Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Cortical Processing of Vestibular Mismatch Information on the Generation of Nystagmus and Vertigo

Objective: Here, we investigate whether vertigo and nystagmus is generated at the first stage of vestibular processing in the parieto-insular vestibular cortex (PIVC). Background: It is believed that the PIVC is the first and most important hub for the cortical processing of vestibular information. In this region of the brain, vestibular information from both hemispheres is integrated with somatosensory and visual information. Mismatches among these inputs have been consistently demonstrated to activate the PIVC and the widespread vestibular network. Such mismatches also cause behavioral responses, such as vertigo and nystagmus. However, the role of the PIVC in the generation of these symptoms remains elusive, particularly because behavioral and cortical responses have been found to follow very different time-courses. It therefore remains unclear at which level of information processing vertigo and nystagmus are generated. Methods: We performed functional magnetic resonance imaging (fMRI) on 20 healthy subjects during caloric stimulation at different temperatures. We were particularly interested in the changes in the strengths of PIVC activity under these stimulus conditions. Results: By using a non-inferiority analysis, we demonstrate that activity in the PIVC did not increase with the occurence of vertigo and nystagmus. Conclusions: The current data suggest that perceptions of vertigo and nystagmus are not generated at the first integrative stage in the PIVC. We further speculate that nystagmus originates via a direct interaction of vestibular signals with somatosensory and visual information at a subcortical level.
Game or measurement? Algorithmic transparency and the Klout score

Klout 1 is an Internet service that claims to measure an individual ′ s inﬂuence by aggregating information from a variety of social media platforms. We brieﬂy examine Klout ′ s approach to measuring inﬂuence and argue that the Klout score ′ s lack of algorithmic transparency undermines its status as a trustworthy metric. We further argue that Klout and similar services “gamify” the notion of inﬂuence in ways that encourage competitive behavior among users in ways which are detrimental to the quality of measurement in a scientiﬁc sense, instead encouraging a gamiﬁed notion of in-ﬂuence. We conclude that only an approach to measurement that is based on transparency has a real chance of gaining trust, and that only a widely trusted metric may serve as a reliable indicator of inﬂuence. Beyond the case of Klout, context, theoretical soundness, algorithmic trans-parency, and user agency are general issues that must be dealt with for any entity attempting to measure inﬂuence in online social networks.
Left Posterior Orbitofrontal Cortex Is Associated With Odor-Induced Autobiographical Memory: An fMRI Study

Autobiographical odor memory (AM-odor) accompanied by a sense of realism of a specific memory elicits strong emotions. AM-odor differs from memory triggered by other sensory modalities, possibly because olfaction involves a unique sensory process. Here, we examined the orbitofrontal cortex (OFC), using functional magnetic resonance imaging (fMRI) to determine which OFC subregions are related to AM-odor. Both AM-odor and a control odor successively increased subjective ratings of comfortableness and pleasantness. Importantly, AM-odor also increased arousal levels and the vividness of memories, and was associated with a deep and slow breathing pattern. fMRI analysis indicated robust activation in the left posterior OFC (L-POFC). Connectivity between the POFC and whole brain regions was estimated using psychophysiological interaction analysis (PPI). We detected several trends in connectivity between L-POFC and bilateral precuneus, bilateral rostral dorsal anterior cingulate cortex (rdACC), and left parahippocampus, which will be useful for targeting our hypotheses for future investigations. The slow breathing observed in AM-odor was correlated with rdACC activation. Odor associated with emotionally significant autobiographical memories was accompanied by slow and deep breathing, possibly involving rdACC processing.
Activation of airway epithelial bitter taste receptors by Pseudomonas aeruginosa quinolones modulates calcium, cyclic-AMP, and nitric oxide signaling

