Miracle-dz/UniFAR-FTUs huggingface dataset:
Leading Edge Review Impulse Control : Temporal Dynamics in Gene Transcription

Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Regulatory circuits controlling gene expression constantly rewire to adapt to environmental stimuli, differentiation cues, and disease. We review our current understanding of the temporal dynamics of gene expression in eukaryotes and prokaryotes and the molecular mechanisms that shape them. We delineate several prototypical temporal patterns, including ''impulse'' (or single-pulse) patterns in response to transient environmental stimuli, sustained (or state-transitioning) patterns in response to developmental cues, and oscillating patterns. We focus on impulse responses and their higher-order temporal organization in regulons and cascades and describe how core protein circuits and cis-regulatory sequences in promoters integrate with chromatin architecture to generate these responses. Introduction The transcriptional program that controls gene expression in cells and organisms is remarkably flexible, constantly reconfi-guring itself to respond and adapt to perturbations. These changes are apparent across a broad range of timescales, from rapid responses to environmental signals (i.e., minutes to hours) to slower events during development and pathogenesis (i.e., hours to days) (Lopez-Maury et al., 2008). Dissecting these dynamic changes, both functionally and mechanistically, is a fundamental challenge in biology and raises several key questions. What is the scope of temporal patterns of gene expression in biological systems? What functions do different patterns serve? What molecular mechanisms underlie the formation of each pattern, and what is their capacity to process the temporal signal into a specific change in gene expression over time? Finally, are any principles, either functional or mechanistic, shared among temporal responses in distinct timescales? Recent parallel advances in genomics and cell biology provide an unprecedented opportunity to map dynamic gene expression and decipher its underlying mechanisms. At the same time, live-cell imaging of fluorescent reporter proteins (Locke and Elowitz, 2009) allows us to study gene expression at fine temporal resolution and at the single-cell level. Such studies, when coupled with molecular manipulations and quantitative modeling, can identify basic mechanisms of temporal patterning. Further, genomic technologies provide global insights on the regulation of gene expression by allowing us to measure and perturb many aspects of the regulatory system, such as mRNA levels, protein-promoter interactions (Badis et al.
Improved survival of biolistically transfected mouse islet allografts expressing CTLA4-Ig or soluble Fas ligand.

BACKGROUND Pancreatic islet transplantation is limited because of immune rejection of the transplanted tissue. Long-term survival of allogeneic pancreatic islet grafts in the absence of systemic immunosuppressive agents should be possible by transfecting the islets directly with DNA encoding immunoregulatory molecules. Localized production of these molecules should affect only the immune cells that come into the vicinity of the foreign tissue. We investigated whether local expression of human CTLA4-Ig or soluble human Fas ligand from biolistically transfected mouse islets would have a protective effect on allograft survival. METHODS Isolated CBA (H2k) islets were biolistically transfected using the gene gun. The experimental groups were naked gold particles (n=6), empty vector DNA (n=5), DNA encoding human CTLA4-Ig (n=8), or soluble human Fas ligand (n=5). Secretion of the transfected gene product was confirmed by screening islet culture supernatants for protein production using a sandwich ELISA. The blasted islets were transplanted under the kidney capsule of alloxan-diabetic BALB/c (H2d) recipients. RESULTS Control grafts survived for 23 days, on average. CTLA4-Ig-transfected islets showed a bimodal distribution: 50% of cases survived > or = 46 days and 50% were similar to the controls. In the soluble human Fas ligand group, 80% of grafts survived > or = 50 days. There was no correlation between graft survival times and pretransplant levels of protein production. CONCLUSION Our results indicate that local production of human CTLA4-Ig or soluble human Fas ligand by biolistically transfected islets can promote allograft survival. This approach should be valuable as a potential immunoprotective therapeutic strategy in tissue transplantation.
The interaction between herpes simplex virus 1 genome and promyelocytic leukemia nuclear bodies (PML-NBs) as a hallmark of the entry in latency

