Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter

Constitutive promoters are used routinely to drive ectopic gene expression. Here, we carried out a systematic comparison of eight commonly used constitutive promoters (SV40, CMV, UBC, EF1A, PGK and CAGG for mammalian systems, and COPIA and ACT5C for Drosophila systems). We also included in the comparison the TRE promoter, which can be activated by the rtTA transcriptional activator in a doxycycline-inducible manner. To make our findings representative, we conducted the comparison in a variety of cell types derived from several species. We found that these promoters vary considerably from one another in their strength. Most promoters have fairly consistent strengths across different cell types, but the CMV promoter can vary considerably from cell type to cell type. At maximal induction, the TRE promoter is comparable to a strong constitutive promoter. These results should facilitate more rational choices of promoters in ectopic gene expression studies.
Intestinal Inflammation in Rats Induces Metallothionein in Colonic Submucosa

The aim of the current study was to determine if induction of metallothionein (MT) via acute or chronic dietary zinc supplementation attenuates intestinal inflammation, and to investigate the relationship with site-specific intestinal MT determined by immunolocalization. Growing rats were assigned to zinc-deficient (ZD), acute zinc-treated (ZT), pair-fed, control or chronic Zn-supplemented (ZS) groups. Half the rats in each dietary group received 5% dextran sulphate sodium (DSS) in their drinking water for 4 days. DSS treatment produced acute intestinal inflammation in the colon only, however, dietary zinc deficiency, acute zinc treatment or chronic zinc supplementation did not alter the severity of ulceration. Serum zinc concentrations were attenuated in the DSS-challenged ZT and ZS groups suggesting that zinc was being utilized in some capacity in response to inflammation. DSS-challenge induced MT immunostaining in the colonic submucosa, however, MT was not associated with histological improvements in the present study. The site-specific MT induction in colonic submucosa during intestinal inflammation requires further clarification as a component of the host defense.
Voltage Collapse Prediction and Voltage Stability Enhancement by Using Static Var Compensator

Voltage instability is gaining importance because of unusual growth in power system. Reactive power limit of power system is one of the reasons for voltage instability. Preventing Voltage Collapsesare one of the challenging tasks present worldwide.This paper presents static methods like Modal Analysis, Two Bus Thevenin Equivalent and Continuation Power Flow methods to predict the voltage collapse of the bus in the power system.These methods are applied on WSCC – 9 Bus and IEEE – 14 Bus Systems and test results are presented. Key Words—Continuation Power Flow, FACTS, QV Modal Analysis, SVC, Two Bus Thevenin Equivalent, Voltage Collapse
The Ral Exchange Factor Rgl2 Promotes Cardiomyocyte Survival and Inhibits Cardiac Fibrosis

Cardiomyocytes compensate to acute cardiac stress by increasing in size and contractile function. However, prolonged stress leads to a decompensated response characterized by cardiomyocyte death, tissue fibrosis and loss of cardiac function. Identifying approaches to inhibit this transition to a decompensated response may reveal important targets for treating heart failure. The Ral guanine nucleotide disassociation (RalGDS) proteins are Ras-interacting proteins that are upregulated by hypertrophic stimuli. The Ral guanine nucleotide dissociation stimulator-like 2 (Rgl2) is a member of the RalGDS family that modulates expression of hypertrophic genes in cardiomyocytes. However, the pathophysiologic consequence of increased Rgl2 expression in cardiomyoctyes remains unclear. To evaluate the effect of increasing Rgl2 activity in the heart, transgenic mice with cardiac-targeted over-expression of Rgl2 were generated. Although Ral activation was increased, there were no apparent morphologic or histological differences between the hearts of Rgl2 transgenic and nontransgenic mice indicating that increased Rgl2 expression had no effect on basal cardiac phenotype. To determine if Rgl2 modulates the cardiac response to stress, mice were infused with the ß-adrenergic receptor agonist, isoproterenol. Isoproterenol infusion increased heart mass in both Rgl2 transgenic and nontransgenic mice. However, unlike nontransgenic mice, Rgl2 transgenic mice showed no morphologic evidence of cardiomyocyte damage or increased cardiac fibrosis following isoproterenol infusion. Increased Rgl2 expression in cultured cardiomyocytes stimulated Ral activation and inhibited staurosporine-induced apoptosis via increased activation of PI3-kinase. Activation of the PI3-kinase signaling pathway was confirmed in hearts isolated from Rgl2 transgenic mice. Increased expression and function of Rgl2 in cardiomyocytes promotes activation of the PI3-kinase signaling cascade and protects from carciomyocyte death and pathologic cardiac fibrosis. Taken further, these results suggest that Rgl2 upregulation in hypertrophic hearts may be a protetive mechanism, and that Rgl2 may be a novel therapeutic target in treating heart disease.
Analysis of the effects of rotating roller speed on a roller electrospinning system

