Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipopolysaccharide variation in Coxiella burnetti: intrastrain heterogeneity in structure and antigenicity

We isolated lipopolysaccharides (LPSs) from phase variants of Coxiella burnetii Nine Mile and compared the isolated LPS and C. burnetii cells by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting. The LPSs were found to be the predominant component which varied structurally and antigenically between virulent phase I and avirulent phase II. A comparison of techniques historically used to extract the phase I antigenic component revealed that the aqueous phase of phenol-water, trichloroacetic acid, and dimethyl sulfoxide extractions of phase I C. burnettii cells all contained phase I LPS, although the efficiency and specificity of extraction varied. Our studies provide additional evidence that phase variation in C. burnetii is analogous to the smooth-to-rough LPS variation of gram-negative enteric bacteria, with phase I LPS being equivalent to smooth LPS and phase II being equivalent to rough LPS. In addition, we identified a variant with a third LPS chemotype with appears to have a structural complexity intermediate to phase I and II LPSs. All three C. burnetii LPS contain a 2-keto-3-deoxyoctulosonic acid-like substance, heptose, and gel Limulus amoebocyte lysates in subnanogram amounts. The C. burnetii LPSs were nontoxic to chicken embryos at doses of over 80 micrograms per embryo, in contrast to Salmonella typhimurium smooth- and rough-type LPSs, which were toxic in nanogram amounts.
Genetic predictors of celiac disease, lactose intolerance, and vitamin D function and presence of peptide morphins in urine of children with neurodevelopmental disorders

Gastrointestinal disturbances, nutritional deficiencies, and food intolerances are frequently observed in children with neurodevelopmental disorders (NDD). To reveal possible association of celiac disease risk variants (HLA-DQ), lactose intolerance associated variant (LCT-13910C>T) as well as variant associated with vitamin D function (VDR FokI) with NDD, polymerase chain reaction-based methodology was used. Additionally, intestinal peptide permeability was estimated in NDD patients and healthy children by measuring the level of peptides in urine using high-performance liquid chromatography. Levels of opioid peptides, casomorphin 8, and gluten exorphin C were significantly elevated in urine samples of NDD patients (P = 0.004 and P = 0.005, respectively), but no association of genetic risk variants for celiac disease and lactose intolerance with NDD was found. Our results indicate that increased intestinal peptide permeability observed in analyzed NDD patients is not associated with genetic predictors of celiac disease or lactose intolerance. We have also found that FF genotype of VDR FokI and lower serum levels of vitamin D (25-OH) showed association with childhood autism (CHA), a subgroup of NDD. We hypothesize that vitamin D might be important for the development of CHA.
Sparse PCA via Bipartite Matchings

We consider the following multi-component sparse PCA problem: given a set of data points, we seek to extract a small number of sparse components with disjoint supports that jointly capture the maximum possible variance. These components can be computed one by one, repeatedly solving the single-component problem and deflating the input data matrix, but as we show this greedy procedure is suboptimal. We present a novel algorithm for sparse PCA that jointly optimizes multiple disjoint components. The extracted features capture variance that lies within a multiplicative factor arbitrarily close to 1 from the optimal. Our algorithm is combinatorial and computes the desired components by solving multiple instances of the bipartite maximum weight matching problem. Its complexity grows as a low order polynomial in the ambient dimension of the input data matrix, but exponentially in its rank. However, it can be effectively applied on a low-dimensional sketch of the data; this allows us to obtain polynomial-time approximation guarantees via spectral bounds. We evaluate our algorithm on real data-sets and empirically demonstrate that in many cases it outperforms existing, deflation-based approaches.
Impacts of chronic wasting disease on a low density mule deer (Odocoileus hemionus) population in the San Andres Mountains, Chihuahuan Desert, New Mexico

