Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletions or duplications in the BtuB protein affect its level in the outer membrane of Escherichia coli

The Escherichia coli btuB product is an outer membrane protein that mediates the TonB-coupled active transport of cobalamins and the uptake of the E colicins and bacteriophage BF23. The roles of various segments of the BtuB protein in its function or cellular localization were investigated by analysis of several genetic constructs. Hybrid proteins in which various lengths from the amino terminus of BtuB were linked to alkaline phosphatase (btuB::phoA genes) were all secreted across the cytoplasmic membrane. The BtuB-PhoA proteins that carried up to 327 amino acids of BtuB appeared to reside in the periplasmic space, whereas hybrid proteins containing at least 399 amino acids of BtuB were associated with the outer membrane. Eleven in-frame internal deletion mutations that spanned more than half of the mature sequence were prepared by combining appropriate restriction fragments from btuB variants with 6-bp linker insertions. None of the deleted proteins was able to complement any BtuB functions, and only three of them were detectable in the outer membrane, suggesting that most of the deletions affected sequences needed for stable association with the outer membrane. Duplications covering the same portions of BtuB were prepared in the same manner. All of these partial duplication variants complemented all BtuB functions, although some gave substantially reduced levels of activity. These proteins were found in the outer membrane, although some were subject to proteolytic cleavage within or near the duplicated segment. These results indicate that the insertion of BtuB into the outer membrane requires the presence of several regions of teh BtuB protein and that the presence of extra or redundant segments of the protein can be tolerated during its insertion and function.
Evaluating the volatility forecasting performance of best fitting GARCH models in emerging Asian stock markets

Problem statement : While modeling the volatility of returns is essential for many areas of finance, it is well known that financial return series exhibit many non-normal characteristics that cannot be captured by the standard GARCH model with a normal error distribution. But which GARCH model and which error distribution to use is still open to question, especially where the model that best fits the in-sample data may not give the most effective out-of-sample volatility forecasting ability. Approach: In this study, six simulated studies in GARCH(p,q) with six different error distributions are carried out. In each case, we determine the best fitting GARCH model based on the AIC criterion and then evaluate its outof sample volatility forecasting performance against that of other models. The analysis is then carried out using the daily closing price data from Thailand (SET), Malaysia (KLCI) and Singapore (STI) stock exchanges. Results : Our simulations show that although the best fitting model does not always provide the best future volatility estimates the differences are so insignificant that the estimates of the best fitting model can be used with confidence. The empirical application to stock markets also indicates that a non normal error distribution tends to improve the volatility forecast of returns. Conclusion : The volatility forecast estimates of the best fitted model can be reliably used for volatility forecasting. Moreover, the empirical studies demonstrate that a skewed error distribution outperforms other error distributions in terms of out-of-sample volatility forecasting.
Prospective change control analysis of transfer of platelet concentrate production from a specialized stem cell transplantation unit to a blood transfusion center

Background and objectives: Specialized centers claim a need for blood component production independent from the general blood transfusion services. We performed a prospective change control analysis of the transfer of platelet (PLT) production for hematological patients at the University Hospital Basel from the Department of Hematology to the Blood Transfusion Centre, Swiss Red Cross, Basel in February 2006. We wanted to demonstrate that neither quality nor transfusion outcome was affected. Material and methods: Production quantity and efficiency, product quality and transfusion outcome were systematically recorded. A 2‐year pretransfer period was compared to a 2 year post‐transfer period. Results: After transfer production quantity at the Blood Transfusion Centre increased from 4,483 to 6,190 PLT concentrates. Production efficiency increased with a significant decrease in the rate of expired products (18% vs. 8%; P < 0.001). Product quality showed a slight decrease in median PLT count per unit (2.84 vs. 2.75 × 1011; P < 0.001) and a slight increase in mean storage time prior to transfusion (3.18 vs. 3.30 days; P < 0.001). Transfusion outcome measured as median corrected count increment one hour post‐transfusion (10.5 vs. 10.7; P = 0.3) and the rate of patients with inadequate post‐transfusion increment (31.5% vs. 32.1%; P = 0.6) did not differ. Conclusion: Supply and quality of PLT products was maintained after the transfer of PLT production to the Blood Transfusion Centre. An optimization of the supply chain process with markedly decreased expiration rates was achieved. These results argue against the need of specialized PLT production sites for selected patient groups. J. Clin. Apheresis, 2012. © 2012 Wiley Periodicals, Inc.
Mechanism of IFN-β-Mediated Inhibition of IL-8 Gene Expression in Astroglioma Cells1