Bitter taste receptors (taste family 2 bitter receptor proteins; T2Rs), discovered in many tissues outside the tongue, have recently become potential therapeutic targets. We have shown previously that airway epithelial cells express several T2Rs that activate innate immune responses that may be important for treatment of airway diseases such as chronic rhinosinusitis. It is imperative to more clearly understand what compounds activate airway T2Rs as well as their full range of functions. T2R isoforms in airway motile cilia (T2R4, -14, -16, and -38) produce bactericidal levels of nitric oxide (NO) that also increase ciliary beating, promoting clearance of mucus and trapped pathogens. Bacterial quorum-sensing acyl-homoserine lactones activate T2Rs and stimulate these responses in primary airway cells. Quinolones are another type of quorum-sensing molecule used by Pseudomonas aeruginosa. To elucidate whether bacterial quinolones activate airway T2Rs, we analyzed calcium, cAMP, and NO dynamics using a combination of fluorescent indicator dyes and FRET-based protein biosensors. T2R-transfected HEK293T cells, several lung epithelial cell lines, and primary sinonasal cells grown and differentiated at the air–liquid interface were tested with 2-heptyl-3-hydroxy-4-quinolone (known as Pseudomonas quinolone signal; PQS), 2,4-dihydroxyquinolone, and 4-hydroxy-2-heptylquinolone (HHQ). In HEK293T cells, PQS activated T2R4, -16, and -38, whereas HHQ activated T2R14. 2,4-Dihydroxyquinolone had no effect. PQS and HHQ increased calcium and decreased both baseline and stimulated cAMP levels in cultured and primary airway cells. In primary cells, PQS and HHQ activated levels of NO synthesis previously shown to be bactericidal. This study suggests that airway T2R-mediated immune responses are activated by bacterial quinolones as well as acyl-homoserine lactones.
Design guidelines for high-performance SCM hierarchies

With emerging storage-class memory (SCM) nearing commercialization, there is evidence that it will deliver the much-anticipated high density and access latencies within only a few factors of DRAM. Nevertheless, the latency-sensitive nature of memory-resident services makes seamless integration of SCM in servers questionable. In this paper, we ask the question of how best to introduce SCM for such servers to improve overall performance/cost over existing DRAM-only architectures. We first show that even with the most optimistic latency projections for SCM, the higher memory access latency results in prohibitive performance degradation. However, we find that deployment of a modestly sized high-bandwidth 3D stacked DRAM cache makes the performance of an SCM-mostly memory system competitive. The high degree of spatial locality that memory-resident services exhibit not only simplifies the DRAM cache's design as page-based, but also enables the amortization of increased SCM access latencies and the mitigation of SCM's read/write latency disparity. We identify the set of memory hierarchy design parameters that plays a key role in the performance and cost of a memory system combining an SCM technology and a 3D stacked DRAM cache. We then introduce a methodology to drive provisioning for each of these design parameters under a target performance/cost goal. Finally, we use our methodology to derive concrete results for specific SCM technologies. With PCM as a case study, we show that a two bits/cell technology hits the performance/cost sweet spot, reducing the memory subsystem cost by 40% while keeping performance within 3% of the best performing DRAM-only system, whereas single-level and triple-level cell organizations are impractical for use as memory replacements.
Acute and Chronic Dopaminergic Modulation of Striatal Circuitry and Function in Health and Disease