Herpes simplex virus 1 (HSV-1) is a human pathogen that establishes latency in the nucleus of infected neurons in the PNS and the CNS. At the transcriptional level latency is characterized by a quasi-complete silencing of the extrachromosomal viral genome that otherwise expresses more than 80 genes during the lytic cycle. In neurons, latency is anticipated to be the default transcriptional program; however, limited information exists on the molecular mechanisms that force the virus to enter the latent state. Our recent study demonstrates that the interaction of the viral genomes with the nuclear architecture and specifically the promyelocytic leukemia nuclear bodies (PML-NBs) is a major determinant for the entry of HSV-1 into latency (Maroui MA, Callé A et al. (2016). Latency entry of herpes simplex virus 1 is determined by the interaction of its genome with the nuclear environment. PLoS Pathogens 12(9): e1005834. ).
Automatic suppression of white noise and repetitive pulses interference in on-site partial discharge monitoring

The on-site partial discharge (PD) monitoring is the most powerful method to detect insulation faults in electrical power components, but it is often severely affected by external interferences. This paper designs two algorithms for automatic detection and suppression of white noise interferences (WNI) and repetitive pulse interferences (RPI) in PD monitoring separately. The first algorithm for WNI suppression is based upon wavelet transform (WT), and it solves the issue of mother wavelet selection, decomposition level determination and threshold selection during WT denoising. The second one makes full use of the differences between PD pulses and RPI in pulse waveform and phase distribution, it takes three key steps including identifying pulses, clustering the similar pulses and analyzing pulse-phase histogram to separate RPI. Both of the two algorithms can be used in on-site PD monitoring, and their performance with practical data is shown in this paper.
Effect of dietary laminarin and fucoidan on selected microbiota, intestinal morphology and immune status of the newly weaned pig

A 2 × 2 factorial experiment was conducted to investigate the interactions between laminarin (LAM; 0 and 300 parts per million (ppm)) and fucoidan (FUC; 0 and 240 ppm) levels on intestinal morphology, selected microbiota and inflammatory cytokine gene expression in the weaned pig. There was an interaction between LAM and FUC supplementation on the Enterobacteriaceae population (P< 0·05) and the abundance of attaching and effacing Escherichia coli (AEEC) strains (P< 0·05) in the colon. Pigs offered the FUC diet had a reduced Enterobacteriaceae population compared with pigs offered the basal diet. However, the effect of FUC on the Enterobacteriaceae population was not observed when combined with LAM. Pigs offered the LAM diet had reduced abundance of AEEC strains compared with pigs offered the basal diet. However, there was no effect of LAM on the abundance of AEEC strains when combined with FUC. There was an interaction between LAM and FUC supplementation on villous height (P< 0·01) and the villous height:crypt depth ratio (P< 0·01) in the duodenum. Pigs offered the LAM or FUC diet had an increased villous height and villous height:crypt depth ratio compared with pigs offered the basal diet. However, there was no effect of the LAM and FUC combination diet on intestinal morphology. Pigs offered the LAM-supplemented diets had a lower IL-6 (P< 0·05), IL-17A (P< 0·01) and IL-1β (P< 0·01) mRNA expression in the colon compared with pigs offered the diets without LAM. In conclusion, supplementation with either LAM or FUC alone modified intestinal morphology and selected intestinal microbiota, but these effects were lost when offered in combination.
The future of financial reporting 2008: measurement and stakeholders

