Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Analysis of the Signal-Sensing Domain of ResE Histidine Kinase from Bacillus subtilis

ABSTRACT The Bacillus subtilis ResD-ResE two-component regulatory system activates genes involved in nitrate respiration in response to oxygen limitation or nitric oxide (NO). The sensor kinase ResE activates the response regulator ResD through phosphorylation, which then binds to the regulatory region of genes involved in anaerobiosis to activate their transcription. ResE is composed of an N-terminal signal input domain and a C-terminal catalytic domain. The N-terminal domain contains two transmembrane subdomains and a large extracytoplasmic loop. It also has a cytoplasmic PAS subdomain between the HAMP linker and C-terminal kinase domain. In an attempt to identify the signal-sensing subdomain of ResE, a series of deletions and amino acid substitutions were generated in the N-terminal domain. The results indicated that cytoplasmic ResE lacking the transmembrane segments and the extracytoplasmic loop retains the ability to sense oxygen limitation and NO, which leads to transcriptional activation of ResDE-dependent genes. This activity was eliminated by the deletion of the PAS subdomain, demonstrating that the PAS subdomain participates in signal reception. The study also raised the possibility that the extracytoplasmic region may serve as a second signal-sensing subdomain. This suggests that the extracytoplasmic region could contribute to amplification of ResE activity leading to the robust activation of genes required for anaerobic metabolism in B. subtilis.
Optimizing software process based on risk assessment and control

Choosing a correct software process and controlling the process effectively has been the key to guarantee the success of a software project. This paper presents a novel approach for assessing and optimizing a software project process based on software risk assessment and control, which evaluates and optimizes software project process from the view of controlling the software risk. A model for optimizing software risk control is given, and then a discrete optimization algorithm based on dynamic programming is proposed. An example of using above method to solve a problem is also included in this paper. By changing afterwards control passively into an effective pre-action actively, this new method can greatly promote the possibility of success of software projects.
Automatic random variate generation for simulation input

We develop and evaluate algorithms for generating random variates for simulation input. One group called automatic, or black-box algorithms can be used to sample from distributions with known density. They are based on the rejection principle. The hat function is generated automatically in a setup step using the idea of transformed density rejection. There, the density is transformed into a concave function and the minimum of several tangents is used to construct the hat function. The resulting algorithms are not too complicated and are quite fast. The principle is also applicable to random vectors. A second group of algorithms is presented that generate random variates directly from a given sample by implicitly estimating the unknown distribution. The best of these algorithms are based on the idea of naive resampling plus added noise. These algorithms can be interpreted as sampling from the kernel density estimates. This method can be also applied to random vectors. There, it can be interpreted as a mixture of naive resampling and sampling from the multi-normal distribution that has the same covariance matrix as the data. The algorithms described in the paper have been implemented in ANSI C in a library called UNURAN which is available via anonymous ftp.
Developmental regulation of ephA4 expression in the chick auditory brainstem

The avian auditory brainstem nuclei nucleus magnocellularis (NM) and nucleus laminaris (NL) display highly precise patterns of neuronal connectivity. NM projects tonotopically to the dorsal dendrites of ipsilateral NL neurons and to the ventral dendrites of contralateral NL neurons. The precision of this binaural segregation is evident at the earliest developmental stage at which connections can be observed. We have begun to examine the possibility that Eph receptor tyrosine kinase signaling is involved in establishing these spatially segregated connections. The expression of the EphA4 tyrosine kinase was examined at several developmental stages. EphA4 is expressed in rhombomere 5, which contains progenitors for both NM and NL. In this rhombomere, the labeling becomes striped during the time that precursor cells migrate to the auditory anlage. At the precise time when NM‐NL projections are forming, EphA4 expression in NL is asymmetric, with markedly higher expression in the dorsal NL neuropil than in the ventral neuropil, suggesting a possible role in guiding growing axons to the appropriate region. At later embryonic ages EphA4 expression is symmetric around NL, and is absent in NM. As auditory function matures, EphA4 expression decreases so that by 4 days after hatch no EphA4 antibody labeling is evident in the auditory brainstem nuclei. J. Comp. Neurol. 426:270–278, 2000. © 2000 Wiley‐Liss, Inc.
Endourologic Management of Upper Tract Transitional Cell Carcinoma following Cystectomy and Urinary Diversion