IL-8 is a chemokine that recruits migrating neutrophils and leukocytes to areas of inflammation. In noninflamed tissue, IL-8 expression is low but can be rapidly induced by proinflammatory cytokines. Typically, inflammation and transient IL-8 expression are beneficial. However, some diseases are characterized by excessive inflammation and high levels of IL-8. Previous studies have shown that IFN-β can inhibit the expression of IL-8, although the mechanism is unknown. Using chromatin immunoprecipitation assays, we define the IL-8 transcriptional program in the absence or presence of inducing stimuli and/or inhibition by IFN-β. In the absence of stimuli, the IL-8 promoter is acetylated but negatively regulated by corepressor proteins. Upon PMA stimulation, the levels of these corepressors are reduced and the promoter is rapidly bound and activated by transcription factors, including NF-κB p65, C/EBPβ, and c-Fos. In addition, RNA polymerase II is recruited to the IL-8 promoter to initiate transcription. However, in the presence of both PMA and IFN-β, there are diminished levels of histone acetylation, reduced levels of transcription factors such as NF-κB p65 and RNA polymerase II, and an increased presence of corepressor proteins such as histone deacetylases 1 and 3 and silencing mediator of retinoic acid and thyroid hormone receptors. IFN-γ-inducible protein-10 and MCP-1 genes, also regulated by NF-κB, are unaffected by IFN-β, and IFN-β does not prevent the activation, nuclear migration, or binding of NF-κB p65 to the κB element of the IFN-γ-inducible protein-10 promoter. As such, these data show that the inhibitory effects of IFN-β are specific to the IL-8 promoter.
Life after Chi-Squared: An Introduction to Log-Linear Analysis

Chi-squared tests are used to examine the relationships among categorical variables. However, they are difficult to use and interpret when more than 2 variables are involved. In such cases, it is better to use a related statistic, called log-linear analysis. This article is an introduction to log-linear models, illustrating how they can be used to tease apart relationships among several variables in looking at the factors associated with photonumerophobia.
Constrained Multivariate Extrapolation Models With Application to Computer Cache Rates

In this article we propose an approach to building multivariate regression models for prediction beyond the range of the data. The extrapolation model attempts to accurately estimate the high-level trend of the data, which can be extended in a natural way. The constraints of monotonicity and convexity/concavity play an important role in restricting the choice of the high level-trend, which otherwise would remain rather arbitrary. Our extrapolation model incorporates these constraints in multiple dimensions. We describe the trend as a nonnegative linear combination of twice-integrated multivariate B-splines and their variations. The specific basis functions in our approach are chosen so that any such combination is a plausible a priori model. As a result, basis function coefficients can be optimized to best fit the data without losing control over the high-level trend of the extrapolation model. Our approach also allows the use of standard model selection techniques. We illustrate this by applying cross-validation to roughness penalty parameter selection. We demonstrate the validity of our approach by successfully applying it to modeling computer cache miss rates—a key problem in computer system performance analysis.
Influence of auditory and haptic feedback on a balancing task