A discussion paper based on the British Accounting Association Financial Accounting and Reporting Special Interest Group (FARSIG) Colloquium, 11 January 2008. Financial accounting and reporting is a curious mix of dynamism and stability. Thinking about the theory and practice of financial accounting and reporting is constantly evolving from generation to generation. Nonetheless, at its core are several key issues that apparently remain eternal, such as a conceptual theory to underpin accounting, how to measure elements within the financial statements and the users of accounting information. A symposium at the ACCA offices in London, on 11 January 2008, explored some modern views on such perennial topics as conceptual theory, measurement and stakeholders. This report aims to synthesise and provide some informed commentary on the five papers presented at the symposium. These five papers were: 1. Conceptual Framework: Revisiting the Basics. A Comment on Hicks and the Concept of Income in the Conceptual Framework (Bromwich, M., Macve, R., and Sunder, S.) 2. Deciding on Basis of Measurement – Users’ Needs or Public Interest? (Chisman, N.) 3. Fair Value – An Ongoing Controversy (Martin, R.) 4. Fair Value and the IASB/FASB Conceptual Framework Project – An Alternative View (Whittington, G.) 5. Communication between Management and Stakeholders: A Case Study (McInnes, B., Beattie, V. and Pierpoint, J.)
Real-Time Heuristic Search with Depression Avoidance

Heuristics used for solving hard real-time search problems have regions with depressions. Such regions are bounded areas of the search space in which the heuristic function is exceedingly low compared to the actual cost to reach a solution. Real-time search algorithms easily become trapped in those regions since the heuristic values of states in them may need to be updated multiple times, which results in costly solutions. State-of-theart real-time search algorithms like LSS-LRTA*, LRTA*(k), etc., improve LRTA*'s mechanism to update the heuristic, resulting in improved performance. Those algorithms, however, do not guide search towards avoiding or escaping depressed regions. This paper presents depression avoidance, a simple real-time search principle to guide search towards avoiding states that have been marked as part of a heuristic depression. We apply the principle to LSS-LRTA* producing aLSS-LRTA*, a new real-time search algorithm whose search is guided towards exiting regions with heuristic depressions. We show our algorithm outperforms LSS-LRTA* in standard real-time benchmarks. In addition we prove aLSS-LRTA* has most of the good theoretical properties of LSS-LRTA*.
A Linear-Complexity Burst Packing Scheme for IEEE 802.16e OFDMA Downlink Frames

The problem of efficiently shaping downlink data bursts into rectangles and packing them in the OFDMA subframe is not addressed by the IEEE 802.16 standard, and is left as an implementation issue. In this paper, we propose a linear complex- ity bursts packing algorithm to maximize radio resources usage on the OFDMA downlink. Our scheme shapes the bursts into identical width, places them in column direction and maximally fills the columns by shifting the bursts on different columns. By simulation, we show that the scheme can push the radio resource usage over 95%, which is on average 20% improvement compared with the simple 2D fixed-bin strip packing and 8% improvement with the exhaustive search. Moreover, the proposed scheme is also power-efficient, because subscriber stations (SSs) do not need to receive a large aggregated burst created for packing problem complexity reduction.
Clinical Usefulness of an Oral Moisture Checking Device (Mucus

Purpose: The aim of this study was to investigate the factors that may influence the results of measurements of oral mucosal moisture using the new oral moisture checking device, especially in relation to the operator and the sensor cover.Methods: Oral mucosal moisture was measured using a new oral moisture checking device (Mucus®). To determine the influence of the operator on the measured values by the oral moisture checking device, 5 operators measured the oral mucosal moisture in 12 subjects. The differences were analyzed using the Friedman test. To determine the influence of the sensor cover, one operator measured the oral mucosal moisture in 12 subjects using two sensor covers. The differences were analyzed by Wilcoxon’s signed-rank test.Results: The result of the Friedman test revealed the absence of any significant influence of the operator on the measured values of oral mucosal moisture by the oral moisture checking device. The results of the Wilcoxon’s signed-rank test revealed that the measured values of oral mucosal moisture by the measuring device differed by about 1.6 % between the two sensor covers (P<0.01). Conclusion: The results of this study suggest that oral mucosal moisture can be measured using the new oral moisture checking device without any inter-operator error. However, there is some possibility of the measured values differing depending on the sensor cover used.
Sequence Folding, Lattice Tiling, and Multidimensional Coding

