Miracle-dz/UniFAR-FTUs huggingface dataset:
Major depression, 5HTTLPR genotype, suicide and antidepressant influences on thalamic volume

Background The 5HTTLPR genetic variant of the serotonin transporter gene (SERT or 5-HTT), which is comprised of a short (SERT-s) and a long (SERT-l) allele, is associated with major depressive disorder and post-traumatic brain disorder. Aims The present study sought to determine whether the total thalamus and major subregions are altered in size in major depressive disorder and in relation to the 5HTTLPR genotype. Method We investigated the influence of 5HTTLPR genotype, psychiatric diagnosis, suicide and other clinical factors on the volume of the entire post-mortem thalamus. Results Major depressive disorder, SERT-ss genotype and suicide emerged as independent factors contributing to an enlargement of the total thalamus. The majority of the volume enlargement associated with the SERT-ss genotype occurred in the pulvinar, whereas enlargement associated with major depressive disorder occurred in the limbic nuclei and in other regions of the thalamus. A history of antidepressant treatment was associated with reduced thalamic volume. Conclusions The 5HTTLPR genetic variation may affect behaviour and psychiatric conditions, in part, by altering the anatomy of the thalamus.
Degradation characteristics of α and β tri-calcium-phosphate (TCP) in minipigs

In seven Goettingen minipigs 3.5--4.7-ml cancellous bone defects were created in the area of the tibial head on both sides. The defects were filled with alpha-TCP or beta-TCP (tricalciumphosphate). ITI implants (Straumann, Freiburg, Germany) of 3.2 x 12-mm length were inserted into the underlying ceramic substitutes. Two additional pigs were used as control. Within the periods of observation (4, 16, 20, 28, 46, 68, and 86 weeks) fluorescent dyes were applied. Nondecalcified thin-sliced sections were examined by means of light and fluorescence microscopy. In addition microangiography and microradiography were performed. Bony regeneration occurred basally and on the sides of the defect according the angiogenetic reossification pattern. Resorption was due to a hydrolytic and cellular degradation process. After 46 weeks histomorphological evaluation showed an incomplete osseointegration of the simultaneously implanted dental implants. The bone contact surface ratio was lower than 25%. After 86 weeks 95--97% of both alpha- and beta-TCP were resorbed. Ceramic residuals stayed within the newly formed trabeculae thus resisting further degradation until remodeling occurred. Both alpha- and beta-TCP show a comparable degradation process. At the 86-week postoperative point only small residuals of the ceramic can be found. These residuals stay within the newly formed trabeculae, which show a functional orientation. In comparison control defects showed only sparse reossification. The beta-TCP material shows an accelerated degradation mode and has an optimal reactivity with the surrounding tissues. According to the results of this animal experiment both materials can be classified as bone-rebuilding materials.
Proton Pump Inhibitor Use and Risk of Hip Fracture in Kidney Transplant Recipients.

BACKGROUND Posttransplantation bone disease is a significant problem, with few well-evidenced therapeutic options. Proton pump inhibitors (PPIs) are associated with hip fracture in the general population and are widely prescribed for kidney transplant recipients. STUDY DESIGN A case-control study. SETTING & PARTICIPANTS From the US Renal Data System, we identified from diagnoses and procedures 231 kidney transplant recipients with a first hip fracture. Cases were matched at the hip fracture index date with 15,575 controls on age, sex, race, and transplantation year. PREDICTOR PPI use. OUTCOMES First hip fracture. RESULTS In the year prior to the index date, a PPI was prescribed to 65.4% of cases and 57.4% of controls. Additionally, in 34.6% of cases and 28.9% of controls, a PPI was prescribed for >80% of the year preceding the index date (higher PPI users). Unadjusted ORs of hip fracture associated with any and higher PPI use were 1.55 (95% CI, 1.18-2.05) and 1.65 (95% CI, 1.2-2.27), respectively. When adjusted for baseline demographic, clinical, and pharmacologic covariables, any and higher PPI use remained associated with hip fracture, with ORs of 1.39 (95% CI, 1.04-1.84) and 1.41 (95% CI, 1.02-1.95), respectively. LIMITATIONS Potential residual confounding through either incorrectly ascertained or unavailable confounders; cohort limited to Medicare beneficiaries receiving low-income subsidy. CONCLUSIONS In summary, PPI use was associated with hip fracture risk in the US kidney transplant population.
Convergence Rates of Evolutionary Algorithms for a Class of Convex Objective Functions

