Miracle-dz/UniFAR-FTUs huggingface dataset:
R/GSEPD Tutorial Gene Set Enrichment and Projection Displays

GSEPD is a package for streamlining RNA-Seq data analysis, targeting complex samples with low replicate count such as human tissues, where all factors (metabolic, genetic, etc) cannot be controlled statistically. As a prerequisite, you need only your multiple samples’ count data as a matrix whose columns are samples and rows are RefSeq NM and NR transcript identifiers. A second matrix associates sample identifiers with treatment/condition. Given both datasets, GSEPD will automate differential expression via DESeq2 [DESeq], functional analysis via GOSeq [GOSeq], generate heatmaps of gene expression for significantly differentially expressed genes, and subsets of genes defined by the significantly enriched GO Terms. After gene sets are detected from a differential expression analysis, the results are merged into a novel ‘projection display’ wherein each sample is scored according to each condition’s multidimensional average expression. When the treatment samples are found to have a perturbed expression profile for a particular GO Term (geneset), all samples are scored on an axis ranging from control to treatment condition, and outliers or anomalous samples are readily apparent. Clustering quality of samples in a given geneset-space is quantified by the cluster’s “Validity score” [Validity] and an empirical permutation derived p-value. GO Terms with more genes than samples in your comparison will randomly appear enriched, so the Segregation P-value is used to determine if a GO Term is significantly segregating your samples.
GABAA Receptors Mediate Trophic Effects of GABA on Embryonic Brainstem Monoamine Neurons In Vitro

The inhibitory neurotransmitter GABA may act as a trophic signal for developing monoamine neurons in embryonic rat brain, because GABA neurons and their receptors appear in brainstem during generation of monoamine neurons. To test this hypothesis, we used dissociated cell cultures from embryonic day 14 rat brainstem, which contains developing serotonin (5-HT), noradrenaline (tyrosine hydroxylase; TH), and GABA neurons. Immunocytochemistry and reverse transcription-PCR (RT-PCR) revealed the presence of multiple α, β, γ, and δ subunits in these cultures. Competitive RT-PCR demonstrated high levels of β3 subunit transcripts. Expression of functional GABAAreceptors was demonstrated using 36Cl− flux assays. To investigate GABAergic regulation of neuronal survival and growth, cultures were treated for 1–3 d in vitro with 10 μm GABA and/or GABAA antagonist (bicuculline or the pesticide dieldrin). The effects of treatments were quantified by analysis of immunoreactive 5-HT, TH, and GABA neurons. GABAA receptor ligands differentially regulated neuronal survival and growth depending on neurotransmitter phenotype. GABA exerted positive effects on monoamine neurons, which were countered by bicuculline (and dieldrin, 5-HT neurons only). By itself, bicuculline produced inhibitory effects on both 5-HT and TH neurons, whereas dieldrin potently inhibited 5-HT neurons only. GABA neurons responded positively to both antagonists, but more strongly to bicuculline. Taken together, these results demonstrate that the activation/inhibition of GABAA receptors produces opposite effects on the development of embryonic monoamine and GABA neurons. This suggests that these neurotransmitter phenotypes may express GABAAreceptors that differ in fundamental ways, and these differences determine the developmental responses of these cells to GABAergic stimuli.
Regulation of the E. coli csgD gene encoding the master regulator of biofilm formation: Interplay between multiple transcription factors

Under stressful conditions in nature, Escherichia coli forms biofilms for long-term survival. Curli fimbriae are an essential architecture for cell-cell contacts within biofilms. Structural components and assembly factors of curli are encoded by two divergently arranged operons, csgBA and csgDEFG, which are regulated by the csgD gene product. Thus, CsgD is a master regulator of bacterial biofilm formation. Reflecting the response of biofilm formation to various external factors and conditions, the csgD promoter is under the control of multiple transcription factors including CRP, CpxR, Crl, H-NS, IHF, MlrA, OmpR, RcsB and RstA. We have conducted a systematic analysis of the regulation mechanism of the csgD promoter by these multiple transcription factors. After the DNA binding assays in vitro of various combinations of these factors with various segments of the csgD promoter as DNA probes, we realized not only competition between positive and negative regulators but also cooperative interplay within both positive and negative factor groups. These findings raise a regulation model, in which the csgD promoter is controlled by the relative levels of functional molecules of these transcription factors.
Control of Transport PDE/Nonlinear ODE Cascades With State-Dependent Propagation Speed