Folding a sequence B into a multidimensional box is a well-known method which is used as a multidimensional coding technique. The operation of folding is generalized in a way that the sequence B can be folded into various shapes and not just a box. The novel definition of folding is based on a lattice tiling for the given shape S and a direction in the D-dimensional integer grid. Necessary and sufficient conditions that a lattice tiling for S combined with a direction define a folding of a sequence into S are derived. The immediate and most impressive applications are some new lower bounds on the number of dots in two-dimensional synchronization patterns. Asymptotically optimal such patterns were known only for rectangular shapes. We show asymptotically optimal such patterns for a large family of hexagons. This is also generalized for multidimensional synchronization patterns. The best known patterns, in terms of dots, for circles and other polygons are also given. The technique and its application for two-dimensional synchronization patterns, raises some interesting problems in discrete geometry. We will also discuss these problems. It is also shown how folding can be used to construct multidimensional error-correcting codes. Finally, by using the new definition of folding, new types of multidimensional pseudo-random arrays with various shapes are generated.
Determinants of moral distress in medical and surgical nurses at an adult acute tertiary care hospital.

AIM To determine the prevalence and contributing factors of moral distress in medical and surgical nurses. BACKGROUND Moral distress from ethical conflicts in the work environment is associated with burnout and job turnovers in nurses. METHOD A prospective cross-sectional survey using the Moral Distress Scale tool was administered to medical and surgical nurses at an adult acute tertiary care hospital. RESULTS The survey was completed by 260 nurses (92% response rate). The intensity of moral distress was uniformly high to situations related to physician practice, nursing practice, institutional factors, futile care, deception and euthanasia. Encounter frequencies for situations associated with futile care and deceptions were particularly high. Encounter frequencies increased with years of nursing experience and caring for oncology and transplant patients. CONCLUSION Moral distress is common among nurses in acute medical and surgical units and can be elicited from different types of situations encountered in the work environment. Nursing experience exacerbated the intensity and frequency of moral distress. IMPLICATIONS FOR NURSING MANAGEMENT Strategies aimed to minimize exposure to situations of moral distress and augment mechanisms mitigating its effect on nurses are necessary to enhance job satisfaction and retention.
Magnetic field sensor based on D-shaped long period fiber gratings

We present a new magnetic field sensor based on D-shaped long-period fiber grating (D-LPFG). Iron thin-film was coated on the polished surface of an LPFG to function as a sensing head. Different levels of magnetic field caused a shift in the grating loss-dip wavelength shift. The sensing section of a D-LPFG causes a change in the effective refractive index both of the core mode and co-propagation cladding modes in response to the different levels of the applied magnetic field. The maximum shift in wavelength of 36 nm was obtained in the case of a magnetic field of 153 kA/m.
Inhibition of endothelial cell proliferation by gamma-interferon

Endothelial cell growth factor (ECGF) is a potent polypeptide mitogen for endothelial cells and fibroblasts. The mitogenic effects of ECGF are inhibited by the lymphokine gamma-interferon (gamma-IFN) in a dose- dependent manner. Gamma-IFN also induces a unique change in endothelial cell morphology which is maximally expressed in the presence of ECGF. The antiproliferative and phenotypic modulatory effects of gamma-IFN on endothelial cells are reversible. Inhibition of ECGF-induced endothelial cell proliferation by gamma-IFN is accompanied by a concentration- and time-dependent decrease in binding of 125I-ECGF to the endothelial cell surface. Scatchard analyses of the binding data in the presence and absence of gamma-IFN demonstrate a decrease in the number of ECGF-binding sites rather than a decrease in ligand affinity for the receptor. Cross-linking experiments with disuccinimidyl suberate demonstrate a decrease in the 170,000 Mr cross-linked receptor- ligand complex. These data suggest that gamma-IFN inhibits endothelial cell proliferation by a mechanism which involves growth factor receptor modulation.
Cache-efficient matrix transposition

