Miracle-dz/UniFAR-FTUs huggingface dataset:
Bed load fluctuations in a steep channel

Bed load transport rate fluctuations have been observed over time in steep rivers and flumes with wide grain size distributions even under constant sediment feeding and water discharge. The observed bed load transport rate pulses are periodic and a consequence of grain sorting. Moreover, the presence of large, relatively immobile boulders, such as erratic stones, which are often present in mountain streams, has an impact on flow conditions. The detailed analysis of a 13 h laboratory experiment is presented in this paper. Boulders were randomly placed in a flume with a steep slope (6.7%), and water and sediment were constantly supplied to the flume. Along with the sediment transport and bulk mean flow velocity, the boulder protrusion, boulder surface, and number of hydraulic jumps, which are indicators of the channel morphology, were measured regularly during the experiment. Periodic bed load transport rate pulses are clearly visible in the data collected during this long‐duration experiment, along with correlated fluctuations in the flow velocity and bed morphology. The links among the bulk velocity, the time evolution of the morphology variables, and the bed load transport rate are analyzed via correlational analysis, showing that the fluctuations are strongly related. A phase analysis of all observed variables is performed, and the average shapes of the time cycles of the fluctuations are shown. Observations indicate that the detected periodic fluctuations correspond to different bed states. Furthermore, the grain size distribution through the channel, which varies in time and space, clearly influences these bed load transport rate pulses. Finally, known bed load transport rate formulae are tested, showing that only the application of a drag shear stress allows a correct estimation of the time fluctuations.
Predicting the natural flow regime: models for assessing hydrological alteration in streams

Understanding the extent to which natural streamflow characteristics have been altered is an important consideration for ecological assessments of streams. Assessing hydrologic condition requires that we quantify the attributes of the flow regime that would be expected in the absence of anthropogenic modifications. The objective of this study was to evaluate whether selected streamflow characteristics could be predicted at regional and national scales using geospatial data. Long‐term, gaged river basins distributed throughout the contiguous US that had streamflow characteristics representing least disturbed or near pristine conditions were identified. Thirteen metrics of the magnitude, frequency, duration, timing and rate of change of streamflow were calculated using a 20–50 year period of record for each site. We used random forests (RF), a robust statistical modelling approach, to develop models that predicted the value for each streamflow metric using natural watershed characteristics. We compared the performance (i.e. bias and precision) of national‐ and regional‐scale predictive models to that of models based on landscape classifications, including major river basins, ecoregions and hydrologic landscape regions (HLR). For all hydrologic metrics, landscape stratification models produced estimates that were less biased and more precise than a null model that accounted for no natural variability. Predictive models at the national and regional scale performed equally well, and substantially improved predictions of all hydrologic metrics relative to landscape stratification models. Prediction error rates ranged from 15 to 40%, but were ≤25% for most metrics. We selected three gaged, non‐reference sites to illustrate how predictive models could be used to assess hydrologic condition. These examples show how the models accurately estimate pre‐disturbance conditions and are sensitive to changes in streamflow variability associated with long‐term land‐use change. We also demonstrate how the models can be applied to predict expected natural flow characteristics at ungaged sites. Copyright © 2009 John Wiley & Sons, Ltd.
Exploring the Relationship between Adherence to Treatment and Viral Load through a New Discrete Simulation Model of HIV Infectivity

Human immunodeficiency virus (HIV) has been a major health problem throughout the world for decades. This paper introduces a new discrete simulation model for the growth of HIV infection within a host body. The model is developed incrementally, and compared at each stage for congruence with real-world observations of disease dynamics. We used the model to get a better understanding of how HIV-infected cells behave, and particularly to assess the importance of medication adherence for effectiveness of treatment. We found that a small lack of adherence could have a proportionally much larger impact on infection as well as trigger negative effects on health sooner. Consequently, improving adherence can be very beneficial (particularly for those whose adherence is already high), and small issues in adherence should be addressed early on. Our work is one step in the development of detailed discrete simulations for HIV dynamics. However, much work remains to be done in order to accurately capture adherence as well as medication schedule, viral resistance, or multiple medication types.
Vascular bifurcation detection in scale-space