In this paper, we present a system based on a wobble board, an instrument used in rehabilitation, augmented with an accelerometer and a pair of actuators. The main idea is to use augmented objects to enhance rehabilitation. Specifically, the accelerometers are manufactured by Phidgets, and connected through USB to a laptop computer. The actuators are manufactured by Tactile labs and are connected through an amplifier to a soundcard and a laptop computer. We used this system in an experiment with the goal of investigating the role of auditory and haptic feedback to facilitate the act of balancing on the board. Specifically, we designed a simple balance task consisting of balancing a box on a tilting virtual platform. The motion of the virtual platform is controlled by the motion of the subjects on the physical board. The experiment was run under eight different conditions: with no feedback, with auditory feedback, with haptic feedback, with visual feedback and with all combinations of the above. Auditory and haptic feedback were generated in software by using a physics-based simulation of friction between the box and the surface. Results show that subjects' ability to perform the task depends merely on their balance skills and not on the feedback they are exposed to.
mTORC1 maintains renal tubular homeostasis and is essential in response to ischemic stress

Significance Mammalian target of rapamycin complex 1 (mTORC1) inhibitors are commonly used as immunosuppressants in solid-organ transplantation and as antiproliferative agents in various cancers. Despite indications of serious renal adverse events caused by mTORC1 inhibition, the role of mTORC1 for renal epithelial function and homeostasis has remained elusive. Unexpectedly, tubular mTORC1 controls energy-driven urine-concentrating mechanisms by maintaining mitochondrial biogenesis. Under pathophysiological conditions, mTORC1-dependent mitochondrial biogenesis is essential for energy supply and adaptation in response to ischemia. These findings identify mTORC1 as an important regulator of tubular energy metabolism, transcellular transport processes, and ischemic stress responses. Mammalian target of rapamycin complex 1 (mTORC1) is a key regulator of cell metabolism and autophagy. Despite widespread clinical use of mTORC1 inhibitors, the role of mTORC1 in renal tubular function and kidney homeostasis remains elusive. By using constitutive and inducible deletion of conditional Raptor alleles in renal tubular epithelial cells, we discovered that mTORC1 deficiency caused a marked concentrating defect, loss of tubular cells, and slowly progressive renal fibrosis. Transcriptional profiling revealed that mTORC1 maintains renal tubular homeostasis by controlling mitochondrial metabolism and biogenesis as well as transcellular transport processes involved in countercurrent multiplication and urine concentration. Although mTORC2 partially compensated for the loss of mTORC1, exposure to ischemia and reperfusion injury exaggerated the tubular damage in mTORC1-deficient mice and caused pronounced apoptosis, diminished proliferation rates, and delayed recovery. These findings identify mTORC1 as an important regulator of tubular energy metabolism and as a crucial component of ischemic stress responses.
A search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoters

We describe a web-based resource to identify, search and analyze sequence patterns conserved in the multiple sequence alignments of orthologous promoters from closely related / distant Saccharomyces spp. The webtool interfaces with a database where conserved sequence patterns (greater than 4 bp) have been previously extracted from genome-wide promoter alignments, allowing one to carry out user-defined genome-wide searches for conserved sequences to assist in the discovery of novel promoter elements based on comparative genomics. The web-based server can be accessed at http://www2.imtech. res.in/ anand/sacch_prom_pat. html.
Diaquabis(ethylenediamine-κ2 N,N′)copper(II) bis(sulfamerazinate)

The asymmetric unit of the title compound, [Cu(C2H8N2)2(H2O)2](C11H11N4O2S)2, contains one sulfamerazinate anion in a general position and one half-cation that is located on a center of inversion. The CuII cation shows a strong Jahn–Teller distortion. It is coordinated by four N atoms of two ethylenediamine ligands in the basal plane and two O atoms at much longer distances in the axial positions in a bipyramidal coordination. In the crystal, the building blocks are connected by N—H⋯N, O—H⋯N, N—H⋯O and O—H⋯O hydrogen bonding into a two-dimensional network parallel to (001).
Studies on the nature of the arterial blood oxygen unsaturation in chronic pulmonary disease.