Chronic wasting disease (CWD), a contagious neurodegenerative disease of cervids, is becoming increasingly prevalent in the arid Southwest including the Chihuahuan Desert ecoregion. Population effects of CWD are uncertain, particularly in arid environments, as previous work has been on relatively high density deer populations in semi-arid or temperate environments. In 2002, CWD was detected in a low density mule deer ( Odocoileus hemionus ) population in the arid San Andres Mountains, a Chihuahuan Desert range in southern New Mexico. We determined prevalence and distribution of CWD, and mortality and movements of deer, to assess the potential impact on low density deer populations in arid environments. Repeated seasonal primarily ante-mortem sampling found stable prevalence of 0.000–0.091, 2003–2008. Annual CWD mortality rate was < 0.02, including deer that were culled. Monitoring of adult radio-collared deer showed no dispersal movements away from home ranges, with maximum movements of ≤20 km; similarly, no juveniles dispersed from maternal ranges. Distribution of infected deer was strongly related to presence of other infected deer. Annual survival rates of mule deer and population rate-of-increase suggested little effect of CWD on population-level mortality given observed prevalence. Transmission and reservoirs of CWD in the SAM were likely limited by low deer densities, patchy distribution, and environmental characteristics (i.e., low clay content of soils) unfavorable to prion persistence, characteristics that are typical of most mule deer populations in the Chihuahuan Desert ecoregion.
Motion History Volumes for Free Viewpoint Action Recognition

Action recognition is an important and challenging topic in computer vision, with many important applications including video surveillance, automated cinematography and understanding of social interaction. Yet, most current work in gesture or action interpretation remains rooted in viewdependent representations. This paper introduces Motion History Volumes (MHV) as a free-viewpoint representation for human actions in the case of multiple calibrated, and background-subtracted, video cameras. We present algorithms for computing, aligning and comparing MHVs of different actions performed by different people in a variety of viewpoints. Alignment and comparisons are performed efficiently using Fourier transforms in cylindrical coordinates around the vertical axis. Preliminary results indicate that this representation can be used to learn and recognize basic human action classes, independently of gender, body size and viewpoint.
Knowledge Extraction from Trained Neural Network Scour Models

This study extends the earlier contribution of Azamathulla et al. in 2005. Artificial neural networks (ANNs), due to their excellent capabilities for modeling complex processes, have been successfully applied to a variety of problems in hydraulics. However, one of the major criticisms of ANNs is that they are just black-box models, since a satisfactory explanation of their behavior has not been offered. They, in particular, do not explain easily how the inputs are related to the output, and also whether the selected inputs have any significant relationship with an output. In this paper, a perturbation analysis for determining the order of influence of the elements in the input vector on the output vector is discussed. The approach is illustrated though networks recommended in Azamathulla et al. 2005 for prediction of scour using neural networks. The analyses of the results suggest that each variable in the input vector (discharge intensity, head, tail water depth, bed material, lip angle and radius of the bucket) influences the depth of scour in different ways. However, the magnitude of the influence cannot be clearly quantified by this approach. Further it adds that the selection of input vector based on linear measures between the variables of interest, which is commonly employed, may still include certain spurious elements that only increase the complexity of the model.
Management of tics and Tourette's disorder: an update

Importance of the field: Tic disorders are fairly prevalent neuropsychiatric disorders. While a proportion of children may not present to the clinician's office for management of tic disorders, another proportion may present with severe symptoms that impair social and occupational functioning. A combination of psychosocial interventions and pharmacological approaches are required in these cases. While alpha-2 agonists and dopamine antagonists constitute the mainstay of pharmacological agents for tic disorders, advances in neurobiology and psychopharmacology have discovered newer avenues for treatment of tic disorders. Areas covered in this review: Apart from reviewing evidence based literature and recent updates on alpha-2 agonists and dopamine antagonists in treating tic disorders, the review also includes novel treatment approaches such as glutamate modulators, nicotinic agents, antiandrogens and botulinum injection. In addition, a brief overview of electroconvulsive therapy (ECT), transcranial magnetic stimulation (TMS), deep brain stimulation (DBS) and habit reversal training is also provided. What the reader will gain: A clear and concise review of the therapeutic options and advances in management of tic disorders. Take home message: In addition to psychosocial interventions, alpha-2 agonists and dopamine antagonists constitute the mainstay of treatment approaches for treating tic disorders. Additional treatment options such as ropinirole, pramipexole and tetrabenazine may be useful if patients do not respond to the primary agents. Severe intractable cases might need a referral to specialist centers to consider the possibility of using ECT, TMS or DBS.
Totally tubeless percutaneous nephrolithotomy.