The complexity of the free surface electrospinning process makes empirical determination of the effects of parameters very difficult. The parameters of the free surface-roller electrospinning process have not been fully defined. In this paper, new electrospinning parameters were suggested and studied. The relationship between rotating roller speed as a dependent parameter and independent parameter was investigated. The effects of rotating roller speed on electrospun nanofiber diameters and the quality of a nano web are determined experimentally. The velocity of the spinning roller and the content of salts in the solutions were selected as independent process parameters. The results show that the velocity of the rotating roller, which is related to the flow rate/feed rate of a solution on the surface of the rotating roller, affects the spinning performance as well as the quality of the fibers. Moreover, the spinnability and spinning behavior of polyurethane and polyethylene oxide solutions mainly depend on the salt content, viscosity and rotating roller speed. The high speed of the rotating roller caused a thick fiber diameter for the polyurethane solutions and polyethylene oxide, while the slow motion of the rotating roller caused low spinning performance. The diameters and diameter distribution of the electrospun nanofibers and quality of the nano web were most significantly affected by the speed of the rotating roller.
Source-space ICA for MEG source imaging

Objective. One of the most widely used approaches in electroencephalography/magnetoencephalography (MEG) source imaging is application of an inverse technique (such as dipole modelling or sLORETA) on the component extracted by independent component analysis (ICA) (sensor-space ICA + inverse technique). The advantage of this approach over an inverse technique alone is that it can identify and localize multiple concurrent sources. Among inverse techniques, the minimum-variance beamformers offer a high spatial resolution. However, in order to have both high spatial resolution of beamformer and be able to take on multiple concurrent sources, sensor-space ICA + beamformer is not an ideal combination. Approach. We propose source-space ICA for MEG as a powerful alternative approach which can provide the high spatial resolution of the beamformer and handle multiple concurrent sources. The concept of source-space ICA for MEG is to apply the beamformer first and then singular value decomposition + ICA. In this paper we have compared source-space ICA with sensor-space ICA both in simulation and real MEG. The simulations included two challenging scenarios of correlated/concurrent cluster sources. Main Results. Source-space ICA provided superior performance in spatial reconstruction of source maps, even though both techniques performed equally from a temporal perspective. Real MEG from two healthy subjects with visual stimuli were also used to compare performance of sensor-space ICA and source-space ICA. We have also proposed a new variant of minimum-variance beamformer called weight-normalized linearly-constrained minimum-variance with orthonormal lead-field. Significance. As sensor-space ICA-based source reconstruction is popular in EEG and MEG imaging, and given that source-space ICA has superior spatial performance, it is expected that source-space ICA will supersede its predecessor in many applications.
Information Value of Two-Prover Games

