Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyrosequencing Reveals the Predominance of Pseudomonadaceae in Gut Microbiome of a Gall Midge

Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of wheat. A total of 3,654 high quality sequences of the V3 hypervariable region of the 16S rRNA gene were obtained through 454-pyrosequencing. From these sequences, 311 operational taxonomic units (OTUs) were obtained at the ≥97% similarity cutoff. In the gut of 1st instar, otu01, a member of Pseudomonas, was predominant, representing 90.2% of total sequences. otu13, an unidentified genus in the Pseudomonadaceae family, represented 1.9% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 2nd instar, otu01 and otu13 decreased to 85.5% and 1.5%, respectively. otu04, a member of Buttiauxella, represented 9.7% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 3rd instar, otu01 and otu13 further decreased to 29.0% and 0%, respectively. otu06, otu08, and otu16, also three members of the Pseudomonadaceae family were 13.2%, 8.6%, and 2.3%, respectively. In addition, otu04 and otu14, two members of the Enterobacteriaceae family, were 4.7% and 2.5%; otu18 and otu20, two members of the Xanthomonadaceae family, were 1.3% and 1.2%, respectively; otu12, a member of Achromobacter, was 4.2%; otu19, a member of Undibacterium, was 1.4%; and otu9, otu10, and otu15, members of various families, were 6.1%, 6.3%, and 1.9%, respectively. The investigation into dynamics of Pseudomonas, the most abundant genera, revealed that its population level was at peak in freshly hatched or 1 day larvae as well as in later developmental stages, thus suggesting a prominent role for this bacterium in Hessian fly development and in its interaction with host plants. This study is the first comprehensive survey on bacteria associated with the gut of a gall midge, and provides a foundation for future studies to elucidate the roles of gut microbes in Hessian fly virulence and biology.
Negative Regulation of Humoral Immunity Due to Interplay between the SLAMF1, SLAMF5, and SLAMF6 Receptors

Whereas the SLAMF-associated protein (SAP) is involved in differentiation of T follicular helper (Tfh) cells and antibody responses, the precise requirements of SLAMF receptors in humoral immune responses are incompletely understood. By analyzing mice with targeted disruptions of the Slamf1, Slamf5, and Slamf6 genes, we found that both T-dependent and T-independent antibody responses were twofold higher compared to those in single knockout mice. These data suggest a suppressive synergy of SLAMF1, SLAMF5, and SLAMF6 in humoral immunity, which contrasts the decreased antibody responses resulting from a defective GC reaction in the absence of the adapter SAP. In adoptive co-transfer assays, both [Slamf1 + 5 + 6]−/− B and T cells were capable of inducing enhanced antibody responses, but more pronounced enhancement was observed after adoptive transfer of [Slamf1 + 5 + 6]−/− B cells compared to that of [Slamf1 + 5 + 6]−/− T cells. In support of [Slamf1 + 5 + 6]−/− B cell intrinsic activity, [Slamf1 + 5 + 6]−/− mice also mounted significantly higher antibody responses to T-independent type 2 antigen. Furthermore, treatment of mice with anti-SLAMF6 monoclonal antibody results in severe inhibition of the development of Tfh cells and GC B cells, confirming a suppressive effect of SLAMF6. Taken together, these results establish SLAMF1, SLAMF5, and SLAMF6 as important negative regulators of humoral immune response, consistent with the notion that SLAM family receptors have dual functions in immune responses.
Atrial fibrillation impairs cardiac sympathetic response to baroreceptor unloading in congestive heart failure.

AIMS In this study, we investigated for a potential mechanism by which atrial fibrillation (AF) might convey a worse prognosis in congestive heart failure (CHF). Specifically, we aimed to determine whether AF impaired cardiac sympathetic response to baroreceptor unloading in comparison to sinus rhythm (SR) in CHF. METHODS AND RESULTS Eighteen CHF patients (ejection fraction 30+/-2%, age 59+/- 2 years), nine in SR and nine in AF, were enrolled. A right heart study and cardiac sympathetic tone assessment by coronary sinus catheter were performed at baseline and after 10 min of 20 degrees and 30 degrees of passive head up tilt (HUT). Filling pressures fell significantly during HUT in both SR and AF groups (AF, P=0.002; SR, P<0.001). The cardiac sympathetic response to HUT was significantly attenuated by AF compared with SR (P=0.014). In conjunction, right atrial appendages were collected from 23 cardiac surgery patients, 12 in SR and 11 in AF to investigate the presence of fibrosis. AF was associated with a significant increase in the collagen density (P=0.025). CONCLUSION AF is associated with impaired cardiac sympathetic response to baroreceptor unloading compared with SR in CHF, possibly secondary to atrial fibrosis.
Serum resistin as an independent marker of aortic stiffness in patients with coronary artery disease