Author(s): Parker, Philip Ross Lutton | Advisor(s): Kreitzer, Anatol C | Abstract: The basal ganglia are an evolutionarily conserved set of nuclei that are crucial for context-dependent learning and selection of appropriate behavioral outputs. The striatum is considered the input nucleus of the basal ganglia because it not only receives the bulk of excitatory synaptic drive from sources outside the basal ganglia, but also contains two populations of medium spiny neurons that give rise to the direct and indirect basal ganglia pathways. The activity of direct and indirect pathway medium spiny neurons (dMSNs and iMSNs) is sufficient to promote or suppress behavioral output, respectively. Changes in synaptic strength at excitatory inputs to MSNs are thought to underlie context-dependent learning, whereas the acute modulation of MSN intrinsic excitability affects motivation or vigor of an ongoing behavior. Previous research has revealed that the neuromodulator dopamine appears to be in a unique position to exert both acute and chronic modulatory effects over MSNs and their excitatory inputs. The differential expression of Gs-coupled D1 and Gi-coupled D2 receptors by dMSNs and iMSNs, respectively, results in opposing changes in direct and indirect pathway function with changes in striatal dopamine levels. However, previous technical limitations have restricted the study of dopamine's acute actions in the striatum and the long-term effects of dopamine on MSN subtypes and excitatory inputs of distinct origins. Here we use recently developed optogenetic and chemogenetic techniques combined with behavior and ex vivo brain slice electrophysiology to study the mechanisms of acute and chronic dopamine signaling in MSNs and their excitatory inputs. In Chapter One, we review the evidence for the dual-pathway model of basal ganglia function and its modulation by dopamine in the context of controlling behavioral output. In Chapter Two, we perform an electrophysiological comparison of common optogenetic proteins to determine the optimal tool for our experiments. We then use optogenetic control of dopamine release to show specific modulation of dMSN intrinsic excitability and D1-mediated invigoration of behavior in Chapter Three. In Chapter Four, we provide evidence that the chronic loss of dopamine in Parkinson's disease results in a reorganization of the thalamostriatal system that has negative outcomes on motor control. Finally, we discuss the overarching implications of these findings in the context of basal ganglia function in health and disease in Chapter Five. These findings not only represent a long overdue reevaluation of the assumptions surrounding the role of dopamine in striatal function, but also provide new testable hypotheses addressing the cellular and synaptic bases of an evolutionarily conserved system for the dynamic regulation of ethologically relevant behaviors.
SNP genotyping data high-resolution copy number variation detection in whole-genome PennCNV : An integrated hidden Markov model designed for Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2007/10/09/gr.6861907. DC1.html Related Content CSH Protocols June 2, 2008 2008: pdb.top46-46pdb.top Kai Wang and Maja Bucan Copy Number Variation Detection via High-Density SNP Genotyping References http://genome.cshlp. org/content/17/11/1665.full. html#related-urls Article cited in: http://genome.cshlp. org/content/17/11/1665.full. html#ref-list-1 This article cites 37 articles, 11 of which can be accessed free at:
Mobile Web Apps - The Non-programmer's Alternative to Native Applications

As the capacity of the mobile web continues to increase with the introduction of new web technologies, a growing number of "non-programming" developers are looking to web-based mobile applications (or "web apps") as an alternative means of creating and deploying content, without the need for code-based programming experience. This paper demonstrates just some of the capabilities of a web-based application built using HTML5 and CSS3. Although this paper focuses on the development process for two web app prototypes built exclusively for the iPhone platform, theoretically, a web application can be presented on other mobile devices with browsers that support HTML5 and CSS3 technologies. It was found that these web apps were capable of producing a comparable standard of user experience as their native application equivalents. The use of the latest web technologies provides "non-programming" developers with a viable alternative for developing apps on mobile devices.
Inhibition of Clostridium perfringens using Bacteriophages and Bacteriocin Producing Strains

In this study, we isolated and characterized a bacteriocin-producing strain and two bacteriophages (P4, A3), showing antimicrobial effects against Clostridium perfringens, from chicken and swine feces by the spot-on-the lawn antagonism method. The selected strain was identified as Streptococcus hyointestinalis by 16S rRNA gene sequencing. The bacteriocin from the isolated strain exhibited strong inhibitory activity against four strains of C. perfringens and all the tested strains of Listeria monocytogenes, and the bacteriocin were highly heat- and pH-stable even at pH 2, pH 10 and 121℃ for 15 min. We also evaluated the combined effects of the isolated bacteriocin and phages. Combining the phage treatments and bacteriocin resulted in a synergetic effect compared with the phage or the bacteriocin alone. In addition, during the probiotic test, the bacteriocin-producing S. hyointestinalis B19 strain reduced the population of C. perfringens significantly. Treatment with S. hyointestinalis B19 and a cocktail of lytic bacteriophages eradicated the C. perfringens KCTC 3269T, completely. Consequently, the isolated bacteriocin and bacteriophages represent candidates for effective biocontrol of C. perfringens, and bacteriocin-producing S. hyointestinalis B19 is a potential probiotic candidate for use in domestic animals.
Chemical organization of the macaque monkey olfactory bulb: III. Distribution of cholinergic markers

