Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibiotic resistance in Neisseria gonorrhoeae: origin, evolution, and lessons learned for the future

The strict human pathogen Neisseria gonorrhoeae has caused gonorrhea for thousands of years, and currently gonorrhea is the second most prevalent bacterial sexually transmitted infection worldwide. Given the ancient nature of N. gonorrhoeae and its unique obligate relationship with humankind over the millennia, its remarkable ability to adapt to the host immune system and cause repeated infections, and its propensity to develop resistance to all clinically useful antibiotics, the gonococcus is an ideal pathogen on which to study the evolution of bacterial pathogenesis, including antimicrobial resistance, over the long term and within the host during infection. Recently, the first gonococcus displaying high‐level resistance to ceftriaxone, identified in Japan, was characterized in detail. Ceftriaxone is the last remaining option for empirical first‐line treatment, and N. gonorrhoeae now seems to be evolving into a true “superbug. ” In the near future, gonorrhea may become untreatable in certain circumstances. Herein, the history of antibiotics used for treatment of gonorrhea, the evolution of resistance emergence in N. gonorrhoeae, the linkage between resistance and biological fitness of N. gonorrhoeae, lessons learned, and future perspectives are reviewed and discussed.
Nuclear Translocated Ehrlichia chaffeensis Ankyrin Protein Interacts with a Specific Adenine-Rich Motif of Host Promoter and Intronic Alu Elements

ABSTRACT Ehrlichiae are obligately intracellular bacteria that reside and replicate in phagocytes by circumventing host cell defenses and modulating cellular processes, including host cell gene transcription. However, the mechanisms by which ehrlichiae influence host gene transcription have largely remained undetermined. Numerous ankyrin and tandem repeat-containing proteins associated with host-pathogen interactions have been identified in Ehrlichia species, but their roles in pathobiology are unknown. In this study, we determined by confocal immunofluorescence microscopy and by immunodetection in purified nuclear extracts that the ankyrin repeat-containing protein p200 is translocated to the nuclei of Ehrlichia-infected monocytes. Chromatin immunoprecipitation (ChIP) with DNA sequencing revealed an Ehrlichia chaffeensis p200 interaction located within host promoter and intronic Alu-Sx elements, the most abundant repetitive elements in the human genome. A specific adenine-rich (mid-A-stretch) motif within Alu-Sx elements was identified using electrophoretic mobility shift and NoShift assays. Whole-genome analysis with ChIP and DNA microarray analysis (ChIP-chip) determined that genes (n = 456) with promoter Alu elements primarily related to transcription, apoptosis, ATPase activity, and structural proteins associated with the nucleus and membrane-bound organelles were the primary targets of p200. Several p200 target genes (encoding tumor necrosis factor alpha, Stat1, and CD48) associated with ehrlichial pathobiology were strongly upregulated during infection, as determined by quantitative PCR. This is the first study to identify a nuclear translocation of bacterially encoded protein by E. chaffeensis and to identify a specific binding motif and genes that are primary targets of a novel molecular strategy to reprogram host cell gene expression to promote survival of the pathogen.
Enabling New Flexibility in the SUNDIALS Suite of Nonlinear and Differential/Algebraic Equation Solvers

In recent years, the SUite of Nonlinear and DIfferential/ALgebraic equation Solvers (SUNDIALS) has been redesigned to better enable the use of application-specific and third-party algebraic solvers and data structures. Throughout this work, we have adhered to specific guiding principles that minimized the impact to current users while providing maximum flexibility for later evolution of solvers and data structures. The redesign was done through the addition of new linear and nonlinear solvers classes, enhancements to the vector class, and the creation of modern Fortran interfaces. The vast majority of this work has been performed “behind-the-scenes,” with minimal changes to the user interface and no reduction in solver capabilities or performance. These changes allow SUNDIALS users to more easily utilize external solver libraries and create highly customized solvers, enabling greater flexibility on extreme-scale, heterogeneous computational architectures.
APEX: A personalization framework to improve quality of experience for DVD-like functions in P2P VoD applications