Traditionally, nephroureterectomy is the gold standard therapy for upper tract recurrence of transitional cell carcinoma (TCC) following cystectomy and urinary diversion. With advances in endoscopic equipment and improvements in technique, conservative endourologic management via a retrograde or antegrade approach is technically feasible with acceptable outcomes in patients with bilateral disease, solitary renal units, chronic renal insufficiency, or significant medical comorbidities. Contemporary studies have expanded the utility of these techniques to include low-grade, low-volume disease in patients with a normal contralateral kidney. The aim of this report is to review the current outcomes of conservative management for upper tract disease and discuss its application and relevance in patients following cystectomy with lower urinary tract reconstruction.
Design and on-line evaluation of type-2 fuzzy logic system-based framework for handling uncertainties in BCI classification

The practical applicability of brain-computer interface (BCI) technology is limited due to its insufficient reliability and robustness. One of the major problems in this regard is the extensive variability and inconsistency of brain signal patterns, observed especially in electroencephalogram (EEG). This paper presents a fuzzy logic (FL) approach to the problem of handling of the resultant uncertainty effects. In particular, it outlines the design of a novel type-2 FL system (T2FLS) classifier within the framework of an EEG-based BCI, and examines its on-line applicability in the presence of short-and long-term nonstationarities of spectral EEG correlates of motor imagery (imagination of left vs. right hand movement). The developed system is shown to effectively cope with real-time constraints. In addition, a comparative post hoc analysis has revealed that the proposed T2FLS classifier outperforms conventional BCI methods, like LDA and SVM, in terms of the maximum classification accuracy (CA) rates by a relatively small, yet statistically significant, margin.
Dictyostelium cell death

Cell death in the stalk of Dictyostelium discoideum, a prototypic vacuolar cell death, can be studied in vitro using cells differentiating as a monolayer. To identify early events, we examined potentially dying cells at a time when the classical signs of Dictyostelium cell death, such as heavy vacuolization and membrane lesions, were not yet apparent. We observed that most cells proceeded through a stereotyped series of differentiation stages, including the emergence of “paddle” cells showing high motility and strikingly marked subcellular compartmentalization with actin segregation. Paddle cell emergence and subsequent demise with paddle-to-round cell transition may be critical to the cell death process, as they were contemporary with irreversibility assessed through time-lapse videos and clonogenicity tests. Paddle cell demise was not related to formation of the cellulose shell because cells where the cellulose-synthase gene had been inactivated underwent death indistinguishable from that of parental cells. A major subcellular alteration at the paddle-to-round cell transition was the disappearance of F-actin. The Dictyostelium vacuolar cell death pathway thus does not require cellulose synthesis and includes early actin rearrangements (F-actin segregation, then depolymerization), contemporary with irreversibility, corresponding to the emergence and demise of highly polarized paddle cells.
In Vitro Surfactant Structure-Toxicity Relationships: Implications for Surfactant Use in Sexually Transmitted Infection Prophylaxis and Contraception

Background The need for woman-controlled, cheap, safe, effective, easy-to-use and easy-to-store topical applications for prophylaxis against sexually transmitted infections (STIs) makes surfactant-containing formulations an interesting option that requires a more fundamental knowledge concerning surfactant toxicology and structure-activity relationships. Methodology/Principal Findings We report in vitro effects of surfactant concentration, exposure time and structure on the viability of mammalian cell types typically encountered in the vagina, namely, fully polarized and confluent epithelial cells, confluent but non-polarized epithelial-like cells, dendritic cells, and human sperm. Representatives of the different families of commercially available surfactants – nonionic (Triton X-100 and monolaurin), zwitterionic (DDPS), anionic (SDS), and cationic (CnTAB (n = 10 to 16), C12PB, and C12BZK) – were examined. Triton X-100, monolaurin, DDPS and SDS were toxic to all cell types at concentrations around their critical micelle concentration (CMC) suggesting a non-selective mode of action involving cell membrane destabilization and/or destruction. All cationic surfactants were toxic at concentrations far below their CMC and showed significant differences in their toxicity toward polarized as compared with non-polarized cells. Their toxicity was also dependent on the chemical nature of the polar head group. Our results suggest an intracellular locus of action for cationic surfactants and show that their structure-activity relationships could be profitably exploited for STI prophylaxis in vaginal gel formulations. The therapeutic indices comparing polarized epithelial cell toxicity to sperm toxicity for all surfactants examined, except C12PB and C12BZK, does not justify their use as contraceptive agents. C12PB and C12BZK are shown to have a narrow therapeutic index recommending caution in their use in contraceptive formulations. Conclusions/Significance Our results contribute to understanding the mechanisms involved in surfactant toxicity, have a predictive value with regard to their safety, and may be used to design more effective and less harmful surfactants for use in topical applications for STI prophylaxis.
Estimating optimal window size for analysis of low-coverage next-generation sequence data