The distribution patterns of choline acetyltransferase (ChAT) and acetylcholinesterase (AChE) were studied in the olfactory bulb (OB) of three species of macaque. AChE was detected by a histochemical method and ChAT immunoreactivity by immunocytochemistry. Similar results were observed in all species analyzed. With the exception of the olfactory nerve layer, all layers of the macaque monkey OB demonstrated a dense innervation of AChE‐ and ChAT‐positive fibers. The distribution patterns of AChE‐ and ChAT‐labeled fibers were similar for both cholinergic markers, although the number of AChE‐labeled fibers was clearly higher than the number of ChAT‐immunoreactive fibers. The highest density of AChE and ChAT‐stained fibers was observed in the interface between the glomerular layer and the external plexiform layer and in the internal plexiform layer. Dense bundles of labeled fibers were observed in the caudal OB, coursing from the olfactory peduncle. All ChAT‐immunopositive elements were identified as centrifugal fibers, derived from neurons caudal to the OB. Neither olfactory fibers nor intrinsic neurons were observed after ChAT immunocytochemistry. However, a few AChE‐positive cells were observed in the glomerular layer and in both external and internal plexiform layers. These neurons were presumably identified as periglomerular cells, superficial short‐axon cells, and/or external tufted cells and deep short‐axon cells. Contrary to other neurotransmitters and neuroactive substances, the distribution patterns of ChAT and AChE activities in the macaque monkey OB closely resembled the patterns described in macrosmatic mammals and showed laminar differences with the distribution pattern observed in humans. J. Comp. Neurol. 501:854–865, 2007. © 2007 Wiley‐Liss, Inc.
Effects of Allogenic Dermal Fibroblasts on Rotator Cuff Healing in a Rabbit Model of Chronic Tear

Background: The failure of rotator cuffs to heal after repair is an unresolved surgical issue. There have been substantial efforts, including the use of biological supplements, to enhance tendon healing. Dermal fibroblasts are a good candidate for tendon tissue engineering because they are similar to the tenocytes used for collagen synthesis. In addition, they are easily accessible because autologous dermal fibroblasts can be obtained from individual skin without major skin defects and allogenic dermal fibroblasts (ADFs) have already been commercialized in the field of skin engineering. Purpose: To determine the effects of dermal fibroblasts on tendon-to-bone healing in a rabbit model of a chronic rotator cuff tear. Study Design: Controlled laboratory study. Methods: A total of 33 rabbits were randomly allocated into 3 groups (n = 11 each). Supraspinatus tendons were detached and left for 6 weeks to establish a chronic rotator tear model. Torn tendons were repaired in a transosseous manner with the injection of 5 × 106 ADFs with fibrin in group A, fibrin only in group B, and saline only in group C. At 12 weeks after repair, the mechanical test and histological evaluation were performed. Results: Seven rabbits died before the evaluation (1 in group A, 2 in group B, 4 in group C). In the final evaluation, the mean ± SD load to failure was 48.1 ± 13.3 N/kg for group A, 34.5 ± 8.9 N/kg for group B, and 31.1 ± 8.3 N/kg for group C, and group A showed significantly higher load-to-failure values than the other groups (P = .011). The midsubstance tear rate, which presented stronger tendon-to-bone healing than insertional tear, was 50.0% in group A, 22.2% in group B, 28.6% in group C, but the differences were not statistically significant (P = .413). In the histological evaluation, group A showed greater collagen fiber continuity and better orientation than the other groups. Conclusion: This controlled laboratory study verified, on the basis of biomechanics and histology, the potential for the use of ADFs in rotator cuff healing. The current results suggest a new biological supplement to increase the rate of rotator cuff healing. Clinical Relevance: The most important finding of this study was the potential for a new biological supplement to enhance rotator cuff healing—a continuing challenge.
Observing vegetation phenology through social media