Background Subjects with higher carotid–femoral pulse wave velocity (cfPWV) will be at an increased risk for cardiovascular (CV) events in future. Resistin is an inflammatory mediator and a biomarker of CV diseases. We evaluated the association between serum resistin and aortic stiffness in patients with coronary artery disease (CAD). Methods A total of 104 patients with CAD were enrolled in this study. cfPWV was measured using the SphygmoCor system. Patients with cfPWV >10 m/s were defined as the high aortic stiffness group. Results Thirty-seven patients (35.6%) had high aortic stiffness and higher percentages of diabetes (p = 0.001), were of older age (p = 0.001) and had higher waist circumference (p < 0.001), systolic blood pressure (p = 0.027), pulse pressure (p = 0.013), high-sensitivity C-reactive protein (p < 0.001) and resistin levels (p < 0.001) but lower estimated glomerular filtration rate (p = 0.009) compared to subjects with low aortic stiffness. After adjusting for factors significantly associated with aortic stiffness by multivariate logistic regression analysis, serum resistin (odds ratio = 1.275, 95% confidence interval: 1.065–1.527, p = 0.008) was also found to be an independent predictor of aortic stiffness in patients with CAD. Conclusions Serum resistin level is a biomarker for aortic stiffness in patients with CAD.
Do We Need Real-Time Hermeneutics? Structures of Meaning in Games

Games differ from most other forms of media by being procedural and interactive. These qualities change how games create and transmit meaning to their players. The concept of “real-time hermeneutics” (Aarseth 2003) is analysed in order to understand how temporality affects the understanding of games. Temporal frames (Zagal and Mateas 2010) are introduced as an alternative way of under standing time in games.
Widening the Sweetgrass Road: Re/Balancing Ways of Knowing for Sustainable Living with a Cree-Nishnaabe Medicine Circle

A Cree-Nishnaabe Medicine Circle, as I have learned about it over the last twenty-eight years in ceremonies, guides this learning journey of an Indigenous way of knowing as it applies to the theory and practice of sustainability, a strategic ideal established to negotiate the complexities of human-nature relationships and balance social, environmental, and economic priorities. The definition and pursuit of sustainability today have been approached primarily from within the dominant Western, neoliberal worldview. In this dissertation, I uphold Indigenous ways of knowing as equal to Western knowledges. If life as we know it is undergoing significant changes due to climate change and stress upon the natural limits to Earth’s life-supporting systems, how can Indigenous ways of knowing and being contribute toward humanity’s adaptation to these changes? The Cree-Nishnaabe Medicine Circle, as I have come to understand it, provides the methodological basis for my dissertation. This distinctly Indigenous framework privileges an Indigenous approach to assessing the above question and comprehending a way forward. As a non-Indigenous woman, I share how I have been able to situate myself within an Indigenous framework to examine dominant approaches to sustainability (distinct from the customary practice of using a Western methodology). The following questions are explored to provide context and propose a way forward: What is the dominant Western approach to the current pursuit of sustainability? What are fundamental Indigenous and Western viewpoints underlying their respective worldviews? How does a Cree-Nishnaabe Medicine Circle provide insights and instruction for living in respectful balance with Creation? The main thesis of this dissertation is that Indigenous ways of knowing integrate holistic perspectives and time-proven wisdom essential for sustainable, relational living, which have endured in learnings of “the Sweetgrass Road,” the miyopimatisiwin (also translated as "the way of the good life" or "the way of an exemplary life"). Metaphorically speaking, “widening the Sweetgrass Road” is one intent of my dissertation, sharing learnings of the Medicine Circle so more people can "walk this road" and appreciate the depth and meanings contained therein. By combining insights and balancing both Indigenous and Western knowledges, I propose a way forward around four themes: raised consciousness, shared responsibility, universal equity, and braided movement.
Opus: University of Bath Online Publication Store Functional Mapping of the Human Auditory Cortex: Fmri Investigation of a Patient with Auditory Agnosia from Trauma to the Inferior Colliculus