In this paper, we deal with the control of a transport partial differential equation/ nonlinear ordinary differential equation (PDE/nonlinear ODE) cascade system in which the transport coefficient depends on the ODE state. We develop a PDE-based predictor-feedback boundary control law, which compensates the transport dynamics of the actuator and guarantees global asymptotic stability of the closed-loop system. The stability proof is based on an infinite-dimensional backstepping transformation and a Lyapunov-like argument. The relation of the PDE–ODE cascade with a state-dependent propagation speed to an ODE system with a state-dependent input delay, which is defined implicitly via an integral of past values of the ODE state, is also highlighted and the corresponding equivalent predictor-feedback design is presented together with an alternative proof of global asymptotic stability of the closed-loop system based on the construction of a Lyapunov functional. The practical relevance of our control framework is illustrated in an example that is concerned with the control of a metal rolling process.
Effects of Manufacturing Deviations on Core Compressor Blade Performance

There has been recent incentive for understanding the possible deleterious effects that manufacturing deviations can have on compressor blade performance. This is of particular importance in today’s age, as compressor designs are pushing operating limits by employing fewer stages with higher loadings and are designed to operate at ever higher altitudes. Deviations in these advanced, as well as legacy designs, could negatively affect the performance and operation of a core compressor; thus, a numerical investigation to quantify manufacturing deviations and their effects is undertaken. Data from three radial sections of every compressor blade in a single row of a production compressor is used as the basis for this investigation. Deviations from the compressor blade design intent to the as-manufactured blades are quantified with a statistical method known as principle component analysis (PCA). MISES, an Euler solver coupled with integral boundary-layer calculations, is used to analyze the effects that the aforementioned deviations have on compressor blade performance when the inlet flow conditions produce a Mach number of approximately 0.7 and a Reynolds number of approximately 6.5 x 10. It was found that the majority of manufacturing deviations were within a range of plus or minus 4% of the design intent, and deviations at the leading edge had a critical effect on performance. Of particular interest is the fact that deviations at the leading edge not only degraded performance but significantly changed the boundary-layer behavior from that of the design case.
Performance evaluation of a coordinated time-domain eICIC framework based on ABSF in heterogeneous LTE-Advanced networks

Enhanced Inter-Cell Interference Coordination (eICIC) is a proposed framework by the 3GPP to handle Inter-Cell Interference (ICI) in heterogeneous network (HetNet) environments. Almost-blank subframe (ABSF) is one of the time-domain techniques proposed in the eICIC framework as a candidate for deployment in LTE release 10 (LTE-Advanced). In this paper, a comprehensive ABSF framework is proposed to mitigate the interference in HetNet environments comprised of macro-cells and femto-cells. The ABSF framework proposes a tracking procedure to mark and unmark the macro-cell victim users. Also, new control message to coordinate between macro-cells and femto-cells is proposed, a novel approach to trigger the ABSF mode at aggressor Home eNBs (HeNBs), and enhancements to the macro-cell scheduling process. Finally, a novel approach for the estimation of victim users' signal-to-interference-plus-noise ratio (SINR) level during ABSF is proposed based on the well-known discrete Kalman filter. The performance evaluation results show that the proposed ABSF framework significantly improves the throughput of the macro-cell victim users with a slight degradation in the throughput of the femto-cells.
Ethics: Problems and Principles