The requirement for supporting DVD-like functions raises new challenges to the design of P2P VoD systems. The uncertainty of frequent user DVD-like interactivity makes it difficult to ensure user perceived Quality of Experience (QoE) for real-time streaming services over distributed self-organized P2P overlay networks. Most existing solutions are based on the unreasonable assumption that all the users in P2P VoD systems have the same preference. Few attention has been paid to personalization, which accommodates the differences between users. In this paper, we present a video model which characterizes the personalization information for users' contents and preferences. Based on this model, we develop APEX, a practical personalization framework for P2P VoD applications. APEX makes the personalization practical by using a hybrid architecture which leverages the offline pattern mining on the server side and online collaborative filtering on the peer side. Furthermore, APEX helps peers to personalize navigation, prefetching and membership management, aiming at improving QoE for DVD-like functions by reducing response latency and optimizing content sharing. Both theoretical analysis and comprehensive simulations show that APEX outperforms most existing schemes in terms of accumulated hit ratio, response latency, and searching efficiency.
An investigation into the relationship between gay activism and the establishment of a gay community in Birmingham, 1967-97

This study charts the establishment of a gay community in Birmingham from the introduction of the Sexual Offences Act 1967, which partially decriminalised male homosexual acts in England and Wales, to the 1997 general election. This saw New Labour end eighteen years of Conservative governments in Britain, which had frequently pursued an anti-gay agenda. This investigation examines the impact of the national Gay Liberation movement in Birmingham and particularly how gay activism, as collective acts of resistance, contributed to the development of a sense of community among the lesbian and gay inhabitants of the city during the 1970s and 1980s. It then documents the developments of a gay ‘village’ in Birmingham in the 1990s, with a brief comparison made to Manchester’s Gay Village. This study blends oral history testimonies with archive material drawn from both local and national gay archives, as well as newspapers and local council records. The thesis ends in 1997 with the organisation of the city’s first official Gay Pride Festival. The Gay Pride Festival represented a watershed for Birmingham’s gay community, symbolising a kind of mass ‘coming out’ process during which Birmingham’s gay community established a long-term physical and cultural location for itself within the city.
The Effects of Cooperative Learning with Intergroup Competition on the Math Achievement of Seventh Grade Students.

There has been a large amount of research on the relative effects of cooperative, competitive, and individualistic learning on achievement and productivity. This paper reports a study designed to determine the effect of cooperative learning strategies on mathematics achievement of 7th graders. Based on school records indicating whether a student had participated in the cooperative learning strategies group or had received individualized/competitive instruction, 50 seventh-grade students were selected from an elementary school located in a low socioeconomic neighborhood in Chicago made up of all minority students. Scores on the mathematics portion of the Iowa Test of Basic Skills administered in the Spring of 1991 and 1992 were utilized to compare the mathematics achievement of the students in the two groups. T-tests performed on the pre-test and post-test data indicated that no differences existed in the groups prior to instruction, but that the cooperative learning groups performed significantly higher on the post-test. These findings confirmed results of similar studies. The paper concluded that cooperative group learning strategies are more effective in promoting mathematics achievement. (MDH) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. *********************************************************************** The Effects Of Cooperative Learning With Intergroup Competition On The Math Achievement of Seventh Grade Students
Communication Theory Spatial frequency scheduling for uplink SC-FDMA based linearly precoded multiuser MIMO systems

This paper investigates the performance of the uplink single carrier (SC) frequency division multiple access (FDMA) based linearly precoded multiuser multiple input multiple output (MIMO) systems with frequency domain packet scheduling. A mathematical expression of the received signal to interference plus noise ratio (SINR) for the studied systems is derived and a utility function based spatial frequency packet scheduling algorithms is investigated. The schedulers are shown to be able to exploit the available multiuser diversity in time, frequency and spatial domains.
Ablation of ceramide synthase 2 exacerbates dextran sodium sulphate‐induced colitis in mice due to increased intestinal permeability

