Miracle-dz/UniFAR-FTUs huggingface dataset:
ATM germline mutations in classical ataxia‐telangiectasia patients in the Dutch population

Germline mutations in the ATM gene are responsible for the autosomal recessive disorder ataxia‐telangiectasia (A‐T). In our study, we have determined the ATM mutation spectrum in 19 classical A‐T patients, including some immigrant populations, as well as 12 of Dutch ethnic origin. Both the protein truncation test (PTT) and the restriction endonuclease fingerprinting (REF) method were used and compared for their detection efficiency, identifying 76% and 60% of the mutations, respectively. Most patients were found to be compound heterozygote. Seventeen mutations were distinct, of which 10 were not reported previously. Mutations are small deletions or point mutations frequently affecting splice sites. Moreover, a 16.7‐kb genomic deletion of the 3′ end of the gene, most likely a result of recombination between two LINE elements, was identified. The most frequently found mutation, identified in three unrelated Turkish A‐T individuals, was previously described to be a Turkish A‐T founder mutation. The presence of a founder mutation among relatively small ethnic population groups in Western Europe could indicate a high carrier frequency in such communities. In patients of Dutch ethnic origin, however, no significant founder effect could be identified. The observed genetic heterogeneity including the relative high percentage of splice‐site mutations had no reflection on the phenotype. All patients manifested classical A‐T and increased cellular radioresistant DNA synthesis. Hum Mutat 12:330–337, 1998. © 1998 Wiley‐Liss, Inc.
Increased arterial stiffness as the marker of vascular involvement in systemic sclerosis.

OBJECTIVE Endothelial dysfunction and vasculopathy of the small and large vessels are crucial pathogenic factors in systemic sclerosis (SSc). Accelerated atherosclerosis and impaired flow-mediated vasodilation have been described in SSc. We evaluated arterial stiffness in patients with SSc compared to healthy controls. METHODS Augmentation index (AI) and pulse wave velocity (PWV) of the brachial artery were measured in 40 patients with SSc and 35 age and sex matched healthy controls using an arteriograph system. RESULTS AI was significantly higher in SSc patients (9.02) compared to controls (-41.15) (p < 0.0001). PWV was similarly higher in patients with SSc (9.67 m/s) than in controls (8.00 m/s) (p = 0.0017). PWV was significantly higher in patients with localized SSc (10.04 +/- 2.01 m/s) compared to those with diffuse SSc (8.39 +/- 1.87 m/s) (p = 0.034). There was a significant, positive linear correlation between AI and PWV (r = 0.32, p = 0.045). We also observed significant correlations between AI and age (r = 0.31, p = 0.048), PWV and age (r = 0.36, p = 0.021), and PWV and disease duration (r = 0.40, p = 0.011) in SSc patients. CONCLUSION Increased AI and PWV of the aorta in comparison to age and sex matched healthy controls indicate increased large-vessel stiffness in patients with SSc. PWV and AI are reproducible indicators of the presence and degree of arterial stiffening. Because arterial stiffness may correlate with disease duration and age in patients with SSc, it may be a useful diagnostic test in the assessment of arterial function. Increased vascular stiffness may be therapeutically targeted by statins and other vasoprotective agents during the management of SSc.
Application-level differentiated multimedia Web services using quality aware transcoding

The ability of a Web service to provide low-latency access to its content is constrained by available network bandwidth. While providing differentiated quality of service (QoS) is typically enforced through network mechanisms, in this paper we introduce a robust mechanism for managing network resources using application-specific characteristics of Web services. We use transcoding to allow Web servers to customize the size of objects constituting a Web page, and hence the bandwidth consumed by that page, by dynamically varying the size of multimedia objects on a per-client basis. We leverage our earlier work on characterizing quality versus size tradeoffs in transcoding JPEG images to supply more information for determining the quality and size of the object to transmit. We evaluate the performance benefits of incorporating this information in a series of bandwidth management policies using realistic workloads and access scenarios to drive our system. The principal contribution of this paper is the demonstration that it is possible to use informed transcoding techniques to provide differentiated service and to dynamically allocate available bandwidth among different client classes, while delivering good quality of information content for all clients. We also show that it is possible to customize multimedia objects to the highly variable network conditions experienced by mobile clients in order to provide acceptable quality and latency depending on the networks used in accessing the service. We show that policies that aggressively transcode the larger images can produce images with quality factor values that closely follow the untranscoded base case while still saving as much as 150 kB. A transcoding policy that has knowledge of the characteristics of the link to the client can avoid as many as 40% of (unnecessary) transcodings.
Stochastic Neural Networks with Monotonic Activation Functions