We introduce a generalization of the standard framework for studying the difficulty of two-prover games. Specifically, we study the model where Alice and Bob are allowed to communicate (with information constraints) - in contrast to the usual two-prover game where they are not allowed to communicate after receiving their respective input. We study the trade-off between the information cost of the protocol and the achieved value of the game after the protocol. In particular, we show the connection of this trade-off and the amortized behavior of the game (i.e. repeated value of the game). We show that if one can win the game with at least (1 - \epsilon)-probability by communicating at most \epsilon bits of information, then one can win n copies with probability at least 2^{-O(\epsilon n)}. This gives an intuitive explanation why Raz's counter-example to strong parallel repetition [Raz2008] (the odd cycle game) is a counter-example to strong parallel repetition - one can win the odd-cycle game on a cycle of length $m$ by communicating O(m^{-2})-bits where m is the number of vertices. Conversely, for projection games, we show that if one can win n copies with probability larger than (1-\epsilon)^n, then one can win one copy with at least (1 - O(\epsilon))-probability by communicating O(\epsilon) bits of information. By showing the equivalence between information value and amortized value, we give an alternative direction for further works in studying amortized behavior of the two-prover games. The main technical tool is the "Chi-Squared Lemma" which bounds the information cost of the protocol in terms of Chi-Squared distance, instead of usual divergence. This avoids the square loss from using Pinsker's Inequality.
Reducing Subjectivity in Code Smells Detection: Experimenting with the Long Method

Guidelines for refactoring are meant to improve software systems internal quality and are widely acknowledged as among software’s best practices. However, such guidelines remain mostly qualitative in nature. As a result, judgments on how to conduct refactoring processes remain mostly subjective and therefore non-automatable, prone to errors and unrepeatable. The detection of the Long Method code smell is an example. To address this problem, this paper proposes a technique to detect Long Method objectively and automatically, using a Binary Logistic Regression model calibrated by expert’s knowledge. The results of an experiment illustrating the use of this technique are reported.
Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life

This article reviews recent advances in ‘microbiome studies’: molecular, statistical and graphical techniques to explore and quantify how microbial organisms affect our environments and ourselves given recent increases in sequencing technology. Microbiome studies are moving beyond mere inventories of specific ecosystems to quantifications of community diversity and descriptions of their ecological function. We review the last 24 months of progress in this sort of research, and anticipate where the next 2 years will take us. We hope that bioinformaticians will find this a helpful springboard for new collaborations with microbiologists.
Alloferon Alleviates Dextran Sulfate Sodium-induced Colitis

Dysfunction of gut immune regulation is involved in mucosal damage in inflammatory bowel disease (IBD). However, there is still no efficacious immune-regulator for the treatment of IBD. Alloferon is a novel immune-modulatory peptide that was originally isolated from infected insects. It shows anti-inflammatory effects by the regulation of cytokine production by immune cells and their activities. Therefore, we investigated the effect of alloferon in a mouse model of colitis using dextran sulfate sodium (DSS). Colitis was induced by administration of DSS in drinking water for 7 consecutive days. It was confirmed by the presence of weight loss, diarrhea, hematochezia, and colon contraction. Alloferon was injected 4 days after DSS administration. We found that alloferon improved the pathogenesis of IBD based on the reduced disease activity index (DAI) and colon contraction. Edema, epithelial erosion, and immune cell infiltration were found in mice administered DSS, but the phenomena were reduced following alloferon treatment. The plasma level of IL-6, a classical pro-inflammatory cytokine in colitis, was also decreased by alloferon. Moreover, alloferon inhibited the TNF-α-induced degradation and phosphorylation of IκB in Colo205 colon cancer cells. Taken together, these results show that alloferon has anti-inflammatory effects and attenuates DSS-induced colitis.
Filterbank learning for deep neural network based polyphonic sound event detection

Deep learning techniques such as deep feedforward neural networks and deep convolutional neural networks have recently been shown to improve the performance in sound event detection compared to traditional methods such as Gaussian mixture models. One of the key factors of this improvement is the capability of deep architectures to automatically learn higher levels of acoustic features in each layer. In this work, we aim to combine the feature learning capabilities of deep architectures with the empirical knowledge of human perception. We use the first layer of a deep neural network to learn a mapping from a high-resolution magnitude spectrum to smaller amount of frequency bands, which effectively learns a filterbank for the sound event detection task. We initialize the first hidden layer weights to match with the perceptually motivated mel filterbank magnitude response. We also integrate this initialization scheme with context windowing by using an appropriately constrained deep convolutional neural network. The proposed method does not only result with better detection accuracy, but also provides insight on the frequencies deemed essential for better discrimination of given sound events.
Introducing Adaptive Incremental Dynamic Analysis: A New Tool for Linking Ground Motion Selection and Structural Response Assessment