(2015) Functional mapping of the human auditory cortex:fMRI investigation of a patient with auditory agnosia from trauma to the inferior colliculus.Functional mapping of the human auditory cortex: fMRI investigation of a patient with auditory agnosia from trauma to the inferior colliculus' Cognitive and Behavioral Neurology, vol 28, no. 3, pp. 160-180. , and available online via This version is made available in accordance with publisher policies. Please cite only the published version using the reference above. Objective: To use functional magnetic resonance imaging to map the auditory cortical fields that are activated, or nonreactive, to sounds in patient M.L. , who has auditory agnosia caused by trauma to the inferior colliculi. Background: The patient cannot recognize speech or environmental sounds. Her discrimination is greatly facilitated by context and visibility of the speaker's facial movements, and under forced-choice testing. Her auditory temporal resolution is severely compromised. Her discrimination is more impaired for words differing in voice onset time than place of articulation. Words presented to her right ear are extinguished with dichotic presentation; auditory stimuli in the right hemifield are mislocalized to the left.
On the Iteration Complexity of Support Recovery via Hard Thresholding Pursuit

Recovering the support of a sparse signal from its compressed samples has been one of the most important problems in high dimensional statistics. In this paper, we present a novel analysis for the hard thresholding pursuit (HTP) algorithm, showing that it exactly recovers the support of an arbitrary s-sparse signal within O (sκ log κ) iterations via a properly chosen proxy function, where κ is the condition number of the problem. In stark contrast to the theoretical results in the literature, the iteration complexity we obtained holds without assuming the restricted isometry property, or relaxing the sparsity, or utilizing the optimality of the underlying signal. We further extend our result to a more challenging scenario, where the subproblem involved in HTP cannot be solved exactly. We prove that even in this setting, support recovery is possible and the computational complexity of HTP is established. Numerical study substantiates our theoretical results.
Wave and vortex dynamics on the surface of a sphere

Motivated by the observed potential vorticity structure of the stratospheric polar vortex, we study the dynamics of linear and nonlinear waves on a zonal vorticity interface in a two-dimensional barotropic flow on the surface of a sphere (interfacial Rossby waves). After reviewing the linear problem, we determine, with the help of an iterative scheme, the shapes of steadily propagating nonlinear waves; a stability analysis reveals that they are (nonlinearly) stable up to very large amplitude. We also consider multi-vortex equilibria on a sphere: we extend the results of Thompson (1883) and show that a (latitudinal) ring of point vortices is more unstable on the sphere than in the plane; notably, no more than three point vortices on the equator can be stable. We also determine the shapes of finite-area multi-vortex equilibria, and reveal additional modes of instability feeding off shape deformations which ultimately result in the complex merger of some or all of the vortices. We discuss two specific applications to geophysical flows: for conditions similar to those of the wintertime terrestrial stratosphere, we show that perturbations to a polar vortex with azimuthal wavenumber 3 are close to being stationary, and hence are likely to be resonant with the tropospheric wave forcing; this is often observed in high-resolution numerical simulations as well as in the ozone data. Secondly, we show that the linear dispersion relation for interfacial Rossby waves yields a good fit to the phase velocity of the waves observed on Saturn's ‘ribbon’.
Eye Movements , Strabismus , Amblyopia and Neuro-Ophthalmology Foveal and Peripapillary Vascular Decrement in Migraine With Aura Demonstrated by Optical Coherence Tomography Angiography

Melinda Y. Chang, Nopasak Phasukkijwatana, Sean Garrity, Stacy L. Pineles, Mansour Rahimi, David Sarraf, Mollie Johnston, Andrew Charles, and Anthony C. Arnold Stein Eye Institute, University of California, Los Angeles, California, United States Doheny Eye Institute, University of California, Los Angeles, California, United States Department of Ophthalmology, University of California, Los Angeles, California, United States Department of Ophthalmology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand Department of Neurology, University of California, Los Angeles, California, United States
The effect of shear span-to-depth ratio and test set-up on the behavior of fibre composite sandwich structure