We propose a Laplace approximation that creates a stochastic unit from any smooth monotonic activation function, using only Gaussian noise. This paper investigates the application of this stochastic approximation in training a family of Restricted Boltzmann Machines (RBM) that are closely linked to Bregman divergences. This family, that we call exponential family RBM (Exp-RBM), is a subset of the exponential family Harmoniums that expresses family members through a choice of smooth monotonic non-linearity for each neuron. Using contrastive divergence along with our Gaussian approximation, we show that Exp-RBM can learn useful representations using novel stochastic units.
Nutrient Acquisition and the Metabolic Potential of Photoferrotrophic Chlorobi

Anoxygenic photosynthesis evolved prior to oxygenic photosynthesis and harnessed energy from sunlight to support biomass production on the early Earth. Models that consider the availability of electron donors predict that anoxygenic photosynthesis using Fe(II), known as photoferrotrophy, would have supported most global primary production before the proliferation of oxygenic phototrophs at approximately 2.3 billion years ago. These photoferrotrophs have also been implicated in the deposition of banded iron formations, the world’s largest sedimentary iron ore deposits that formed mostly in late Archean and early Proterozoic Eons. In this work we present new data and analyses that illuminate the metabolic capacity of photoferrotrophy in the phylum Chlorobi. Our laboratory growth experiments and biochemical analyses demonstrate that photoferrotrophic Chlorobi are capable of assimilatory sulfate reduction and nitrogen fixation under sulfate and nitrogen limiting conditions, respectively. Furthermore, the evolutionary histories of key enzymes in both sulfur (CysH and CysD) and nitrogen fixation (NifDKH) pathways are convoluted; protein phylogenies, however, suggest that early Chlorobi could have had the capacity to assimilate sulfur and fix nitrogen. We argue, then, that the capacity for photoferrotrophic Chlorobi to acquire these key nutrients enabled them to support primary production and underpin global biogeochemical cycles in the Precambrian.
Elastomer viscoelasticity and performance of seals in coldclimate applications

The Ph.D. thesis addresses the issues of elastomer seals operating in cold climate areas like Arctic. The work is devoted to a better understanding of low-temperature behaviour of elastomer seals near the glass transition Tg. The main objective of the work is to understand the causes for seal failures in cold environment and to establish a correlation between the low-temperature performance of hydrogenated nitrile butadiene rubber (HNBR) seals and the composition and the properties of the material. The basic material studied is HNBR with 96 % saturated polybutadiene with 36 % acrylonitrile content and varied carbon black (CB) content from 0 to 50 phr (parts per hundred rubber). A set of material and seal experiments was designed and carried out together with a finite element analysis (FEA) approach in order to accomplish the set goal. The major findings and novel results are as follows: 1. The relaxation function of the HNBR is found to be independent of strain at low temperatures down to −15 °C (≈ Tg + 8 °C) or times higher than ≈ 10−3 s. Therefore, the relaxation function of HNBR needed for FEA or other modelling can be measured at one single strain relevant for the application using the most convenient deformation mode. The relaxation function is also unaffected by the CB at the indicated temperatures and times, however it exhibits an increasing strain or CB dependency if the material is brought deeper into the glass transition region. 2. Compression set as a measure of elastic recovery in HNBR is found to increase with cooling. Below Tg, the HNBR compression strain field in HNBR is "frozen-in", i.e. the HNBR compounds demonstrate no recovery regardless of the presence of CB. Equivalence of time and temperature on the cold compression set is also shown. A viscoelastic model for prediction of the cold compression set using the stress relaxation data is proposed and validated against the FEA and experimental results.
Analysis of a correlated queue in a communication system

A family of queues for which the service time B/sub n/ of customer n depends on the interarrival time I/sub n/ between customers n-1 and n and the random variables I/sub n/ and B/sub n/ exhibit a proportionality relation is studied. In particular, the focus is on dependencies that arise naturally in communication systems, where the finite speed of the communication links constrains the amount of data that can be received in a given time interval. The simple case of a deterministic proportionality relation between the service time of a customer and its preceding interarrival time is considered and extended to allow the addition of an independent, generally distributed overhead to the service time. Several models that capture the on-off behavior of communication links in packet networks are then addressed. In all cases, expressions for the delay experienced by a packet in the system and illustrative numerical examples are provided. <<ETX>>
Prediction of Type III Secretion Signals in Genomes of Gram-Negative Bacteria