Ceramides mediate crucial cellular processes including cell death and inflammation and have recently been implicated in inflammatory bowel disease. Ceramides consist of a sphingoid long‐chain base to which fatty acids of various length can be attached. We now investigate the effect of alerting the ceramide acyl chain length on a mouse model of colitis. Ceramide synthase (CerS) 2 null mice, which lack very‐long acyl chain ceramides with concomitant increase of long chain bases and C16‐ceramides, were more susceptible to dextran sodium sulphate‐induced colitis, and their survival rate was markedly decreased compared with that of wild‐type littermates. Using mixed bone‐marrow chimeric mice, we showed that the host environment is primarily responsible for intestinal barrier dysfunction and increased intestinal permeability. In the colon of CerS2 null mice, the expression of junctional adhesion molecule‐A was markedly decreased and the phosphorylation of myosin light chain 2 was increased. In vitro experiments using Caco‐2 cells also confirmed an important role of CerS2 in maintaining epithelial barrier function; CerS2‐knockdown via CRISPR‐Cas9 technology impaired barrier function. In vivo myriocin administration, which normalized long‐chain bases and C16‐ceramides of the colon of CerS2 null mice, increased intestinal permeability as measured by serum FITC‐dextran levels, indicating that altered SLs including deficiency of very‐long‐chain ceramides are critical for epithelial barrier function. In conclusion, deficiency of CerS2 influences intestinal barrier function and the severity of experimental colitis and may represent a potential mechanism for inflammatory bowel disease pathogenesis.
Validation Experiments with the NCAR Spectral Element Dynamical Core

Traditionally, climate model dynamical cores have been based on the spectral transform method because the global spherical harmonic basis functions provide an isotropic representation on the sphere. It is trivial to implement semi-implicit time stepping schemes, as the spherical harmonics are eigenfunctions of the Laplacian on the sphere and the resulting Helmholtz problem is diagonalized in spectral space. Spectral elements maintain the accuracy and exponential convergence rate exhibited by the spectral transform method and have proven to be effective in geophysical fluid dynamics by Taylor et al. (1997) and Iskandarani et al. (1995). The explicit time step is limited by the Courant condition for gravity waves. For spectral elements, stability is determined by the eigenvalues of the discrete spatial operators. With quadratic clustering of Gauss points at element boundaries, these eigenvalues scale as 1/KN, where K is the number of elements and N is the polynomial degree. For the spectral transform, the explicit time step decreases linearly with increased resolution. Consequently, the explicit time step is more restrictive in the case of spectral elements. A semi-implicit scheme removes the stability constraint related to gravity waves (Thomas et al 2003). The advection stability constraint can be avoided with a semi-Lagrangian scheme as described in Giraldo and Perot (2001).
Reptile: representative tiling for short read error correction

MOTIVATION Error correction is critical to the success of next-generation sequencing applications, such as resequencing and de novo genome sequencing. It is especially important for high-throughput short-read sequencing, where reads are much shorter and more abundant, and errors more frequent than in traditional Sanger sequencing. Processing massive numbers of short reads with existing error correction methods is both compute and memory intensive, yet the results are far from satisfactory when applied to real datasets. RESULTS We present a novel approach, termed Reptile, for error correction in short-read data from next-generation sequencing. Reptile works with the spectrum of k-mers from the input reads, and corrects errors by simultaneously examining: (i) Hamming distance-based correction possibilities for potentially erroneous k-mers; and (ii) neighboring k-mers from the same read for correct contextual information. By not needing to store input data, Reptile has the favorable property that it can handle data that does not fit in main memory. In addition to sequence data, Reptile can make use of available quality score information. Our experiments show that Reptile outperforms previous methods in the percentage of errors removed from the data and the accuracy in true base assignment. In addition, a significant reduction in run time and memory usage have been achieved compared with previous methods, making it more practical for short-read error correction when sampling larger genomes. AVAILABILITY Reptile is implemented in C++ and is available through the link: http://aluru-sun.ece. iastate.edu/doku.php? id=software CONTACT aluru@iastate.edu.
Chronic ethanol drinking by alcohol-preferring rats increases the sensitivity of the mesolimbic dopamine system to the reinforcing and stimulating effects of cocaine