The shear strength of the core material is a critical parameter and is an important consideration when designing a composite sandwich structure in construction application. In this paper, the shear behaviour of a new generation composite sandwich panel made up of glass fibre composite skins and phenolic core was investigated under three-point loading short beam (SB) and asymmetrical beam shear (ABS) tests. The effect of the shear span-to-depth ratio (a/D) was examined on the shear strength and failure behaviour of the fibre composite sandwich beams. The results showed that the shear behaviour of the beams is affected strongly by the a/D ratios. The beams with a lower a/D ratio failed at a higher load compare to the beams with larger a/D ratio. In general, the sandwich beams tested under ABS failed at a significantly higher load than that of the sandwich beams tested under SB for the same a/D ratio. The results also showed that the behaviour of the fibre composite sandwich beams is governed by the strength of the phenolic core material. In all the tested sandwich beams, the failure of the core occurred under the loading point where the shear force and bending moment are maximum.
Androgen Receptor Gene Aberrations in Circulating Cell-Free DNA: Biomarkers of Therapeutic Resistance in Castration-Resistant Prostate Cancer

Purpose: Although novel agents targeting the androgen–androgen receptor (AR) axis have altered the treatment paradigm of metastatic castration-resistant prostate cancer (mCRPC), development of therapeutic resistance is inevitable. In this study, we examined whether AR gene aberrations detectable in circulating cell-free DNA (cfDNA) are associated with resistance to abiraterone acetate and enzalutamide in mCRPC patients. Experimental Design: Plasma was collected from 62 mCRPC patients ceasing abiraterone acetate (n = 29), enzalutamide (n = 19), or other agents (n = 14) due to disease progression. DNA was extracted and subjected to array comparative genomic hybridization (aCGH) for chromosome copy number analysis, and Roche 454 targeted next-generation sequencing of exon 8 in the AR. Results: On aCGH, AR amplification was significantly more common in patients progressing on enzalutamide than on abiraterone or other agents (53% vs. 17% vs. 21%, P = 0.02, χ2). Missense AR exon 8 mutations were detected in 11 of 62 patients (18%), including the first reported case of an F876L mutation in an enzalutamide-resistant patient and H874Y and T877A mutations in 7 abiraterone-resistant patients. In patients switched onto enzalutamide after cfDNA collection (n = 39), an AR gene aberration (copy number increase and/or an exon 8 mutation) in pretreatment cfDNA was associated with adverse outcomes, including lower rates of PSA decline ≥ 30% (P = 0.013, χ2) and shorter time to radiographic/clinical progression (P = 0.010, Cox proportional hazards regression). Conclusions: AR gene aberrations in cfDNA are associated with resistance to enzalutamide and abiraterone in mCRPC. Our data illustrate that genomic analysis of cfDNA is a minimally invasive method for interrogating mechanisms of therapeutic resistance in mCRPC. Clin Cancer Res; 21(10); 2315–24. ©2015 AACR.
Modern-day naturopathic medicine and traditional Ayurveda in a combined attack against Parkinson's disease

In Parkinson’s disease, the neuronal cells that produce the neurotransmitter dopamine deteriorate. As a consequence, dopamine levels decline and symptoms appear. Treatment has traditionally involved dopamine’s chemical precursor, L-dopa. Although widely used, this treatment is accompanied by unpleasant toxic effects and causes only symptomatic relief while the disease progresses. The legume Mucuna pruriens (L) DC. (Fabaceae) has been used in Ayurveda as a naturopathic medicine for the treatment of Parkinson’s disease (then known as Kampavata). The results from more recent clinical studies suggest that this nutraceutical may be more effective than L-dopa against the symptoms of Parkinson’s disease, may possess neuroprotective properties, and may even cure patients suffering from this condition. This indicates a need for further in vitro as well as clinical research with M. pruriens.
Defenses against Oxidative Stress in Neisseria gonorrhoeae: a System Tailored for a Challenging Environment