This unique text focuses on ethical puzzles and hypothetical problems to help students at all levels understand and refine their moral principles and see how they apply to various situations. An extensive, thoughtfully written introduction provides the theoretical background and lays out numerous moral puzzle cases that are analyzed and discussed throughout the text. Challenging follow-up articles argue a variety of stances on the ethical puzzles set forth in the introduction.
Antagonism of Azole Activity against Candida albicans following Induction of Multidrug Resistance Genes by Selected Antimicrobial Agents

ABSTRACT Antifungal azoles (e.g., fluconazole) are widely used for prophylaxis or treatment of Candida albicans infections in immunocompromised individuals, such as those with AIDS. These individuals are frequently treated with a variety of additional antimicrobial agents. Potential interactions between three azoles and 16 unrelated drugs (antiviral, antibacterial, antifungal, and antiprotozoal agents) were examined in vitro. Two compounds, tested at concentrations achievable in serum, demonstrated an antagonistic effect on azole activity against C. albicans. At fluconazole concentrations two to four times the 50% inhibitory concentration,C. albicans growth (relative to treatment with fluconazole alone) increased 3- to 18-fold in the presence of albendazole (2 μg/ml) or sulfadiazine (50 μg/ml). Antagonism (3- to 78-fold) of ketoconazole and itraconazole activity by these compounds was also observed. Since azole resistance has been correlated with overexpression of genes encoding efflux proteins, we hypothesized that antagonism results from drug-induced overexpression of these same genes. Indeed, brief incubation of C. albicans with albendazole or sulfadiazine resulted in a 3-to->10-fold increase in RNAs encoding multidrug transporter Cdr1p or Cdr2p. Zidovudine, trimethoprim, and isoniazid, which were not antagonistic with azoles, did not induce these RNAs. Fluphenazine, a known substrate for Cdr1p and Cdr2p, strongly induced their RNAs and, consistent with our hypothesis, strongly antagonized azole activity. Finally, antagonism was shown to require a functional Cdr1p. The possibility that azole activity against C. albicans is antagonized in vivo as well as in vitro in the presence of albendazole and sulfadiazine warrants investigation. Drug-induced overexpression of efflux proteins represents a new and potentially general mechanism for drug antagonism.
Automating Morphological Profiling with Generic Deep Convolutional Networks

Morphological profiling aims to create signatures of genes, chemicals and diseases from microscopy images. Current approaches use classical computer vision-based segmentation and feature extraction. Deep learning models achieve state-of-the-art performance in many computer vision tasks such as classification and segmentation. We propose to transfer activation features of generic deep convolutional networks to extract features for morphological profiling. Our approach surpasses currently used methods in terms of accuracy and processing speed. Furthermore, it enables fully automated processing of microscopy images without need for single cell identification.
In reply: the severity of basilar invagination and atlantoaxial dislocation correlates with sagittal joint inclination, coronal joint inclination, and craniocervical tilt: a description of new indices for the craniovertebral junction.

compression and extension reduction of basilar invagination and atlanto-axial dislocation: a novel pilot technique. Neurosurgery. 2013;72(6):1040-1053. 7. Yin YH, Qiao GY, Yu XG, Tong HY, Zhang YZ. Posterior realignment of irreducible atlantoaxial dislocation with C1-C2 screw and rod system: a technique of direct reduction and fixation. Spine J. 2013;13(12):1864-1871. 8. Guo SL, Zhou DB, Yu XG, Yin YH, Qiao GY. Posterior C1-C2 screw and rod instrument for reduction and fixation of basilar invagination with atlantoaxial dislocation. Eur Spine J. 2014;23(8):1666-1672. doi: 10.1007/s00586-014-3409-5.
Value Proposition of Agility in Software Development - An Empirical Investigation

Agile Development Methods have received much attention since their inception, being regarded as an alternative to plan"based, phased methodologies, which are guided by a waterfall process model. These practices have evolved and developed over time, culminating in 2001 with the Agile Manifesto. Since that time, preferred methodologies, implementations, and best practices have continued to evolve with a focus on doing what works best for the individual company or project. However, the concept of agility in software development has remained quite nebulous, lacking in clarity particularly about its underlying dimensions. In this research we conceive agility in terms of four distinct underlying dimensions. Drawing from the theoretical perspective of holographic organization, we develop a model explaining how each of these underlying dimensions of agility contributes to project value in software teams. We test the model using survey data collected from industry practitioners and discuss findings.
Regional differences and metabolic changes in normal aging of the human brain: proton MR spectroscopic imaging study.