Oster, Scott M. Ph.D., Purdue University, May, 2012. Chronic Ethanol Drinking by Alcohol-Preferring Rats Increases the Sensitivity of the Mesolimbic Dopamine System to the Reinforcing and Stimulating Effects of Cocaine. Major Professor: James M. Murphy. Alcohol and cocaine are commonly co-abused drugs, and those meeting criteria for both cocaine and alcohol use disorders experience more severe behavioral and health consequences than those with a single disorder. Chronic alcohol (ethanol) drinking increased the reinforcing and dopamine (DA) neuronal stimulating effects of ethanol within mesolimbic regions of the central nervous system (CNS) of alcohol-preferring (P) rats. The objectives of the current study were to determine if chronic continuous ethanol drinking produced: (1) alterations in the sensitivity of the nucleus accumbens shell (AcbSh) to the reinforcing effects of cocaine, (2) changes in the magnitude and time course of the local stimulating effects of cocaine on posterior ventral tegmental area (pVTA) DA neurons, and (3) a persistence of alterations in the stimulating effects of cocaine after a period of protracted abstinence. Female P rats received continuous, free-choice access to water and 15% v/v ethanol for at least 10 wk (continuous ethanol-drinking; CE) or access to water alone (ethanol-naïve; N). A third group of rats received the same period of ethanol access followed by 30 d of protracted abstinence from ethanol (ethanolabstinent; Ab). CE and Ab rats consumed, on average, 6-7 g/kg/d of ethanol. Animals with a single cannula aimed at the AcbSh responded for injections of cocaine into the AcbSh during four initial operant sessions. Cocaine was not present in the self-infused solution for the subsequent three sessions, and
Use of multiple digital libraries: a case study

The aim of the work reported here was to better understand the usabili ty issues raised when digital libraries are used in a natural setting. The method used was a protocol analysis of users working on a task of their own choosing to retrieve documents from publicly available digital libraries. Various classes of usability difficulties were found. Here, we focus on use in context - that is, usability concerns that arise from the fact that libraries are accessed in particular ways, under technically and organisationally imposed constraints, and that use of any particular resource is discretionary. The concepts from an Interaction Framework, which provides support for reasoning about patterns of interaction between users and systems, are applied to understand interaction issues.
Characterizing Water Diffusion In Fixed Baboon Brain

In the Biomedical Medical Research laboratory in St. Louis Missouri there is an ongoing project to characterize water diffusion in fixed baboon brain using diffusion weighted magnetic res- onance imaging as a means of monitoring development throughout gestation. Magnetic resonance images can be made sensitive to diffusion by applying magnetic field gradients during the pulse sequence. Results from the analysis of diffusion weighted magnetic resonance images using a full diffusion tensor model do not fit the data well. The estimated standard deviation of the noise exhibit structures corresponding to known baboon brain anatomy. However, the diffusion tensor plus a con- stant model overfits the data: the residuals in the brain are smaller than in regions where there is no signal. Consequently, the full diffusion tensor plus a constant model has too many parameters and needs to be simplified. This model can be simplified by imposing axial symmetry on the diffusion tensor. There are three axially symmetric diffusion tensor models, prolate, oblate, and isotropic; and two other models, no signal and full diffusion tensor, that could characterize the diffusion weighted images. These five models may or may not have a constant offset, giving 10 total models that poten- tially describe the diffusion process. In this paper the Bayesian calculations needed to select which of the 10 models best characterizes the diffusion data are presented. The various outputs from the analysis are illustrated using one of our baboon brain data sets.
Subtraction Based on a Robust Consensus Method

Statistical background modeling is a fundamental and important part of many visual tracking systems and of other computer vision applications. In this paper, we presents an effective and adaptive background modeling method for detecting foreground objects in both static and dynamic scenes. The proposed method computes SAmple CONsensus (SACON) of the background samples and estimates a statistical model per pixel. Numerous experiments on both indoor and outdoor video sequences show that the proposed method, compared with several state-of-theart methods, can achieve very promising performance.
Automatic adaptive grid refinement for the Euler equations