SUMMARY Neisseria gonorrhoeae is a host-adapted pathogen that colonizes primarily the human genitourinary tract. This bacterium encounters reactive oxygen and reactive nitrogen species as a consequence of localized inflammatory responses in the urethra of males and endocervix of females and also of the activity of commensal lactobacilli in the vaginal flora. This review describes recent advances in the understanding of defense systems against oxidative stress in N. gonorrhoeae and shows that while some of its defenses have similarities to the paradigm established with Escherichia coli, there are also some key differences. These differences include the presence of a defense system against superoxide based on manganese ions and a glutathione-dependent system for defense against nitric oxide which is under the control of a novel MerR-like transcriptional regulator. An understanding of the defenses against oxidative stress in N. gonorrhoeae and their regulation may provide new insights into the ways in which this bacterium survives challenges from polymorphonuclear leukocytes and urogenital epithelial cells.
Development of Postural Control in Healthy Children: A Functional Approach

From a set of experimental studies showing how intersegmental coordination develops during childhood in various posturokinetic tasks, we have established a repertoire of equilibrium strategies in the course of ontogenesis. The experimental data demonstrate that the first reference frame used for the organization of balance control during locomotion is the pelvis, especially in young children. Head stabilization during posturokinetic activities, particularly locomotion, constitutes a complex motor skill requiring a long time to develop during childhood. When studying the emergence of postural strategies, it is essential to distinguish between results that can be explained by biomechanical reasons strictly and those reflecting the maturation of the central nervous system (CNS). To address this problem, we have studied our young subjects in situations requiring various types of adaptation. The studies dealing with adaptation of postural strategies aimed at testing short and long-term adaptation capacity of the CNS during imposed transient external biomechanical constraints in healthy children, and during chronic internal constraints in children with skeletal pathologies. In addition to maintenance of balance, another function of posture is to ensure the orientation of a body segment. It appears that the control of orientation and the control of balance both require the trunk as an initial reference frame involving a development from egocentric to exocentric postural control. It is concluded that the first step for children consists in building a repertoire of postural strategies, and the second step consists in learning to select the most appropriate postural strategy, depending on the ability to anticipate the consequence of the movement in order to maintain balance control and the efficiency of the task.
Macrophages Promote Oxidative Metabolism To Drive Nitric Oxide Generation in Response to Trypanosoma cruzi

ABSTRACT Trypanosoma cruzi is the causative agent of chronic chagasic cardiomyopathy. Why macrophages (mφs), the early responders to infection, fail to achieve parasite clearance is not known. Mouse (RAW 264.7) and human (THP-1 and primary) mφs were infected for 3 h and 18 h with T. cruzi TcI isolates, SylvioX10/4 (SYL, virulent) and TCC (nonpathogenic), which represent mφ stimulation and infection states, respectively. Mφs incubated with lipopolysaccharide and gamma interferon (LPS/IFN-γ) and with interleukin-4 (IL-4) were used as controls. We monitored the cytokine profile (using enzyme-linked immunosorbent assay [ELISA]), reactive oxygen species (ROS; fluorescent probes), nitric oxide (·NO; Griess assay), and metabolic state using a custom-designed mitoxosome array and Seahorse XF24 Analyzer. LPS/IFN-γ treatment of mφs elicited a potent increase in production of tumor necrosis alpha (TNF-α) at 3 h and of ROS and ·NO by 18 h. Upon SYL infection, murine mφs elicited an inflammatory cytokine profile (TNF-α ≫ TGF-β + IL-10) and low levels of ·NO and ROS production. LPS/IFN-γ treatment resulted in the inhibition of oxidative metabolism at the gene expression and functional levels and a switch to the glycolytic pathway in mφs, while IL-4-treated mφs utilized oxidative metabolism to meet energy demands. SYL infection resulted in an intermediate functional metabolic state with increased mitoxosome gene expression and glycolysis, and IFN-γ addition shut down the oxidative metabolism in SYL-infected mφs. Further, TCC- and SYL-stimulated mφs exhibited similar levels of cell proliferation and production of TNF-α and ROS, while TCC-stimulated mφs exhibited up to 2-fold-higher levels of oxidative metabolism and ·NO production than SYL-infected mφs. Inhibiting ATP-coupled O2 consumption suppressed the ·NO generation in SYL-infected mφs. Mitochondrial oxygen consumption constitutes a mechanism for stimulating ·NO production in mφs during T. cruzi infection. Enhancing the oxidative metabolism provides an opportunity for increased ·NO production and pathogen clearance by mφs to limit disease progression.