Several methods have been proposed over the years for segmentation of vessels, many of them based on scale-space. However, none of the existing methods for blood vessel segmentation is appropriate for extension to bifurcation detection. Other existing bifurcation detection algorithms use an inherently serial “track and detect” approach, which also requires a seed point. We present for the first time a comprehensive scale-space analysis of vascular bifurcations, resulting in a simple, novel algorithm for direct detection of blood vessel bifurcation points based not only on spatial variation across scales, but also on the variation at a single spatial point across scales, without requiring training data or seed points. We present an analytical model for the bifurcation evolution with increasing scale, which was combined with eigenvalue analysis to create a bifurcation-Ness filter. We reveal, for the first time, a hybrid structure of bifurcations in scale-space. The algorithm was tested for validation in both 2D and 3D, with synthetic data as well as medical and non-medical images.
Identification of the Major Molecular Types of Cryptococcus neoformans and C. gattii by Hyperbranched Rolling Circle Amplification

The agents of cryptococcosis C. neoformans and C. gattii are important agents of meningoencephalitis in immunocompromised and immunocompetent hosts, respectively. They are grouped into eight major molecular types, VNI-VNIV for C. neoformans and VGI-VGIV for C. gattii. These major molecular types differ in their host range, epidemiology, antifungal susceptibility and geographic distribution. To enable a rapid identification of the major molecular types and potential hybrids within the two species specific probes based on the PLB1 gene in combination with hyperbranched rolling circle amplification (HRCA) were developed. HRCA was applied to 76 cryptococcal strains, 10 strains each representing the 7 haploid major molecular types, 4 VNIII hybrid strains and 2 inter-species hybrid strains. All strains were correctly identified to the major molecular type and or hybrid type using HRCA alone. To increase the sensitivity a semi-nested PCR step was developed, which will enable the identification of the molecular types/hybrids directly from clinical samples, harboring a low copy number of DNA (40 copies). Thus, HRCA based on the PLB1 locus alone and in combination with a semi-nested PCR showed to be a specific and sensitive methodology, with a great potential to be used on clinical specimens for the direct diagnosis of the agents of cryptococcosis, including hybrid strains, enabling a rapid and patient tailored treatment choice of this disease.
A Cross-Cultural Study of Major Depression and Family Functioning *

Patterns of family functioning in families with a depressed member from two cultures (North America and Hungary) were compared. In both cultural settings, families with a depressed member reported poorer family functioning than the control families. Comparisons between the two depressed groups, however, showed that the response to family dysfunction by the two cultures differed. While depressed families in Hungary reported difficulties in setting family rules and boundaries, those in North America experienced impaired functioning in solving problems, communicating, being involved with each other, and in overall functioning. These results are discussed in terms of the interplay between culture, depression and family functioning.
The application of an automated fabric analyzer system to the textural evolution of folded ice layers in shear zones

Abstract Layered ice has been used to investigate the initiation of fabrics in shear zones where there is preservation of a refolded layering The fabrics were measured using an apparatus that acquires pixel-based images that illustrate the variation of c-axis orientation within and between grains. In the centre of the shear zones there is dynamic recrystallization with the production of an asymmetric two-maxima fabric. The way dynamic recrystallization modifies the inherited folds and microstructure suggests that there is little effect of inheritance from a precursor grain microstructure or fabric No obvious evidence has been found for the occurrence of sub-grains, which implies that the role of sub-grain rotation is minimal or is obliterated by the recrystallization process. The final c-axis pattern is asymmetric with respect to the direction of shortening, with a strong maximum at ~5° to the pole of the shear zone, and a sense of asymmetry in the direction of the shear, and a secondary maximum inclined at ~45° to the plane of shearing. Distinct sets of nearest-neighbour c-axis distributions, namely, intermediate-angle (10–25°), high-angle (50–65°) and very high-angle (120–150°), suggest there may be special grain-boundary relationships.
Over-Expression of Cysteine Leucine Rich Protein Is Related to SAG Resistance in Clinical Isolates of Leishmania donovani