PURPOSE To establish if totally tubeless percutaneous nephrolithotomy (PCNL) is a safe management technique. PCNL is a well-established option for upper tract stones. The procedure traditionally concludes with the placement of a nephrostomy drainage tube but in those patients in whom there has been minimal blood loss and complete stone clearance, it may not be necessary to place a nephrostomy. PATIENTS AND METHODS Totally tubeless PCNL was performed in uncomplicated cases, when there was no significant bleeding or residual stone load, an intact pelvicaliceal system, and no evidence of a residual ureteral stone. RESULTS 100 procedures were analyzed during a 10-year period from 1996 to 2006. The mean stone size was 15.9 mm (range 7-40 mm). Mean residual stone load was 1.74 mm (range 1-10 mm). Access was considered difficult in 2%. Transfusion rate was 1% with a mean fall in hemoglobin of 1.4 g/dL ([-0.4] - [+5.6] g/dL), and a mean rise in creatinine level of 0.3 micromol/L ([-43] - [+52] micromol/L). The minor sepsis rate was 5%, and the major sepsis rate was 1%. The readmission rate was 1%. The mean length of stay was 2.9 days (range 1-10 d). Secondary treatment was required in 5%, and stone clearance rate at 3 months was 90%. CONCLUSION This study demonstrates that PCNL without nephrostomy or stent is a safe and well-tolerated procedure in selected patients. It is the authors' belief that totally tubeless PCNL may be considered an accepted standard of care for selected patients, and it is possible to reserve placement of a nephrostomy tube or internal ureteral stent for specific indications.
Spherical Diffusion for 3D Surface Smoothing

A diffusion-based approach to surface smoothing is presented. Surfaces are represented as scalar functions defined on the sphere. The approach is equivalent to Gaussian smoothing on the sphere and is computationally efficient since it does not require iterative smoothing. Furthermore, it does not suffer from the well-known shrinkage problem. Evolution of important shape features (parabolic curves) under diffusion is demonstrated. A nonlinear modification of the diffusion process is introduced in order to improve smoothing behavior of elongated and poorly centered objects.
Adiponectin and resistin in relationship with skeletal status in women from the RAC-OST-POL study.

INTRODUCTION The aim of this study was to establish adiponectin and resistin serum levels and their relationship with skeletal status in women from the RAC-OST-POL study. MATERIAL AND METHODS 40 women with the lowest and 40 women with the highest value of bone mineral density (BMD) measured at the femoral neck (FN) were selected from a total of 625 women after dividing them into six age categories. Mean age in the whole group of 80 women was 66.1 ± 8.0 years. 22 women had osteoporotic fractures. Adiponectin and resistin were measured, and skeletal assessment included measurements of BMD of FN and total hip (TH) using Lunar DPX (USA) and quantitative ultrasound (QUS) of hand phalanges by means of DBM Sonic 1200 (IGEA, Italy). RESULTS Mean age did not differ between the subgroups, whereas height, weight, BMI and BMD were significantly higher in women with high BMD values. In women with high and low BMD, adiponectin concentration [μg/mL] was 24.81 ± 12.7 and 31.04 ± 12.64 respectively, and differed significantly (p 〈 0.05). Respective values for resistin concentration [ng/mL] were 3.29 ± 1.37 and 3.62 ± 1.45, and did not differ. Adiponectin negatively correlated with weight (r = -0.34, p 〈 0.01), BMI (r = -0.37, p 〈 0.01), FN BMD (r = -0.26, p 〈 0.05), TH BMD (r = -0.33, p 〈 0.01), and did not correlate with QUS result. Stepwise multiple regression analysis showed that TH BMD was negatively influenced by age and adiponectin and positively by weight, and that FN BMD was dependent on age and weight only. CONCLUSIONS Our results suggest that adiponectin may be an independent factor influencing skeletal status in women aged over 55 years.
Factors influencing radiation therapy student clinical placement satisfaction

Radiation therapy students at Queensland University of Technology (QUT) attend clinical placements at five different clinical departments with varying resources and support strategies. This study aimed to determine the relative availability and perceived importance of different factors affecting student support while on clinical placement. The purpose of the research was to inform development of future support mechanisms to enhance radiation therapy students’ experience on clinical placement.
Serum ferritin, sex hormones, and cardiovascular risk factors in healthy women.