Adaptive Incremental Dynamic Analysis (AIDA) is a novel ground motion selection scheme that adaptively changes the ground motion suites at different ground motion intensity levels to match hazardconsistent properties for structural response assessment. Incremental Dynamic Analysis (IDA), a current dynamic response history analysis practice in Performance-Based Earthquake Engineering (PBEE), uses the same suite of ground motions at all Intensity Measure (IM) levels to estimate structural response. Probabilistic Seismic Hazard Analysis (PSHA) deaggregation tells us, however, that the target distributions of important ground motion properties change as the IM levels change. To match hazard-consistent ground motion properties, ground motions can be re-selected at each IM level, but ground motion continuity is lost when using such “stripes” (i.e., individual analysis points at each IM level). Alternatively, the data from the same ground motions in IDA can be re-weighted at various IM levels to match their respective target distributions of properties, but this implies potential omission of data and curse of dimensionality. Adaptive Incremental Dynamic Analysis, in contrast, gradually changes ground motion records to match ground motion properties as the IM level changes, while also partially maintaining ground motion continuity without the omission of useful data. AIDA requires careful record selection across IM levels. Potential record selection criteria include ground motion properties from deaggregation, or target spectrum such as the Conditional Spectrum. Steps to perform AIDA are listed as follows: (1) obtain target ground motion properties for each IM level; (2) determine “bin sizes” (i.e., tolerance for acceptable ground motion properties) and identify all candidate ground motions that fall within target bins; (3) keep ground motions that are usable at multiple IM levels, to maintain continuity; (4) use each ground motion for IDA within its allowable IM range. As a result, if we keep increasing the “bin sizes”, AIDA will approach IDA asymptotically; on the other hand, if we decrease the “bin sizes”, AIDA will approach the other end of “stripes”. This paper addresses the challenges of changing records across various IM levels. Different ground motion selection schemes are compared with AIDA to demonstrate the advantages of using AIDA. Example structural analyses are used to illustrate the impact of AIDA on the estimation of structural response in PBEE. By combining the benefits of IDA and PSHA without the omission of useful data, AIDA is a promising new tool for linking ground motion selection and structural response assessment.
Human Genome Epidemiology ( HuGE ) Review Factor XIII Val 34 Leu Variant Is Protective against Venous Thromboembolism : A HuGE Review and Meta-Analysis

It has been suggested that a G-to-T transition in exon 2 of the factor XIIIA gene resulting in a substitution of leucine for valine at amino acid 34 (FXIII Val34Leu) protects against venous thromboembolism (VTE). However, the evidence to date is insufficient to incorporate testing for the FXIII Val34Leu variant into clinical practice. To determine whether genotypes with the FXIII Val34Leu variant are protective against VTE, the authors performed a meta-analysis of 12 studies with genotyping for the FXIII Val34Leu variant (3,165 objectively diagnosed VTE cases and 4,909 controls). When a random-effects model was used, the combined odds ratios for VTE were 0.63 (95% confidence interval: 0.46, 0.86) for the homozygotes of the FXIII Val34Leu variant, 0.89 (95% confidence interval: 0.80, 0.99) for the heterozygotes, and 0.85 (95% confidence interval: 0.77, 0.95) for the homozygotes and heterozygotes combined. Potential sources of heterogeneity and potential bias were explored. The meta-analysis provided evidence that the FXIII Val34Leu variant has a small, but significant protective effect against VTE. Since VTE is a complex disorder, this information, along with results of ongoing studies to identify additional genetic factors underlying VTE, will be crucial in developing accurate risk profiles to identify individuals at higher risk of VTE.
Cranioplasty After Severe Traumatic Brain Injury: Effects of Trauma and Patient Recovery on Cranioplasty Outcome