Background Resistance emergence against antileishmanial drugs, particularly Sodium Antimony Gluconate (SAG) has severely hampered the therapeutic strategy against visceral leishmaniasis, the mechanism of resistance being indistinguishable. Cysteine leucine rich protein (CLrP), was recognized as one of the overexpressed proteins in resistant isolates, as observed in differential proteomics between sensitive and resistant isolates of L. donovani. The present study deals with the characterization of CLrP and for its possible connection with SAG resistance. Methodology and Principal Findings In pursuance of deciphering the role of CLrP in SAG resistance, gene was cloned, over-expressed in E. coli system and thereafter antibody was raised. The expression profile of CLrP and was found to be over-expressed in SAG resistant clinical isolates of L. donovani as compared to SAG sensitive ones when investigated by real-time PCR and western blotting. CLrP has been characterized through bioinformatics, immunoblotting and immunolocalization analysis, which reveals its post-translational modification along with its dual existence in the nucleus as well as in the membrane of the parasite. Further investigation using a ChIP assay confirmed its DNA binding potential. Over-expression of CLrP in sensitive isolate of L. donovani significantly decreased its responsiveness to SAG (SbV and SbIII) and a shift towards the resistant mode was observed. Further, a significant increase in its infectivity in murine macrophages has been observed. Conclusion/Significance The study reports the differential expression of CLrP in SAG sensitive and resistant isolates of L. donovani. Functional intricacy of CLrP increases with dual localization, glycosylation and DNA binding potential of the protein. Further over-expressing CLrP in sensitive isolate of L. donovani shows significantly decreased sensitivity towards SAG and increased infectivity as well, thus assisting the parasite in securing a safe niche. Results indicates the possible contribution of CLrP to antimonial resistance in L. donovani by assisting the parasite growth in the macrophages.
Time-space consistency in large-scale distributed virtual environments

Maintaining a consistent view of the simulated world among different simulation nodes is a fundamental problem in large-scale distributed virtual environments (DVEs). In this paper, we characterize this problem by quantifying the time-space inconsistency in a DVE. To this end, a metric is defined to measure the time-space inconsistency in a DVE. One major advantage of the metric is that it may be estimated based on some characteristic parameters of a DVE, such as clock asynchrony, message transmission delay, the accuracy of the dead reckoning algorithm, the kinetics of the moving entity, and human factors. Thus the metric can be used to evaluate the time-space consistency property of a DVE without the actual execution of the DVE application, which is especially useful in the design stage of a DVE. Our work also clearly shows how the characteristic parameters of a DVE are interrelated in deciding the time-space inconsistency, so that we may fine-tune the DVE to make it as consistent as possible. To verify the effectiveness of the metric, a Ping-Pong game is developed. Experimental results show that the metric is effective in evaluating the time-space consistency property of the game.
Cigarette Smoking and Effects on Hormone Function in Premenopausal Women

Cigarette smoke contains compounds that are suspected to cause reproductive damage and possibly affect hormone activity; therefore, we examined hormone metabolite patterns in relation to validated smoking status. We previously conducted a prospective study of women of reproductive age (n = 403) recruited from a large health maintenance organization, who collected urine daily during an average of three to four menstrual cycles. Data on covariates and daily smoking habits were obtained from a baseline interview and daily diary, and smoking status was validated by cotinine assay. Urinary metabolite levels of estrogen and progesterone were measured daily throughout the cycles. For the present study, we measured urinary levels of the pituitary hormone follicle-stimulating hormone (FSH) in a subset of about 300 menstrual cycles, selected by smoking status, with the time of transition between two cycles being of primary interest. Compared with nonsmokers, moderate to heavy smokers (≥ 10 cigarettes/day) had baseline levels (e.g., early follicular phase) of both steroid metabolites that were 25–35% higher, and heavy smokers (≥ 20 cigarettes/day) had lower luteal-phase progesterone metabolite levels. The mean daily urinary FSH levels around the cycle transition were increased at least 30–35% with moderate smoking, even after adjustment. These patterns suggest that chemicals in tobacco smoke alter endocrine function, perhaps at the level of the ovary, which in turn effects release of the pituitary hormones. This endocrine disruption likely contributes to the reported associations of smoking with adverse reproductive outcomes, including menstrual dysfunction, infertility, and earlier menopause.
Developing health information literacy: a needs analysis from the perspective of preprofessional health students.