The protective effect of endogenous sex hormones is commonly believed to explain the gender gap in the risk of coronary heart disease and the diminished protection in women when menopause occurs. Recent reports indicate that iron overload, due to cessation of menstrual bleeding, may be an important factor. We therefore investigated iron stores by serum ferritin measurements in healthy premenopausal (n = 113) and postmenopausal (n = 46) women. Ferritin levels were higher in postmenopausal than in premenopausal women, both in blood donors (43.4 versus 23.1 micrograms/L, P < .001) and in nondonors (71.7 versus 32.8 micrograms/L, P < .001). Serum ferritin was positively correlated with age (r = .36, P < .001). After age adjustment, serum ferritin was positively correlated with hemoglobin, hematocrit, serum total cholesterol, and low-density lipoprotein (LDL) cholesterol. Total cholesterol was correlated with age (r = .66, P < .001), as were LDL cholesterol (r = .60, P < .01) and high-density lipoprotein cholesterol (r = .32, P < .01). Neither ferritin nor serum lipids were directly associated with female sex hormone levels. The mutual relation between ferritin, hemoglobin, and hematocrit probably only indicates their usefulness as measures of body iron. The parallel rise in serum ferritin, total cholesterol, and LDL cholesterol might contribute to the increased risk of coronary heart disease among postmenopausal women.
Losses of functional opsin genes, short-wavelength cone photopigments, and color vision—A significant trend in the evolution of mammalian vision

Abstract All mammalian cone photopigments are derived from the operation of representatives from two opsin gene families (SWS1 and LWS in marsupial and eutherian mammals; SWS2 and LWS in monotremes), a process that produces cone pigments with respective peak sensitivities in the short and middle-to-long wavelengths. With the exception of a number of primate taxa, the modal pattern for mammals is to have two types of cone photopigment, one drawn from each of the gene families. In recent years, it has been discovered that the SWS1 opsin genes of a widely divergent collection of eutherian mammals have accumulated mutational changes that render them nonfunctional. This alteration reduces the retinal complements of these species to a single cone type, thus rendering ordinary color vision impossible. At present, several dozen species from five mammalian orders have been identified as falling into this category, but the total number of mammalian species that have lost short-wavelength cones in this way is certain to be much larger, perhaps reaching as high as 10% of all species. A number of circumstances that might be used to explain this widespread cone loss can be identified. Among these, the single consistent fact is that the species so affected are nocturnal or, if they are not technically nocturnal, they at least feature retinal organizations that are typically associated with that lifestyle. At the same time, however, there are many nocturnal mammals that retain functional short-wavelength cones. Nocturnality thus appears to set the stage for loss of functional SWS1 opsin genes in mammals, but it cannot be the sole circumstance.
The Rupture Process of the 2018 Mw 6.9 Hawaiʻi Earthquake as Imaged by a Genetic Algorithm‐Based Back‐Projection Technique

An episode of unrest began at Kīlauea in April 2018 that produced both significant volcanic output and high rates of seismicity, including a Mw 6.9 earthquake on 4 May 2018. In this study, we image the rupture process of this earthquake using a genetic algorithm‐based back‐projection technique. The dominant feature of the earthquake is a slowly propagating western rupture, which shares similar characteristics with the region's largest recorded event in 1975 (Mw 7.7). The location of this western segment suggests that small asperities on this section of the décollement that frequently fail as slow slip events may achieve seismic slip rates when rupture is initiated on adjacent sections of the fault. Given the interaction between volcanic and seismic activity in this region, imaging the rupture properties of these events can improve our understanding of future geologic hazards in this region.
Theoretical and experimental evaluation of vector control for doubly-fed reluctance generators