Probabilistic optimization algorithms that mimic the process of biological evolution are usually subsumed under the termèvolutionary algorithms. ' This work extends the convergence theory of evolutionary algorithms by presenting a suucient convergence condition for those evolutionary algorithms that do not necessarily generate a sequence of feasible points such that the associated objective function values decrease monotonically to the global minimum. Moreover, it is investigated how fast the sequence of objective function values generated by an evolutionary algorithm approaches the minimum of strongly convex functions in a probabilistic sense. The theoretical analysis presented here distinguishes from related studies in three points: First, it does not require advanced calculus. Second, only the rst partial derivatives of the objective function are assumed to exist. Third, one obtains sharp bounds on the convergence rates for a class of functions being a superset of the class of quadratic functions with positive deenite Hessian matrix.
Space-Efficient Boundary Representation of Volumetric Objects

In this paper we present a compression technique for efficiently representing boundary objects from volumetric data-sets. Exploiting spatial coherency within object contours, we are able to reduce the size of the volumetric boundary down to the size of just a few images. Allowing for direct volume rendering of the down-scaled data in addition to compression ratios up to 250:1, interactive volume visualization becomes possible, even over the Internet and on low-end hardware.
Modeling Energy Consumption of Lock-Free Queue Implementations

This paper considers the problem of modelling the energy behaviour of lock-free concurrent queue data structures. Our main contribution is a way to model the energy behaviour of lock-free queue implementations and parallel applications that use them. Focusing on steady state behaviour we decompose energy behaviour into throughput and power dissipation which can be modeled separately and later recombined into several useful metrics, such as energy per operation. Based on our models, instantiated from synthetic benchmark data, and using only a small amount of additional application specific information, energy and throughput predictions can be made for parallel applications that use the respective data structure implementation. To model throughput we propose a generic model forlock-free queue throughput behaviour, based on combination of the dequeuers' throughput and enqueuers' throughput. To model power dissipation we commonly split the contributions from the various computer components into static, activation and dynamic parts, where only the dynamic part depends on the actual instructions being executed. To instantiate the models a synthetic benchmark explores each queue implementation over the dimensions of processor frequency and number of threads. Finally, we show how to make predictions of application throughput and power dissipation for a parallel application using lock-free queue requiring only a limited amount of information about the application work done between queue operations. Our case study on a Mandelbrot application shows convincing prediction results.
Commercial enzyme-linked immunosorbent assay versus polymerase chain reaction for the diagnosis of chronic Chagas disease: a systematic review and meta-analysis

Chronic Chagas disease diagnosis relies on laboratory tests due to its clinical characteristics. The aim of this research was to review commercial enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) diagnostic test performance. Performance of commercial ELISA or PCR for the diagnosis of chronic Chagas disease were systematically searched in PubMed, Scopus, Embase, ISI Web, and LILACS through the bibliography from 1980-2014 and by contact with the manufacturers. The risk of bias was assessed with QUADAS-2. Heterogeneity was estimated with the I2 statistic. Accuracies provided by the manufacturers usually overestimate the accuracy provided by academia. The risk of bias is high in most tests and in most QUADAS dimensions. Heterogeneity is high in either sensitivity, specificity, or both. The evidence regarding commercial ELISA and ELISA-rec sensitivity and specificity indicates that there is overestimation. The current recommendation to use two simultaneous serological tests can be supported by the risk of bias analysis and the amount of heterogeneity but not by the observed accuracies. The usefulness of PCR tests are debatable and health care providers should not order them on a routine basis. PCR may be used in selected cases due to its potential to detect seronegative subjects.
CUni Multilingual Matrix in the WMT 2013 Shared Task

We describe our experiments with phrase-based machine translation for the WMT 2013 Shared Task. We trained one system for 18 translation directions between English or Czech on one side and English, Czech, German, Spanish, French or Russian on the other side. We describe a set of results with different training data sizes and subsets. For the pairs containing Russian, we describe a set of independent experiments with slightly different translation models.
Knowledge Transfer in Deep convolutional Neural Nets

Knowledge transfer is widely held to be a primary mechanism that enables humans to quickly learn new complex concepts when given only small training sets. In this paper, we apply knowledge transfer to deep convolutional neural nets, which we argue are particularly well suited for knowledge transfer. Our initial results demonstrate that components of a trained deep convolutional neural net can constructively transfer information to another such net. Furthermore, this transfer is completed in such a way that one can envision creating a net that could learn new concepts throughout its lifetime. The experiments we performed involved training a Deep Convolutional Neural Net (DCNN) on a large training set containing 20 different classes of handwritten characters from the NIST Special Database 19. This net was then used as a foundation for training a new net on a set of 20 different character classes from the NIST Special Database 19. The new net would keep the bottom layers of the old net (i.e. those nearest to the input) and only allow the top layers to train on the new character classes. We purposely used small training sets for the new net to force it to rely as much as possible upon transferred knowledge as opposed to a large and varied training set to learn the new set of hand written characters. Our results show a clear advantage in relying upon transferred knowledge to learn new tasks when given small training sets, if the new tasks are sufficiently similar to the previously mastered one. However, this advantage decreases as training sets increase in size.
Thin magnetic conductor substrate for placement-immune, electrically-small antennas.