Background Pathogenic bacteria infecting both animals as well as plants use various mechanisms to transport virulence factors across their cell membranes and channel these proteins into the infected host cell. The type III secretion system represents such a mechanism. Proteins transported via this pathway (“effector proteins”) have to be distinguished from all other proteins that are not exported from the bacterial cell. Although a special targeting signal at the N-terminal end of effector proteins has been proposed in literature its exact characteristics remain unknown. Methodology/Principal Findings In this study, we demonstrate that the signals encoded in the sequences of type III secretion system effectors can be consistently recognized and predicted by machine learning techniques. Known protein effectors were compiled from the literature and sequence databases, and served as training data for artificial neural networks and support vector machine classifiers. Common sequence features were most pronounced in the first 30 amino acids of the effector sequences. Classification accuracy yielded a cross-validated Matthews correlation of 0.63 and allowed for genome-wide prediction of potential type III secretion system effectors in 705 proteobacterial genomes (12% predicted candidates protein), their chromosomes (11%) and plasmids (13%), as well as 213 Firmicute genomes (7%). Conclusions/Significance We present a signal prediction method together with comprehensive survey of potential type III secretion system effectors extracted from 918 published bacterial genomes. Our study demonstrates that the analyzed signal features are common across a wide range of species, and provides a substantial basis for the identification of exported pathogenic proteins as targets for future therapeutic intervention. The prediction software is publicly accessible from our web server (www.modlab.org).
Randomized Nonlinear Component Analysis

Classical methods such as Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA) are ubiquitous in statistics. However, these techniques are only able to reveal linear relationships in data. Although nonlinear variants of PCA and CCA have been proposed, these are computationally prohibitive in the large scale. In a separate strand of recent research, randomized methods have been proposed to construct features that help reveal nonlinear patterns in data. For basic tasks such as regression or classification, random features exhibit little or no loss in performance, while achieving drastic savings in computational requirements. In this paper we leverage randomness to design scalable new variants of nonlinear PCA and CCA; our ideas extend to key multivariate analysis tools such as spectral clustering or LDA. We demonstrate our algorithms through experiments on real-world data, on which we compare against the state-of-the-art. A simple R implementation of the presented algorithms is provided.
Repetitive Control of Electrical Stimulation for Tremor Suppression

Tremor is a rapid involuntary movement often seen in patients with neurological conditions such as multiple sclerosis and Parkinson’s disease. This debilitating oscillation can be suppressed by applying functional electrical stimulation (FES) within a closed-loop control system. However, conventional implementations use classical control methods and have proved capable of only limited performance. This paper establishes the feasibility of embedding repetitive control (RC) action to exploit the capability of learning from experience to completely suppress tremor at the wrist via FES regulated co-contraction of wrist extensors/flexors. A nonlinear model structure and associated identification procedure are first proposed to guarantee stability and performance of the RC system. Then a linearizing control approach is developed to facilitate transparent RC design, together with a mechanism to preserve patients’ voluntary intention. Experimental evaluation is performed with both unimpaired and neurologically impaired participants using a validated wrist-rig. For the former group, a novel electromechanical system is employed to induce tremor artificially. Results are bench-marked against a well-known classical filtering technique to establish the efficacy of the RC approach. These confirm that the proposed control system with the developed model identification procedure can increase tremor suppression by 43.3% compared with conventional filtering. In addition, the mechanism reduces the interference of RC action with voluntary motion by 20.2% compared with conventional filtering.
Multistep joint bilateral depth upsampling