OBJECTIVE The research identified the skills, if any, that health preprofessional students wished to develop after receiving feedback on skill gaps as well as any strategies they intended to use to address these gaps. METHODS A qualitative approach was used to elicit students' reflections on building health information literacy skills. First, the students took the Research Readiness Self-Assessment instrument, which measured their health information literacy, and then they received individually tailored feedback about their scores and skill gaps. Second, students completed a post-assessment survey asking how they intended to close identified gaps in their skills on these. Three trained coders analyzed qualitative comments by 181 students and grouped them into themes relating to "what skills to improve" and "how to improve them. " RESULTS Students intended to develop library skills (64% of respondents), Internet skills (63%), and information evaluation skills (63%). Most students reported that they would use library staff members' assistance (55%), but even more respondents (82%) planned to learn the skills by practicing on their own. Getting help from librarians was a much more popular learning strategy than getting assistance from peers (20%) or professors (17%). CONCLUSIONS The study highlighted the importance of providing health preprofessional students with resources to improve skills on their own, remote access to library staff members, and instruction on the complexity of building health literacy skills, while also building relationships among students, librarians, and faculty.
Expressive Agents: Non-verbal Communication in Collaborative Virtual Environments

The premise of this paper is that agent technology in collaborative virtual environments (CVEs) may be enriched by incorporating an emotional channel alongside the conventional informational content, and that this would be best achieved through an associated visual human embodiment or avatar. Since humans express emotion in face-to-face encounters primarily through facial expression, an investigation was undertaken in order to establish how such expressions might be effectively and efficiently captured and represented in an avatar. The study involved consulting socio-psychological research relating to face-to-face encounters, followed by a controlled experiment to investigate user ability to interpret the faces of the avatars pre-prepared to express specific emotions. Effectiveness was demonstrated through good recognition rates for all but one of the emotion categories, and efficiency was established since a reduced feature set was found to be sufficient to build the successfully recognised core set of avatar facial expressions
Randomized, Double-Blind, Parallel-Group, 48-Week Study for Efficacy and Safety of a Higher-Dose Rivastigmine Patch (15 vs. 10 cm2) in Alzheimer’s Disease

Aim: Determine whether patients with Alzheimer’s disease demonstrating functional and cognitive decline, following 24–48 weeks of open-label treatment with 9.5 mg/24 h (10 cm2) rivastigmine patch, benefit from a dose increase in a double-blind (DB) comparative trial of two patch doses. Methods: Patients meeting prespecified decline criteria were randomized to receive 9.5 or 13.3 mg/24 h (15 cm2) patch during a 48-week, DB phase. Coprimary outcomes were change from baseline to week 48 on the Instrumental Activities of Daily Living domain of the Alzheimer’s Disease Cooperative Study–Activities of Daily Living (ADCS-IADL) scale and the Alzheimer’s Disease Assessment Scale–cognitive subscale (ADAS-cog). Safety and tolerability were assessed. Results: Of 1,584 patients enrolled, 567 met decline criteria and were randomized. At all timepoints, ADCS-IADL and ADAS-cog scores favoured the 13.3 mg/24 h patch. The 13.3 mg/24 h patch was statistically superior to the 9.5 mg/24 h patch on the ADCS-IADL scale from week 16 (p = 0.025) onwards including week 48 (p = 0.002), and ADAS-cog at week 24 (p = 0.027), but not at week 48 (p = 0.227). No unexpected safety concerns were observed. Conclusions: The 13.3 mg/24 h rivastigmine patch significantly reduced deterioration in IADL, compared with the 9.5 mg/24 h patch, and was well tolerated.
Racial and geographic disparities in the utilization of parenteral nutrition among inflammatory bowel disease inpatients diagnosed with malnutrition in the United States