SUMMARY 1.Our studies indicate that shunting producing arterial blood oxygen unsaturation is one of varying magnitude whether it be due to an arteriovenous fistula of the lung, intracardiac shunting from right to left or at the alveolar level in chronic pulmonary diseases such as: pulmonary fibrosis, collagen diseases, sarcoidosis, pneumoconiosis and emphysema. The decrease noted in the arterial blood oxygen saturation with exercise on air breathing was not restored to a normal level on a high oxygen breathing mixture (such as 32.0 per cent oxygen) as one would expect if the major difficulty were alveolar capillary-membrane block. 2.The use of (1) graded levels of oxygen breathing, especially 32.0 per cent oxygen and 40.0 per cent oxygen, and (2) the use of intermittent positive pressure breathing on compressed air only constitute simple tests indicating the nature of the arterial blood oxygen unsaturation. 3.The use of 100 per cent oxygen breathing at rest in an inadequate test to rule out shunting, as this not only obscures shunting at the alveolar level, but in some cases if measured with exercise a decreased saturation results in the presence of a normal resting saturation (100 per cent). 4.These studies indicate that in chronic pulmonary disease in general (except beryllosis) that the primary cause of the arterial blood oxygen unsaturation is due to the presence of poorly ventilated alveoli or to the perfusion of blood through nonventilated or poorly ventilated areas and that an alveolar-capillary membrane block is not a significant factor producing the hypoxia.
Knowledge Based Concept Analysis Method using Concept Maps and UML: Security Notion Case

One of the most ancient humankind concerns is knowledge formalization i.e. what a concept is. Concept Analysis, a branch of analytical philosophy, relies on the purpose of decompose the elements, relations and meanings of a concept. This paper aims at presenting a method to make a concept analysis obtaining a knowledge representation suitable to be processed by a computer system using either object-oriented or ontology technologies. Security notion is, usually, known as a set of different concepts related to “some kind of protection”. Our method concludes that a more general framework for the concept, despite it is dynamic, is possible and any particular definition (instantiation) depends on the elements used by its construction instead of the concept itself. Keywords—Concept analysis, Knowledge representation, Security, UML.
Considerations on the biological effect of laser induced radiation with high dose rates

Values for the number of DNA damages of different types caused by sparsely ionizing radiation produced by conventional accelerators are well known. Table II shows approximate yields of DNA damages per Gy and cell and in compasion the calculated additional multiple DNA damages due to stochastic independent ionizations. It is obvious, that for dose fractions applied in radiation therapy the number of additional double-strand breaks induced by accidental single hits is negligible small. This is even the case for fraction doses as high as 24 Gy, a dose fraction, which is applied in stereotactic radio surgery for example. In reality it should be even smaller because it was assumed that all ionization events would take place at the same time what is especially due to the temporal spread of the dose pulse when interacting with matter not the case. The temporal spread of a 20MeV electron beam in water in a depth of 6 cm was also calculated using GEANT4 and can be seen in Fig. 6. As this figure shows the radiation pulse needs around 200 ps to reach a depth of 6 cm. At this depth the temporal spread of the pulse has become so broad, that it takes a time of ca 13 ps to deposit 50% of the total dose. During this period of time it could be possible, that recombination takes place and that cracked chemical bonds are stabilized before further ionizations can cause a complex damages. This makes it clear, that the calculated values are upper limits anyway. However this predication is valid for direct radiation effects. It should be noticed that this investigation is restricted to the direct radiation effect. The influence of the indirect radiation effect on the relative biological effectiveness of ultra shortly pulsed radiation was not assessed by these calculations.
End-to-End Neural Speech Synthesis