An antenna is considered to be placement-immune when the antenna operates effectively regardless of where it is placed. By building antennas on magnetic conductor materials, the radiated fields will be positively reinforced in the desired radiation direction instead of being negatively affected by the environment. Although this idea has been discussed thoroughly in theoretical research, the difficulty in building thin magnetic conductor materials necessary for in-phase field reflections prevents this technology from becoming more widespread. This project's purpose is to build and measure an electrically-small antenna on a new type of non-metallic, thin magnetic conductor. This problem has not been previously addressed because non-metallic, thin magnetic conductor materials have not yet been discovered. This work proposed the creation of an artificial magnetic conductor (AMC) with in-phase field reflections without using internal electric conductors, the placement of an electrically-small antenna on this magnetic conductor, and the development of a transmit-receive system that utilizes the substrate and electrically-small antenna. By not using internal electric conductors to create the AMC, the substrate thickness can be minimized. The electrically-small antenna will demonstrate the substrate's ability to make an antenna placement immune, and the transmit-receive system combines both the antenna and the substrate while addingmore » a third layer of system complexity to demonstrate the complete idea. « less
The statistical mechanics of complex signaling networks: nerve growth factor signaling

The inherent complexity of cellular signaling networks and their importance to a wide range of cellular functions necessitates the development of modeling methods that can be applied toward making predictions and highlighting the appropriate experiments to test our understanding of how these systems are designed and function. We use methods of statistical mechanics to extract useful predictions for complex cellular signaling networks. A key difficulty with signaling models is that, while significant effort is being made to experimentally measure the rate constants for individual steps in these networks, many of the parameters required to describe their behavior remain unknown or at best represent estimates. To establish the usefulness of our approach, we have applied our methods toward modeling the nerve growth factor (NGF)-induced differentiation of neuronal cells. In particular, we study the actions of NGF and mitogenic epidermal growth factor (EGF) in rat pheochromocytoma (PC12) cells. Through a network of intermediate signaling proteins, each of these growth factors stimulates extracellular regulated kinase (Erk) phosphorylation with distinct dynamical profiles. Using our modeling approach, we are able to predict the influence of specific signaling modules in determining the integrated cellular response to the two growth factors. Our methods also raise some interesting insights into the design and possible evolution of cellular systems, highlighting an inherent property of these systems that we call ‘sloppiness. ’
Somatosensation, circulation and stance balance in elderly dysvascular transtibial amputees

Objective: To establish the relationship between poor lower limb somatosensory and circulatory status with standing balance, falls history, age and mobility level in dysvascular transtibial amputees (TTAs). Design: Within-subjects evaluation of somatosensation, circulation and stance balance measures in dysvascular transtibial amputees. Setting: Physiotherapy department of a tertiary metropolitan hospital in Australia. Participants: Twenty-two community-dwelling unilateral dysvascular transtibial amputee volunteers, aged between 54 and 86 recruited from a metropolitan hospital outpatient amputee clinic. Main outcome measures: Lower limb vibration sense, light touch sensation and circulatory status were related to centre of pressure excursion during quiet stance, dynamic balance measures of forward and lateral reach distance, and demographic information such as falls history and mobility level. Results: Overall, poor somatosensory status was associated with poor stance balance. There was an association between poor vibration and circulation and increased centre of pressure excursion in quiet stance and reduced reach distance, whereas poor light touch was linked with even weight-bearing in quiet stance. Poor vibration sense was associated with a history of frequent falls. Conclusions: Compromised lower limb somatosensation and circulation was linked with poor balance and a history of frequent falls in the elderly dysvascular amputee population.
FEA Modelling of Weld-deposition based Additive Manufacturing for the Residual Stress Prediction

Research in the development of additive manufacturing process employing direct metal deposition for the fabrication of fully functional parts and tooling has generated significant interest in the recent years. Three-dimensional welding is being investigated as an additive manufacturing technique for the production of real metallic parts using gas metal arc welding (GMAW) principles. The temperature field distribution during weld based rapid prototyping induces complex thermal stress evolutions and plays a big role in residual stress distributions. The present work is to investigate the temperature field and thermal stress distributions in the multi-pass single-layer weld-deposition based additive manufacturing using twin wire welding. A three-dimensional finite element model with the temperature-dependent material properties and moving heat source is modelled for the same. A double ellipsoidal heat source model is applied to calculate the twin wire welding‟s temperature field is used. The filler metal deposition is taken into account by implementing the birth-and-death functionality for the finite elements. The temperature distribution pattern and magnitude is subsequently obtained. This result is then used for estimation of residual stress and distortion due to the twin wire welding.
Estimating phosphate removal in haemodialysis: an additional tool to quantify dialysis dose.