MOTIVATION Current high-throughput sequencing has greatly transformed genome sequence analysis. In the context of very low-coverage sequencing (<0.1×), performing 'binning' or 'windowing' on mapped short sequences ('reads') is critical to extract genomic information of interest for further evaluation, such as copy-number alteration analysis. If the window size is too small, many windows will exhibit zero counts and almost no pattern can be observed. In contrast, if the window size is too wide, the patterns or genomic features will be 'smoothed out'. Our objective is to identify an optimal window size in between the two extremes. RESULTS We assume the reads density to be a step function. Given this model, we propose a data-based estimation of optimal window size based on Akaike's information criterion (AIC) and cross-validation (CV) log-likelihood. By plotting the AIC and CV log-likelihood curve as a function of window size, we are able to estimate the optimal window size that minimizes AIC or maximizes CV log-likelihood. The proposed methods are of general purpose and we illustrate their application using low-coverage next-generation sequence datasets from real tumour samples and simulated datasets. AVAILABILITY AND IMPLEMENTATION An R package to estimate optimal window size is available at http://www1.maths. leeds.ac. uk/∼arief/R/win/.
How do American's think about the enviornment and what does it mean for public policy: A re-assessment

How do American's think about the enviornment and what does it mean for public policy: A re-assessment" (2012). Abstract Research within the social sciences has attempted to explain what individuals perceive, why they perceive it the way that they do and what are their attitudes, intentions and behavior. This issue is at the root of the contention that surrounds many environmental issues, with individuals worrying about some risks that dramatically exceed the danger they actually pose while ignoring others. Moreover, this fact of the non-rational element in policy decision-making has led researchers to study how to effectively communicate with a public that is emotionally driven. Using the 2010 General Social Survey, this paper attempts to reassess the bases of environmental concern and why it matters for public policy. This paper highlights the significance of social psychological factors in influencing environmental attitudes, intentions and behavior and how policy decision makers can benefit through a localized discourse when communicating risks or formulating public policy. iii Acknowledgements
The Role of Multimodel Climate Forecasts in Improving Water and Energy Management over the Tana River Basin, Kenya

The Masinga Reservoir located in the upper Tana River basin, Kenya, is extremely important in supplying the country’s hydropower and protecting downstream ecology. The dam serves as the primary storage reservoir, controlling streamflow through a series of downstream hydroelectric reservoirs. The Masinga dam’s operation is crucial in meeting power demands and thus contributing significantly to the country’s economy. La Ni~ prolonged droughts of 1999‐2001 resulted in severe power shortages in Kenya. Therefore, seasonal streamflow forecasts contingent on climate information are essential to estimate preseason water allocation. Here, the authors utilize reservoir inflow forecasts downscaled from monthly updated precipitation forecasts from ECHAM4.5 forced with constructed analog SSTs and multimodel precipitation forecastsdevelopedfromtheEnsemble-BasedPredictionsofClimateChangesandtheirImpacts(ENSEMBLES) project to improve water allocation during the April‐June and October‐December seasons for the Masinga Reservoir. Three-month-ahead inflow forecasts developed from ECHAM4.5, multiple GCMs, and climatological ensembles are used in a reservoir model to allocate water for power generation by ensuring climatological probability of meeting the end-of-season target storage required to meet seasonal water demands. Retrospective reservoir analysis shows that inflow forecasts developed from single GCM and multiple GCMs perform better than use of climatological values by reducing the spill and increasing the allocation for hydropower during above-normal inflow years. Similarly, during below-normal inflow years, both of these forecasts could be effectively utilized to meet the end-of-season target storage by restricting releases for power generation. The multimodel forecasts preserve the end-of-season target storage better than the singlemodel inflow forecasts by reducing uncertainty and the overconfidence of individual model forecasts.
Bound entangled states with secret key and their classical counterpart

Entanglement is a fundamental resource for quantum information processing. In its pure form, it allows quantum teleportation and sharing classical secrets. Realistic quantum states are noisy and their usefulness is only partially understood. Bound-entangled states are central to this question--they have no distillable entanglement, yet sometimes still have a private classical key. We present a construction of bound-entangled states with a private key based on classical probability distributions. From this emerge states possessing a new classical analogue of bound entanglement, distinct from the long-sought bound information. We also find states of smaller dimensions and higher key rates than previously known. Our construction has implications for classical cryptography: we show that existing protocols are insufficient for extracting private key from our distributions due to their "bound-entangled" nature. We propose a simple extension of existing protocols that can extract a key from them.
Accelerating FPGA routing using architecture-adaptive A* techniques