BACKGROUND— Racial disparities have been described in the utilization of a diverse spectrum of surgical procedures. Our objectives were to determine whether disparities also exist for the use of parenteral nutrition (PN) in IBD. METHODS— We analyzed the Nationwide Inpatient Sample from the U. S. between 1998 and 2003 to determine PN utilization among IBD inpatients diagnosed with protein-calorie malnutrition and assessed if utilization patterns differed by race and geographical region. RESULTS— The proportion of African American IBD admissions with protein-calorie malnutrition who received PN was significantly lower than that in whites (19.9% vs. 28.1%, p =0.001), while there was no difference between Hispanics and non-Hispanic whites. After adjustment for gender, comorbidity, health insurance status, geographic region, and median neighborhood income, African Americans remained less likely than whites to receive PN (OR 0.67; 95% CI: 0.50 – 0.89) while the difference between Hispanics and non-Hispanic whites was marginally significant (OR 0.65; 95% CI: 0.41 – 1.04). PN use varied geographically, with highest rates in the Northeast (44.3%) and lowest in the Midwest (17.3%). Uninsured patients were less than half as likely to receive PN as those with insurance (OR 0.46; 95% CI: 0.31 – 0.69). Compared to whites, Hispanics experienced a longer time interval between admission and initiation of PN (3.5 vs. 4.8 days, p =0.02) and had higher rates of catheter-related complications (5.1% vs. 12.2%, p =0.04). CONCLUSIONS— Among IBD inpatients with clinically diagnosable malnutrition, PN utilization was lower among African Americans compared to whites. The underlying mechanisms of these racial variations merit further investigation.
AMPA-selective glutamate receptor subunits GluR2 and GluR4 in the cat retina: An immunocytochemical study

(article appeared in Visual Neuroscience (1999), 16, 1105–1114. ) Due to an oversight, Table 2 that appeared on p. 1106 of Visual Neuroscience 16:6 had errors in the body of the Table. A corrected version of Table 2 is printed below. Cambridge University Press and the authors regret any inconvenience that this inadvertent error may have caused.
On the Semidiurnal Internal Tide at a Shelf-Break Region on the Australian North West Shelf

Abstract The properties of the semidiurnal internal tide, in the region of the shelf-break, at a location on the Australian North West Shelf are discussed. Information is derived from an analysis of thermistor chain and current meter data, collected over six months at the shelf-break and slope locations. The work is an extension of an earlier study. The internal tide is described in terms of modes, finding that the firm mode dominates, propagating onshore at an angle of ∼30° from normal to the bathymetry, with a rapid decay in amplitude of nearly five times from the shelf-slope to the shelf-break, a distance of 22.5 km or approximately one wavelength. The loss of energy flux from this decay gives rise to vertical mixing with a vertical eddy viscosity of 1.4 × 10−4 m2 s−1. The amplitude at the M2 tidal frequency dominates over the S2 amplitude giving an S2/M2 amplitude ratio significantly smaller than for the barotropic tidal motion. The internal tide appears to have a three-dimensional structure at the sh.
Palaeozoic Lachlan orogen, Australia; accretion and construction of continental crust in a marginal ocean setting: isotopic evidence from Cambrian metavolcanic rocks

Abstract The Lachlan orogen developed as a classic accretionary orogen in an oceanic setting between the palaeo-Pacific subduction zone and the Australian craton. Direct evidence for the composition and age of the lower crust and the basement to the thick Palaeozoic turbidite fan of the Lachlan orogen is limited. Exposures of Cambrian metavolcanic rocks and geophysical data suggest that most of the basement is the mafic oceanic crust along with possible small fragments of older continental crust. The trace element compositions of Cambrian metavolcanic rocks in the western and central Lachlan orogen are similar to those of volcanic rocks formed in modern back-arc and forearc settings. Pb, Nd and Sr isotopic data from these Cambrian rocks suggest a supra-subduction zone setting with little or no influence of continental crust other than subducted sediment.