BACKGROUND AND PURPOSE Aging is recognized to originate from a diversity of mechanisms that blur the limits between normal and pathologic processes. The purpose of this study was to determine the early effect of normal aging on the regional distribution of brain metabolite concentrations, including N-acetylaspartate (NAA), a major neuronal marker, choline (Cho), and creatine (Cr). METHODS Thirty-two healthy participants, ages 21 to 61 years, were examined by proton MR spectroscopic (1H MRS) imaging. 1H MRS imaging acquisitions were performed in two brain locations: the centrum semiovale and the temporal lobe. Thirty voxels were selected in four cerebral regions, cortical, semioval, temporal, and hippocampal, and 1H MR spectra were processed to determine the metabolite ratios. RESULTS With advancing age of the participants, the ratios of %NAA, NAA:Cho, and NAA:Cr were significantly decreased, whereas the ratios of %Cho and %Cr were significantly increased in the cortical, semioval, and temporal regions. On the basis of the significant metabolic difference determined by cluster analysis, two groups of 16 participants with ages ranging from 21 to 39 years (younger group) and 40 to 61 years (older group) were compared. Repeated measures analysis of variance tests, with multiple comparison procedures between the two age groups and among the four brain region groups, showed significant decreases of the %NAA, NAA:Cho, and NAA:Cr ratios in the semioval and temporal regions of the older group compared with the younger group. When compared with other cerebral regions, %NAA and %Cho ratios were significantly decreased in the hippocampal and cortical regions, respectively. CONCLUSION These metabolic changes suggest that brain aging is characterized by a reduction in neuronal viability or function associated with an accelerated membrane degradation and/or an increase in glial cell numbers.
The impact of preapheresis white blood cell count on autologous peripheral blood stem cell collection efficiency and HSC infusion side effect rate

Autologous peripheral blood hematopoietic stem cell (PBSC) collection efficiency (CE) is reportedly affected by the patient's blood properties; however, studies to identify factors correlated with CE have shown inconsistent results. Additionally, variables such as stem cell graft granulocyte content and patient age, sex, and underlying disease, may be associated with hematopietic stem cell (HSC) infusion‐related adverse reactions. In this study, we evaluated the correlation of preleukapheresis PB granulocyte count and PBSC harvest variables with CD34+collection yield and efficiency, and thawed HSC infusion side effect occurrence.
A framework to introduce flexibility in crop modelling: from conceptual modelling to software engineering and back

Keywords: model structure, uncertainty, modularity, software design patterns, good modelling practices, crop growth and development. This thesis is an account of the development and use of a framework to introduce flexibility in crop modelling. The construction of such a framework is supported by two main beams: the implementation and the modelling beam. Since the beginning of the 1990s, the implementation beam has gained increasing attention in the crop modelling field, notably with the development of APSIM (Agricultural Production Systems sIMulator) in Australia, OMS (Object Modelling System) in the United States, and APES (Agricultural Production and Externalities Simulator) in Europe. The main focus of this thesis is on the modelling beam and how to combine it with the implementation beam. I first explain how flexibility is adopted in crop modelling and what is required for the implementation beam of the framework, namely libraries of modules representing the basic crop growth and development processes and of crop models (i.e. modelling solutions). Then, I define how to deal with this flexibility (i.e. modelling beam) and more specifically I describe systematic approaches to facilitate the selection of the appropriate model structure (i.e. a combination of modules) for a specific simulation objective. While developing the framework, I stress the need for better documentation of the underlying assumptions of the modules and of the criteria applied in the selection of these modules for a particular simulation objective. Such documentation should help to point out the sources of uncertainties associated with the development of crop models and to reinforce the role of the crop modeller as an intermediary between the software engineer, coding the modules, and the end users, using the model for a specific objective. Finally, I draw conclusions for the prospects of such a framework in the crop modelling field. I see its main contribution to (i) a better understanding in crop physiology through easier testing of alternatives hypotheses, and (ii) integrated studies by facilitating model reuse.
Orientation and affect directed towards social and nonsocial targets in infant siblings of children with Autistic Spectrum Disorder (ASD)