BACKGROUND Half of the dialysis population suffers from hyperphosphataemia, which is now recognized as a major factor of haemodialysis (HD) morbidity and mortality. Current control is focussed on reducing dietary phosphate intake and diminishing absorption using phosphate binders, whereas control and quantification of phosphate removal by HD is undervalued. The aim of this prospective study was to develop a simple, bedside formula to estimate dialytic phosphate removal in stable HD patients. METHODS This was a prospective, randomized trial. Phosphate and urea elimination were assessed in a representative group of patients at two dialysis centres using randomly different dialysers (1.3-2.4 m(2)). Quantification was performed by partial dialysate collection, concentration measurements in blood and effluent dialysate spot samples, and Kt/V(urea) during standard high-flux HD. Multiple linear regression analyses were used in 77% of all data sets to generate an equation to predict phosphate removal. The formula was validated in the remaining 23% of data sets, in the same group of patients using a large capillary filter, and in diabetic patients treated with a small dialyser at different blood flows (200, 250, and 300 ml/min). RESULTS A formula allowing quantification of phosphate removal within one HD session was developed in 18 of 74 patients during 41 treatments (137 out of 177 data sets) and was determined as: M(PO4pred)=0.1t -17+50c(ds60)+11c(b60), where t is treatment time in min, c(ds60) and c(b60) are phosphate concentrations in dialysate and plasma measured 60 min into HD in mmol/l, and M(PO4pred) is estimated phosphate removed in mmol. The precision was remarkable (r(2)=0.92-0.94). The comparison of phosphate and Kt/V(urea) showed a significant association (r(2)=0.28), albeit with remarkable scatter. CONCLUSIONS We present the first approach to quantify phosphate removal during high-flux HD by a bedside formula. Only 28% of the variation in phosphate removal was explained by Kt/V(urea). It appears that other factors not adequately accounted for by Kt/V(urea) affect phosphate removal. Therefore, we propose an individual control and quantification of phosphate removal in HD.
Bifurcation Analysis of the Hodgkin-Huxley Model Exposed to External DC Electric Field

Based on the modified Hodgkin-Huxley (HH) model exposed to extremely low frequency (ELF) electric field, we study Hopf and saddle-node bifurcations of the modified HH model in two dimensional parameter space of externally applied DC current and trans-membrane voltage induced by external DC electric field. The bifurcation sets are calculated by employing the generalized algebra criterion in high dimensional system. The obtained bifurcation sets partition the two dimensional parameter space in terms of the qualitatively different behaviors of the HH model. Thus the neuron's information encodes the stimulus information, and vice versa, which is significant in neuron control. The study is of some biological significance and suggest that the aberration of dynamics in bio-systems may account for diseases caused by electric exposure.
ChloroplastDB: the Chloroplast Genome Database

The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene locations, RNA-editing sites, putative protein families and alignments (). With recent technical advances, the rate of generating new organelle genomes has increased dramatically. However, the established ontology for chloroplast genes and gene features has not been uniformly applied to all chloroplast genomes available in the sequence databases. For example, annotations for some published genome sequences have not evolved with gene naming conventions. ChloroplastDB provides unified annotations, gene name search, BLAST and download functions for chloroplast encoded genes and genomic sequences. A user can retrieve all orthologous sequences with one search regardless of gene names in GenBank. This feature alone greatly facilitates comparative research on sequence evolution including changes in gene content, codon usage, gene structure and post-transcriptional modifications such as RNA editing. Orthologous protein sets are classified by TribeMCL and each set is assigned a standard gene name. Over the next few years, as the number of sequenced chloroplast genomes increases rapidly, the tools available in ChloroplastDB will allow researchers to easily identify and compile target data for comparative analysis of chloroplast genes and genomes.
Analog, Digital and Mixed-Signal Design Flows

There are still no reference design flow for mixed-signal circuits. The aim of this paper is to present distinct analog and digital design flows in the context of a mixed-signal environment. A top-level mixed mode design flow is presented showing different levels of interaction between the analog and digital domains. Examples of CAD tools are also indicated. Finally a case study of a USB 2.0 physical layer is given that shows the efficiency of such flows.