Depth maps are used in many applications, e.g. 3D television, stereo matching, segmentation, etc. Often, depth maps are available at a lower resolution compared to the corresponding image data. For these applications, depth maps must be upsampled to the image resolution. Recently, joint bilateral filters are proposed to upsample depth maps in a single step. In this solution, a high-resolution output depth is computed as a weighted average of surrounding low-resolution depth values, where the weight calculation depends on spatial distance function and intensity range function on the related image data. Compared to that, we present two novel ideas. Firstly, we apply anti-alias prefiltering on the high-resolution image to derive an image at the same low resolution as the input depth map. The upsample filter uses samples from both the high-resolution and the low-resolution images in the range term of the bilateral filter. Secondly, we propose to perform the upsampling in multiple stages, refining the resolution by a factor of 2×2 at each stage. We show experimental results on the consequences of the aliasing issue, and we apply our method to two use cases: a high quality ground-truth depth map and a real-time generated depth map of lower quality. For the first use case a relatively small filter footprint is applied; the second use case benefits from a substantially larger footprint. These experiments show that the dual image resolution range function alleviates the aliasing artifacts and therefore improves the temporal stability of the output depth map. On both use cases, we achieved comparable or better image quality with respect to upsampling with the joint bilateral filter in a single step. On the former use case, we feature a reduction of a factor of 5 in computational cost, whereas on the latter use case, the cost saving is a factor of 50.
Acoustic and surface EMG diagnosis of pediatric muscle disease

The ratio of acoustic myography (AMG) amplitude to surface electromyography (EMG) amplitude is proposed as a measure of mechanical output compared with electrical activity of the contractile system. AMG to EMG ratios were measured from 16 children with muscle disease diagnosed by clinical criteria, EMG, and/or muscle biopsy. These were compared with the ratios from 11 normal volunteers spanning the same age range (7‐16 years). AMG to EMG ratios were significantly (P > 0.01) different for the two populations. Using a linear discriminant function to define the normal range for AMG to EMG ratios yielded a sensitivity of 82% (13 of 16 abnormals diagnosed) and a specificity of 91% (10 of 11 normals). These findings suggest that surface recordings may provide significant diagnostic information in muscle disease. The accuracy may be improved further by using additional muscles (e.g., paraspinals) and evoked twitches.
Pay, Working Conditions, and Teacher Quality

Eric Hanushek and Steven Rivkin examine how salary and working conditions affect the quality of instruction in the classroom. The wages of teachers relative to those of other college graduates have fallen steadily since 1940. Today, average wages differ little, however, between urban and suburban districts. In some metropolitan areas urban districts pay more, while in others, suburban districts pay more. But working conditions in urban and suburban districts differ substantially, with urban teachers reporting far less administrator and parental support, worse materials, and greater student problems. Difficult working conditions may drive much of the difference in turnover of teachers and the transfer of teachers across schools. Using rich data from Texas public schools, the authors describe in detail what happens when teachers move from school to school. They examine how salaries and student characteristics change when teachers move and also whether turnover affects teacher quality and student achievement. They note that both wages and student characteristics affect teachers' choices and result in a sorting of teachers across schools, but they find little evidence that teacher transitions are detrimental to student learning. The extent to which variations in salaries and working conditions translate into differences in the quality of instruction depends importantly on the effectiveness of school personnel policies in hiring and retaining the most effective teachers and on constraints on both entry into the profession and the firing of low performers. The authors conclude that overall salary increases for teachers would be both expensive and ineffective. The best way to improve the quality of instruction would be to lower barriers to becoming a teacher, such as certification, and to link compensation and career advancement more closely with teachers' ability to raise student performance.
Early nasogastric feeding versus parenteral nutrition in severe acute pancreatitis: A retrospective study

Objective: To compare the efficacy and safety of early nasogastric enteral nutrition (EN) with total parenteral nutrition (TPN) in patients with severe acute pancreatitis (SAP). Methods: From July 2008 to July 2014,185 patients with SAP admitted to our centre were enrolled in this retrospective study. They were divided into EN group (n=89) and TPN group (n=96) based on the nutrition support modes. Patients in EN group received nasogastric EN support, while patients in TPN group received TPN support within 72 hours of disease onset. The medical records were reviewed and clinical factors were retrospectively analyzed. Results: There were no significant differences in baseline characteristics between two groups. EN group had significantly lower incidence of pancreatic infections (P=0.0333) and extrapancreatic infections (P=0.0431). Significantly shorter hospital stay (P=0.0355) and intensive-care stay (P=0.0313) were found in EN group. TPN group was found to have significantly greater incidence of multiple organ dysfunction syndrome (MODS) (P=0.0338) and mortality (P=0.0382). Moreover, the incidence of hyperglycemia was significantly higher in TPN group (P=0.0454). Conclusions: Early nasogastric EN was feasible and significantly decreased the incidence of infectious complications as well as the frequency of MODS and mortality caused by SAP.