We investigate the memory system performance of several algorithms for transposing an N/spl times/N matrix in-place, where N is large. Specifically, we investigate the relative contributions of the data cache, the translation lookaside buffer, register tiling, and the array layout function to the overall running time of the algorithms. We use various memory models to capture and analyze the effect of various facets of cache memory architecture that guide the choice of a particular algorithm, and attempt to experimentally validate the predictions of the model. Our major conclusions are as follows: limited associativity in the mapping from main memory addresses to cache sets can significantly degrade running time; the limited number of TLB entries can easily lead to thrashing; the fanciest optimal algorithms are not competitive on real machines even at fairly large problem sizes unless cache miss penalties are quite high: low-level performance tuning "hacks", such as register tiling and array alignment, can significantly distort the effects of improved algorithms; and hierarchical non-linear layouts are inherently superior to the standard canonical layouts (such as row- or column-major) for this problem.
A Real Option Model Suitable for Real Estate Project Investment Decision

Real estate investment is distinctively different from others with its high input capital, long period of recycling, huge fluctuation of house price and high sensitivity to other factors. The traditional decision method could not make a rational judgment of the flexible management value in real estate project investment. With regards to the policy and market features of real estate investment in China, a real option model suitable for real estate project investment decision under high uncertainty in China is constructed. At last, a case of a real estate company is studied to test the real estate investment decision model.
The physiological role of the amyloid precursor protein as an adhesion molecule in the developing nervous system

The amyloid precursor protein (APP) is a type I transmembrane glycoprotein better known for its participation in the physiopathology of Alzheimer disease as the source of the beta amyloid fragment. However, the physiological functions of the full length protein and its proteolytic fragments have remained elusive. APP was first described as a cell‐surface receptor; nevertheless, increasing evidence highlighted APP as a cell adhesion molecule. In this review, we will focus on the current knowledge of the physiological role of APP as a cell adhesion molecule and its involvement in key events of neuronal development, such as migration, neurite outgrowth, growth cone pathfinding, and synaptogenesis. Finally, since APP is over‐expressed in Down syndrome individuals because of the extra copy of chromosome 21, in the last section of the review, we discuss the potential contribution of APP to the neuronal and synaptic defects described in this genetic condition.
A high density 3.3 kW isolated on-vehicle battery charger using SiC SBDs and SiC DMOSFETs

We present a 3.3kW on-vehicle battery charger (OBC) for plug-in hybrid electrical vehicles and battery electric vehicles. The OBC is developed with a semi-bridgeless front-end PFC boost converter followed by a ZVS full bridge DC-DC converter. The performance of the PFC boost is analyzed and measured using different switching power devices. The test data is measured in the same system, at the same points of operation, using the conventional Si SJMOSFETs and Silicon Carbide (SiC) DMOSFETs. With the SiC DMOSFET at 200kHz switching frequency, the measured maximum power conversion efficiency of the PFC boost front-end converter is 97.7%. The full OBC efficiency is 94.7%.
Evidence for the Complexity of MicroRNA-Mediated Regulation in Ovarian Cancer: A Systems Approach

MicroRNAs (miRNAs) are short (∼22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. Previous studies have shown that miRNAs inhibit the translation and facilitate the degradation of their targeted messenger RNAs (mRNAs) making them attractive candidates for use in cancer therapy. However, the potential clinical utility of miRNAs in cancer therapy rests heavily upon our ability to understand and accurately predict the consequences of fluctuations in levels of miRNAs within the context of complex tumor cells. To evaluate the predictive power of current models, levels of miRNAs and their targeted mRNAs were measured in laser captured micro-dissected (LCM) ovarian cancer epithelial cells (CEPI) and compared with levels present in ovarian surface epithelial cells (OSE). We found that the predicted inverse correlation between changes in levels of miRNAs and levels of their mRNA targets held for only ∼11% of predicted target mRNAs. We demonstrate that this low inverse correlation between changes in levels of miRNAs and their target mRNAs in vivo is not merely an artifact of inaccurate miRNA target predictions but the likely consequence of indirect cellular processes that modulate the regulatory effects of miRNAs in vivo. Our findings underscore the complexities of miRNA-mediated regulation in vivo and the necessity of understanding the basis of these complexities in cancer cells before the therapeutic potential of miRNAs can be fully realized.