Background In patients with severe traumatic brain injury (sTBI) treated with decompressive craniectomy (DC), factors affecting the success of later cranioplasty are poorly known. Objective We sought to investigate if injury- and treatment-related factors, and state of recovery could predict the risk of major complications in cranioplasty requiring implant removal, and how these complications affect the outcome. Methods A retrospective cohort of 40 patients with DC following sTBI and subsequent cranioplasty was studied. Non-injury-related factors were compared with a reference population of 115 patients with DC due to other conditions. Results Outcome assessed 1 day before cranioplasty did not predict major complications leading to implant removal. Successful cranioplasty was associated with better outcome, whereas a major complication attenuates patient recovery: in patients with favorable outcome assessed 1 year after cranioplasty, major complication rate was 7%, while in patients with unfavorable outcome the rate was 42% (p = 0.003). Of patients with traumatic subarachnoid hemorrhage (tSAH) on admission imaging 30% developed a major complication, while none of patients without tSAH had a major complication (p = 0.014). Other imaging findings, age, admission Glasgow Coma Scale, extracranial injuries, length of stay at intensive care unit, cranioplasty materials, and timing of cranioplasty were not associated with major complications. Conclusion A successful cranioplasty after sTBI and DC predicts favorable outcome 1 year after cranioplasty, while stage of recovery before cranioplasty does not predict cranioplasty success or failure. tSAH on admission imaging is a major risk factor for a major complication leading to implant removal.
Looking for symmetric Bell inequalities

Finding all Bell inequalities for a given number of parties, measurement settings and measurement outcomes is in general a computationally hard task. We show that all Bell inequalities which are symmetric under the exchange of parties can be found by examining a symmetrized polytope which is simpler than the full Bell polytope. As an illustration of our method, we generate 238 885 new Bell inequalities and 1085 new Svetlichny inequalities. We find, in particular, facet inequalities for Bell experiments involving two parties and two measurement settings that are not of the Collins–Gisin–Linden–Massar–Popescu type.
Degrees-of-freedom reduction for wave-particle systems : Comparison of Pierce equivalent circuit and recent discrete model for traveling-wave tubes

To perform accurate numerical simulations of the wave-particle interaction as it occurs in particular in traveling wave tubes, a new approach using field decomposition with large reduction of degrees of freedom has been proposed: the discrete model. To assess its validity, we compare it with the well-established Pierce equivalent circuit model in small signal regime. Before the comparison, the beam-wave interaction in both models is reformulated using a new pedagogical approach, dealing with associated beam, circuit-beam, and circuit impedances. We show analytically and with a numerical example that the newly developed reduced model is very close to the Pierce model. Interestingly, small deviations do exist at the edges of the amplification band, for which the reduced model offers a physical interpretation.
A $\mu $-Rhythm Matched Filter for Continuous Control of a Brain-Computer Interface

A brain-computer interface (BCI) is a system that provides an alternate nonmuscular communication/control channel for individuals with severe neuromuscular disabilities. With proper training, individuals can learn to modulate the amplitude of specific electroencephalographic (EEG) components (e.g., the 8-12 Hz mu rhythm and 18-26 Hz beta rhythm) over the sensorimotor cortex and use them to control a cursor on a computer screen. Conventional spectral techniques for monitoring the continuous amplitude fluctuations fail to capture essential amplitude/phase relationships of the mu and beta rhythms in a compact fashion and, therefore, are suboptimal. By extracting the characteristic mu rhythm for a user, the exact morphology can be characterized and exploited as a matched filter. A simple, parameterized model for the characteristic mu rhythm is proposed and its effectiveness as a matched filter is examined online for a one-dimensional cursor control task. The results suggest that amplitude/phase coupling exists between the mu and beta bands during event-related desynchronization, and that an appropriate matched filter can provide improved performance