The A* algorithm is a well-known path-finding technique that is used to speed up FPGA routing. Previously published A*-based techniques are either targeted to a class of architecturally similar devices, or require prohibitive amounts of memory to preserve architecture adaptability. This work presents architecture-adaptive A* techniques that require significantly less memory than previously published work. Our techniques are able to produce routing runtimes that are within 7% (on an island-style architecture) and 9% better (on a hierarchical architecture) than targeted heuristic techniques. Memory improvements range between 30/spl times/ (island-style) and 140/spl times/ (hierarchical architecture).
PARENTAL BODY CONDITION DOES NOT CORRELATE WITH OFFSPRING SEX RATIO IN CORY'S SHEARWATERS

Abstract We analyzed offspring sex ratio variation in Mediterranean Cory's Shearwater (Calonectris d. diomedea) during two consecutive breeding seasons in two colonies. We test for differential breeding conditions between years and colonies looking at several breeding parameters and parental condition. We then explored the relationship between offspring sex ratio and parental condition and breeding parameters. This species is sexually dimorphic with males larger and heavier than females; consequently we expected differential parental cost in rearing sexes, or a greater sensitivity of male chicks to adverse conditions, which may lead to biased sex ratios. Chicks were sexed molecularly by the amplification of the CHD genes. Offspring sex ratio did not differ from parity, either at hatching or fledging, regardless of the colony or year. However, parental body condition and breeding parameters such as egg size and breeding success were different between years and colonies. Nevertheless, neither nestling mortality nor body condition at fledging varied between years or colonies, suggesting that male and female chicks were probably not differentially affected by variability in breeding conditions. La Condición Parental no está Correlacionada con las Proporciones de Sexos en los Pollos de Calonectris d. diomedea Resumen. Se analizaron las proporciones de sexos en la descendencia en dos colonias mediterráneas de Calonectris d. diomedea, durante dos temporadas de cría consecutivas. Se estudió la relación entre la proporción de sexos de los pollos y la condición parental y algunos parámetros reproductivos durante la cría. La especie es dimórfica, siendo los machos mayores y más pesados que las hembras; en consecuencia, se esperarían costos parentales diferenciales en la cría de los sexos, o una sensibilidad mayor de los pollos machos a condiciones adversas, que se traduciría en un sesgo en la proporción de sexos. Se determinó el sexo de los pollos por medio de técnicas moleculares, mediante la amplificación del gen CHD. Las proporciones de sexos en los pollos no se desviaron del 50% ni en la eclosión, ni en los volantones, independientemente de la colonia o el año de estudio. Sin embargo, la condición parental y algunos parámetros reproductivos como el tamaño del huevo o el éxito reproductivo sí variaron entre años y colonias. La mortalidad o la condición física de los volantones tampoco mostraron ninguna variación en función de la colonia o del año de estudio, sugiriendo que los pollos de los dos sexos probablemente no se vieron afectados de manera diferencial por la variabilidad en las condiciones de cría.
Generalized Compute-Compress-and-Forward

Compute-and-forward (CF) harnesses interference in wireless communications by exploiting structured coding. The key idea of CF is to compute integer combinations of code words from multiple source nodes, rather than to decode individual code words by treating others as noise. Compute-compress-and-forward (CCF) can further enhance the network performance by introducing compression operations at receivers. In this paper, we develop a more general compression framework, termed generalized CCF (GCCF), where the compression function involves the selection of message segments over finite fields. We show that GCCF achieves a broader compression rate region than CCF. We also compare our compression rate region with the fundamental Slepian–Wolf (SW) region. We show that GCCF is optimal in the sense of achieving the minimum total compression rate. We also establish the criteria under which GCCF achieves the SW region. In addition, we consider a two-hop relay network employing the GCCF scheme. We formulate a sum-rate maximization problem and develop an approximate algorithm to solve the problem. Numerical results are presented to demonstrate the performance superiority of GCCF over CCF and other schemes.
Understanding awareness in mixed presence collaboration

Mixed presence collaboration combines distributed and collocated collaboration -- there are multiple distributed sites, each with a collocated group. While collocated collaboration and purely distributed collaboration are each the subject of rich bodies of research, the combination is less well explored. In this paper we present our initial concepts of awareness support in mixed presence collaboration. We present this as a first version model of awareness. The selected literature we have used to inform the model is drawn from collocated research and distributed research as well as the small body of work addressing mixed presence collaboration directly. In this paper we present a discussion of this relevant literature and use it to explain our model. We also offer a sample of applying the model through the use of a scenario.