The paper deals with flux and voltage vector oriented control of a brushless doubly-fed reluctance generator (BDFRG) for grid-connected wind turbines. The BDFRG features the low operation & maintenance costs afforded by using a smaller inverter and the high reliability of brushless structure at potentially competitive performance to its popular slip-ring cousin, the doubly-fed induction generator (DFIG). The simulation and experimental studies have evaluated the two parameter independent speed and reactive power control algorithms on a custom-built BDFRG under the maximum torque per inverter ampere (MTPIA) conditions for various loading profiles.
Unbiased generative semi-supervised learning

Reliable semi-supervised learning, where a small amount of labelled data is complemented by a large body of unlabelled data, has been a long-standing goal of the machine learning community. However, while it seems intuitively obvious that unlabelled data can aid the learning process, in practise its performance has often been disappointing. We investigate this by examining generative maximum likelihood semi-supervised learning and derive novel upper and lower bounds on the degree of bias introduced by the unlabelled data. These bounds improve upon those provided in previous work, and are specifically applicable to the challenging case where the model is unable to exactly fit to the underlying distribution a situation which is common in practise, but for which fewer guarantees of semi-supervised performance have been found. Inspired by this new framework for analysing bounds, we propose a new, simple reweighing scheme which provides a provably unbiased estimator for arbitrary model/distribution pairs--an unusual property for a semi-supervised algorithm. This reweighing introduces no additional computational complexity and can be applied to very many models. Additionally, we provide specific conditions demonstrating the circumstance under which the unlabelled data will lower the estimator variance, thereby improving convergence.
Efficacy of an Emotion Self-regulation Program for Promoting Development in Preschool Children

This work reports the results of an evaluation study to assess the efficacy of the Early HeartSmarts (EHS) program in schools of the Salt Lake City, Utah, School District. The EHS program is designed to guide teachers with methods that support young children (3—6 y old) in learning emotion self-regulation and key age-appropriate socioemotional competencies with the goal of facilitating their emotional, social, and cognitive development. The study was conducted over one school year using a quasiexperimental longitudinal field research design with 3 measurement points (baseline, preintervention, and postintervention) using The Creative Curriculum Assessment (TCCA), a teacher-scored, 50-item instrument measuring students growth in 4 areas of development: social/emotional, physical, cognitive, and language development. Children in 19 preschool classrooms in the Salt Lake City School District were divided into intervention and control group samples (n = 66 and n = 309, respectively; mean age = 3.6 y). The intervention classes were specifically selected to target children of lower socioeconomic and ethnic minority backgrounds. Overall, there is compelling evidence of the efficacy of the EHS program in increasing total psychosocial development and each of the 4 development areas measured by the TCCA: the results of a series of analyses of covariance found a strong, consistent pattern of large, significant differences on the development measures favoring preschool children who received the EHS program over those in the control group.
Renal Transplantation in Hepatitis C Positive Patients: A Single Centre Experience

Introduction. Hepatitis C virus (HCV) infection is an independent risk factor for renal transplantation (RTx). Immunosuppression minimization can render better quality of life to these patients. Methods. We analyzed 132 HCV-positive RTx patients (group A) transplanted under tolerance induction protocol (TIP) and compared them with 79 controls (group B) transplanted using standard triple drugs. TIP consisted of 1 donor-specific transfusion, peripheral blood stem cell infusion, portal infusion of bone marrow, and target-specific irradiation. Their immunosuppression was cyclosporin, 2 ± 1 mg/kg BW/day + prednisone, 10 mg/day. Results. TIP had no side effects. Although unequal in size, the groups were well balanced. Group A patient survival at 1, 5, and 10 years was 92.4%, 70.4%, and 63.7%, respectively, versus 75.6%, 71.7%, and 55.7% in later, and graft survival was 92.9%, 81.5%, and 79.1% versus 91.7%, 75.7%, and 67.7%, respectively. Mean serum creatinine (mg/dL) at these time periods in former was 1.38, 1.72, and 1.87, versus 1.3, 1.75, and 2.1 in later. Altered liver functions were noted in 22% patients in former versus 31% in later. Group A had lesser rejection episodes. Conclusion. RTx using TIP in HCV-positive patients is a viable option with acceptable outcome.