The widespread use of social media has created a valuable but underused source of data for the environmental sciences. We demonstrate the potential for images posted to the website Twitter to capture variability in vegetation phenology across United States National Parks. We process a subset of images posted to Twitter within eight U.S. National Parks, with the aim of understanding the amount of green vegetation in each image. Analysis of the relative greenness of the images show statistically significant seasonal cycles across most National Parks at the 95% confidence level, consistent with springtime green-up and fall senescence. Additionally, these social media-derived greenness indices correlate with monthly mean satellite NDVI (r = 0.62), reinforcing the potential value these data could provide in constraining models and observing regions with limited high quality scientific monitoring.
Demographic Responses to Oxidative Stress and Inflammation in the Wandering Albatross (Diomedea exulans)

One of the major challenges in ecological research is the elucidation of physiological mechanisms that underlie the demographic traits of wild animals. We have assessed whether a marker of plasma oxidative stress (TBARS) and plasma haptoglobin (protein of the acute inflammatory phase response) measured at time t predict five demographic parameters (survival rate, return rate to the breeding colony, breeding probability, hatching and fledging success) in sexually mature wandering albatrosses over the next four years (Diomedea exulans) using a five-year individual-based dataset. Non-breeder males, but not females, having higher TBARS at time t had reduced future breeding probabilities; haptoglobin was not related to breeding probability. Neither TBARS nor haptoglobin predicted future hatching or fledging success. Haptoglobin had a marginally positive effect on female survival rate, while TBARS had a marginally negative effect on return rate. Our findings do not support the role for oxidative stress as a constraint of future reproductive success in the albatross. However, our data point to a potential mechanism underlying some aspects of reproductive senescence and survival. Our results also highlight that the study of the consequences of oxidative stress should consider the life-cycle stage of an individual and its reproductive history.
Relationship between dietary quality, tinnitus and hearing level: data from the national health and nutrition examination survey, 1999–2002

Abstract Objective: To examine the relationship between the healthy eating index (HEI), a measure of dietary quality based on United States Department of Agriculture recommendations and report of tinnitus. Design: This cross-sectional analysis was based on HEI data and report of tinnitus. Study sample: Data for adults between 20 and 69 years of age were drawn from the National Health and Nutrition Examination Survey (NHANES), 1999–2002. The NHANES is a programme of studies, to assess the health and nutritional status of adults and children in the United States. Two thousand one hundred and seventy-six participants were included in the analytic sample. Results: Of the sample, 21.1% reported tinnitus within the past year and 11.7% reported persistent tinnitus, defined as tinnitus experienced at least monthly or greater. Controlling for age, sex, race/ethnicity, diabetes, noise exposure and smoking status, we found that with healthier diet (poorer vs. better HEI) there was decreased odds of reported persistent tinnitus [odds ratio (OR); 0.67; 95% confidence interval (CI) 0.45–0.98; p = 0.03]. Conclusions: The current findings support a possible relationship between healthier diet quality and reported persistent tinnitus.
Generation of coherent acoustic beams in solids by mixing of counterpropagating , detuned optical beams [ invited ]

We model the generation of coherent acoustic beams in a homogeneous solid from the interference of two oppositely propagating, detuned, optical laser beams. This configuration is reciprocal to Brillouin light scattering in the backward interaction arrangement. Generation of a confined ultrasound beam is predicted, close to the Brillouin frequency. Optoacoustic gain spectra and beam shapes are obtained numerically using a finite element model. The acoustic spectra are non-symmetrical, i.e. non-Lorentzian, and result from excitation of the continuum of bulk elastic waves. The acoustic beam width correspondingly varies with detuning frequency and optical beam waist. © 2018 Optical Society of America