In recent years, end-to-end neural networks have become the state of the art for speech recognition tasks and they are now widely deployed in industry (Amodei et al., 2016). Naturally, this has led to the creation of systems to do the opposite – end-to-end speech synthesis from raw text. Very recently, neural TTS systems have become highly competitive with their conventional counterparts, showing high naturalness scores in a variety of incarnations. The flexibility and relative simplicity of these models is compelling and their potential for transfer learning (Arik et al., 2017) suggests the future existence of high quality voice mimicking algorithms. Here, we present an open source end-to-end TTS system, based on Google’s Tacotron, which uses freely available datasets to train a working voice with reasonable naturalness.
Anomalous diffusion in random media of any dimensionality

We show, through physical arguments and a renormalization group analysis, that in the presence of long-range correlated random forces, diffusions is anomalous in any dimension. We obtain in general surdiffusive behaviours, except when the random force is the gradient of a potential. In this last situation, with either short or long-range correlations, a subdiffusive behaviour with a disorder dependent exponent is found in the upper critical case (D = 2 for short-range correlations). This is because the β-function vanishes, which is explicitly proven at all orders of the perturbation theory. Apart from this case, a potential force is expected to lead to logarithmic diffusion (1/f noise), as suggested by simple arguments.
Beta‐Amyloid, Phospho‐Tau and Alpha‐Synuclein Deposits Similar to Those in the Brain Are Not Identified in the Eyes of Alzheimer's and Parkinson's Disease Patients

Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative disorders, and are characterized by deposition of specific proteins in the brain. If similar abnormal protein deposits are present in the eye, it would facilitate noninvasive diagnosis and monitoring of disease progression. We therefore evaluated expression of proteins associated with AD and PD pathology in postmortem eyes and brains in a case‐control study. Eyes from 11 cases of AD, 6 cases of PD or PD with dementia, and 6 age‐matched controls were retrieved from the autopsy archives of The Johns Hopkins Hospital. Immunostains for β‐amyloid, phospho‐tau and α‐synuclein and Congo red stains were performed in the same laboratory in both brains and eyes. No amyloid deposits or abnormal tau accumulations were detected in the lens, retina or other structures in the eyes of AD patients. Eyes also lacked definite Lewy bodies or Lewy neurites in either PD or AD cases. Patchy cytoplasmic α‐synuclein positivity was seen in the retina of AD, PD and control cases, but did not correlate with the presence or extent of Lewy body pathology in the brain. Abnormal protein aggregations characteristic of AD and PD are thus not commonly present in the retinas or lens of affected patients when assayed using the same protocols as in the brain. This suggests that β‐amyloid, phospho‐tau and α‐synuclein either do not deposit in the eye in a manner analogous to brain, or are present at lower levels or in different forms.
Simultaneous MR Acquisition of Arterial and Brain Signal‐Time Curves

Regional cerebral blood flow (rCBF) provides important information about local neuronal functional and cerebrovascular status. Determination of rCBF requires sequential measurements of tracer concentration in arterial blood and brain tissue unless the tracer is trapped in the brain in proportion to rCBF. Since gadopentate dimeglumine is not trapped within brain tissue, we have developed the simultaneous dual FLASH pulse sequence (SDFLASH) which sequentially measures the MR signal change in both the internal carotid artery and brain parenchyma simultaneously during the passage of a bolus of paramagnetic contrast material. © 1992 Academic Press,Inc.
Tsunami and Storm Surge Simulation Using Low Power Architectures - Concept and Evaluation

Performing a tsunami or storm surge simulation in real time is a highly challenging research topic that calls for a collaboration between mathematicians and computer scientists. One must combine mathematical models with numerical methods and rely on computational performance and code parallelization to produce accurate simulation results as fast as possible. The traditional modeling approaches require a lot of computing power and significant amounts of electrical energy; they are also highly dependent on uninterrupted access to a reliable power supply. This paper presents a concept how to develop suitable low power hardware architectures for tsunami and storm surge simulations based on cooperative software and hardware simulation. The main goal is to be able - if necessary - to perform simulations in-situ and battery-powered. For flood warning systems installed in regions with weak or unreliable power and computing infrastructure, this would significantly decrease the risk of failure at the most critical moments.