased by fivefold. The postprandial increases in metabolism and gastrointestinal morphology and function of N. rhombifer are of a lower magnitude than is characteristic of infrequently feeding snakes and are more similar to the responses observed for other frequently feeding species. In support of an adaptive interplay between feeding habits and digestive physiology, this study demonstrates that the regulation of gastrointestinal structure and function for the frequently feeding N. rhombifer is generally modest and matched in magnitude.
The Effect of Extracellular Potassium Concentration on Muscle Fiber Conduction Velocity Examined Using Model Simulation

During fatiguing contractions muscle fiber conduction velocity (CV) decreases progressively. The exact cause of this is not yet fully known, although recent studies suggest that changes in extracellular potassium concentration play an important role. A model was developed to examine the effect of accumulation of extracellular potassium ions on the muscle fiber action potential and its CV. As the extracellular potassium concentration was increased, the action potential progressively broadened, reduced in peak-peak amplitude and its CV decreased. However, when the inward rectifier channels were blocked, the changing shape of the action potential and the reduction of its CV with increasing extracellular potassium were dramatically reduced. The simulation results support the hypothesis that the reduction in muscle fiber CV observed during sustained fatiguing contractions may be due in part, to increased accumulation of extracellular potassium ions and suggest that the inward rectifier currents play an important role on the relationships observed.
How air influences radiation dose deposition in multiwell culture plates: a Monte Carlo simulation of radiation geometry

Radiation of experimental culture cells on plates with various wells can cause a risk of underdosage as a result of the existence of multiple air–water interfaces. The objective of our study was to quantify this error in culture plates with multiple wells. Radiation conditions were simulated with the GAMOS code, based on the GEANT4 code, and this was compared with a simulation performed with PENELOPE and measured data. We observed a slight underdosage of ∼4% on the most superficial half of the culture medium. We believe that this underdosage does not have a significant effect on the dose received by culture cells deposited in a monolayer and adhered to the base of the wells.
Impact of Fiber Nonlinearity on 5G Backhauling via Mixed FSO/Fiber Network

The inherently high bandwidth of fiber and free-space optical (FSO) links make them ideally suited to provide broadband backhaul in fifth-generation (5G) mobile networks. However, both fiber and FSO systems suffer from a variety of impairments, which must be properly modeled in order to design the network. In this paper, we present analytical results for mixed FSO/fiber amplify-and-forward backhauling systems, where the impacts of radio-frequency (RF) co-channel interference, FSO pointing errors, and both fiber and FSO modulator nonlinearity are modeled and taken into consideration. Closed-form and asymptotic expressions are derived for the outage probability, the average bit-error rate, and the cumulative distribution function (CDF) of the channel capacity for mixed FSO/fiber backhauling systems. Our results reveal an optimal average-launched power for the fiber, which balances the impact of fiber nonlinear distortion with the receiver noise. In particular, when using the optimal fiber average-launched power, our estimated user capacity CDF results show that the 50th percentile user rates using mm-wave RF access can reach over 1.5 Gb/s in ideal conditions. However, user rates are more sensitive to the FSO backhaul channel characteristics.
Accounting for Surface Wave Distortion of the Marine Wind Profile in Low-Level Ocean Storms Wind Measurements

Abstract Marine wind measurements at three heights (3.0,4.5, and 5.0 m) from both moored and drifting buoys during the Ocean Storms Experiment are described. These winds are compared with each other, with winds from ships, from subsurface ambient acoustic noise, and from the analyses of three numerical weather prediction centers. In the mean, wind directions generally differ by only a small constant offset of a few degrees. No wave influence on the wind direction is evident, because the differences are not systematic and, with few exceptions, they are less than the expected error. After correcting for some apparent calibration and instrument bias, the Ocean Storms wind speeds display similar behavior when compared to the analyzed wind products. There is excellent agreement up to a transition wind speed between 7 and 10 m s−1, above which all the measured winds tend to be relatively low. The transition speed is found to increase with anemometer height, so this behavior is interpreted as being due to the di.
Hedgehog signaling is required for formation of the notochord sheath and patterning of nuclei pulposi within the intervertebral discs

The vertebrae notochord is a transient rod-like structure that produces secreted factors that are responsible for patterning surrounding tissues. During later mouse embryogenesis, the notochord gives rise to the middle part of the intervertebral disc, called the nucleus pulposus. Currently, very little is known about the molecular mechanisms responsible for forming the intervertebral discs. Here we demonstrate that hedgehog signaling is required for formation of the intervertebral discs. Removal of hedgehog signaling in the notochord and nearby floorplate resulted in the formation of an aberrant notochord sheath that normally surrounds this structure. In the absence of the notochord sheath, small nuclei pulposi were formed, with most notochord cells dispersed throughout the vertebral bodies during embryogenesis. Our data suggest that the formation of the notochord sheath requires hedgehog signaling and that the sheath is essential for maintaining the rod-like structure of the notochord during early embryonic development. As notochord cells form nuclei pulposi, we propose that the notochord sheath functions as a “wrapper” around the notochord to constrain these cells along the vertebral column.
STRONG NEBULAR LINE RATIOS IN THE SPECTRA of z ∼ 2–3 STAR FORMING GALAXIES: FIRST RESULTS FROM KBSS-MOSFIRE

We present initial results of a deep near-IR spectroscopic survey covering the 15 fields of the Keck Baryonic Structure Survey using the recently commissioned MOSFIRE spectrometer on the Keck 1 telescope. We focus on a sample of 251 galaxies with redshifts 2.0 < z < 2.6, star formation rates (SFRs) 2 ≲ SFR ≲ 200 M☉ yr−1, and stellar masses 8.6 < log (M*/M☉) < 11.4, with high-quality spectra in both H- and K-band atmospheric windows. We show unambiguously that the locus of z ∼ 2.3 galaxies in the “BPT” nebular diagnostic diagram exhibits an almost entirely disjointed, yet similarly tight, relationship between the line ratios [N ii] λ6585/Hα and [O iii]/Hβ as compared to local galaxies. Using photoionization models, we argue that the offset of the z ∼ 2.3 BPT locus relative to that at z ∼ 0 is caused by a combination of harder stellar ionizing radiation field, higher ionization parameter, and higher N/O at a given O/H compared to most local galaxies, and that the position of a galaxy along the z ∼ 2.3 star-forming BPT locus is surprisingly insensitive to gas-phase oxygen abundance. The observed nebular emission line ratios are most easily reproduced by models in which the net stellar ionizing radiation field resembles a blackbody with effective temperature Teff = 50, 000–60, 000 K, the gas-phase oxygen abundances lie in the range 0.2 < Z/Z☉ < 1.0, and the ratio of gas-phase N/O is close to the solar value. We critically assess the applicability at high redshift of commonly used strong line indices for estimating gas-phase metallicity, and consider the implications of the small intrinsic scatter of the empirical relationship between excitation-sensitive line indices and M* (i.e., the “mass–metallicity” relation) at z ≃ 2.3.