A method of adaptive grid refinement for the solution of the steady Euler equations for transonic flow is presented. The algorithm automatically decides where the coarse grid accuracy is insufficient, and creates locally uniform refined grids in these regions. This typically occurs at the leading and trailing edges. The solution is then integrated to steady state using the same integrator (FLO52) in the interior of each grid. The boundary conditions needed on the fine grids are examined, and the importance of treating the fine/coarse grid interface conservatively is discussed. Numerical results indicate substantial computational savings for the same solution accuracy can be achieved.
An improved adaptive propagation chaotic particle swarm optimization algorithm based on immune selection

The particle swarm optimization algorithm is improved by introducing the immune selection, adaptive propagation, multi-population evolution. An improved adaptive propagation chaotic particle swarm optimization algorithm based on immune selection (IS-APCPSO algorithm for short) is proposed in this paper. The performance of several algorithms has been compared by a classic example of traffic network optimization. It is proved that the improved algorithm in accelerating convergence rate, increasing the diversity of particles, and preventing premature phenomenon is effective. The novel algorithm is expected to be used in the model solution of large-scale complex traffic network optimization problem.
Chords , scales , and divisor lattices

In this paper I study musical harmony from the rational point of view, stressing the significance of integer ratios. The main concept is the divisor set of an integer. A divisor set is the set of all divisors of a number and it has the algebraic structure of a lattice with greatest common divisor and least common multiple as the lattice operations. A divisor set can also be interpreted as a geometric lattice, a set of points with integer coordinates in the space of prime exponent sequences (‘tonal space’), with the shape of a parallelepiped (‘shoebox’, ‘brick’). Divisor lattices can also be seen as set intersections of harmonic (‘overtone’) series with subharmonic (‘undertone’) sequences. I shall concentrate in particular on the divisor lattices of three numbers, 60, 8640, and 345600 with 12, 56, and 120 divisors, respectively. In the tonal space they are bricks with side lengths 2μ1μ1, 6μ3μ1, and 9μ3μ2, respectively. Projecting these point sets on the ‘pitch line’ gives the following musically recognizable sets: major and minor triad chords and the tonic seventh chord, the diatonic scale, and the just chromatic scale, respectively. The equation of the pitch line in parametric form is p log pi where pi is the ith prime and p is the pitch parameter.
Association of TBX2 and P21 expression with clinicopathological features and survival of laryngeal squamous cell carcinoma.

BACKGROUND The expression of P21 and TBX2 in laryngeal squamous cell carcinoma (LSCC) and their corresponding adjacent normal laryngeal tissues, as well as their association with clinical pathological features and survival remain unclear. METHOD we used the RT-PCR and immunohistochemistry to detect their mRNA and protein levels in 75 LSCC patients. We also use log-rank test and Cox models to compare survival among different groups. RESULTS The mRNA expression level of TBX2 was up-regulated, while P21 was down-regulated in LSCC compared with their matched adjacent laryngeal tissues (All P < 0.001). The expression of P21 was correlated with tumor stage, lymph node metastasis and smoking; and TBX2 expression was associated with lymph node metastasis, differentiation degree and smoking (All P < 0.05). Patients with high TBX2 and low P21 expression had significantly worse survival than those with low TBX2 and high P21 expression, respectively (All P < 0.05). A significant correlation between expression of TBX2 and P21 (Pearson, P < 0.05) was observed. Furthermore, multivariable analysis showed that patients with low TBX2 and high P21 expression alone had a significantly reduced risk for overall death compared with those with low TBX2 and high P21 expression. The risk for overall death was even lower for patients with both low and high expression of both genes than any other co-expression status of both genes (HR, 0.1; 95% CI, 0.0-0.9). CONCLUSION These results suggest that abnormal expression of P21 and TBX2 in tumors may jointly, or individually, predict poor prognosis of LSCC.