This study contributes to a growing body of work aimed at documenting and defining behavioral markers associated with early autism spectrum disorder (ASD) and its broader phenotype. A total of 19 infants (sib-ASD), who have a sibling diagnosed with ASD were seen at 6.5 months, and 23 infants were seen at 9 months. Sib-ASD infants were matched in age and gender with low-risk infants (sib-TD), who have a typically developing sibling. Infants were simultaneously presented two stimuli, a person’s face (the social stimulus) and a brightly colored toy (the nonsocial stimulus). We found there were no significant differences between at-risk infants and low-risk infants in their responsiveness to and disengagement from the stimuli. However, a significant group difference did appear in the 9 month infants’ time smiling. Sib-TD infants spent more time smiling at the nonsocial as compared to the social stimulus relative to the sib-ASD infants, who showed no preference in time smiling for one stimulus over the other. This unexpected finding contradicted our initial predictions that sib-TD infants would prefer the social stimulus and thus spend more time smiling at the experimenter’s face, while sib-ASD infants would prefer the nonsocial stimulus, and thus spend more time smiling at the toy.
In the Wake of 9-11: The Psychology of Terror

Terror in America - The Day our World Changed Terror Management Theory - An Evolutionary Existential Account of Human Behaviour Terror Management Research - Coping with Conscious and Unconscious Death Related Thoughts Terror Management Research on Prejudice and Self-Esteem Striving Black Tuesday - The Psychology Impact of 9/11 Managing the Terror The Roots of Islamic Terrorism Giving Peace a Chance In the Wake of 9/11 Rising Above the Terror.
Investigating False Positive Reduction in HTTP via Procedure Analysis

This paper focuses on high false-positive rate of attacks. First, the merits and demerits of research work in curbing false positive rate of attacks in intrusion detection systems (IDSs) are discussed. Then we present our research efforts in the form of an IDS called NetHost-Sensor, recap on past NetHost-Sensor research contributions and discusses in detail its novel procedure analysis technique in curbing false-positive. We discuss in detail, the NetHost-Sensor methodology, its procedure analysis technique and report on our experimental investigation that shows the reduction of false-positives, using HTTP network communication as a medium for analysis. Finally, we validate our research work by comparing false-positives with Snort IDS
Architectural Knowledge for Technology Decisions in Developer Communities: An Exploratory Study with StackOverflow

Architectural decisions have a big influence on basic properties of a software system, and are difficult to change once implemented. Technology decisions deserve special attention because they are one of the most frequently occurring types of architectural decisions. Architectural knowledge is crucial for good decisions. Current architecture knowledge management approaches try to support architects by offering a rich base of architectural solutions and design decision rules. However, they mostly depend on manually capturing and maintaining the architectural knowledge. In this paper, we utilize the most popular online software development community (StackOverflow) as a source of knowledge for technology decisions to support architecture knowledge management approaches with a more efficient methods for knowledge capturing. We conducted an exploratory study, and followed a qualitative and quantitative content analysis approach. We analysed the posts in this community to identify architecture-relevant and technology-related knowledge, and to classify the posts into different types for the purpose of knowledge structuring. In addition, we evaluated our findings through feedback from practitioners.