bluuebunny/crossref_metadata_2025 huggingface dataset:
Longitudinal, Nationwide, Cohort Study to Assess Incidence, Outcomes, and Costs Associated with Complicated Urinary Tract Infection
Authors: Carreno Joseph J , Tam Iris M , Meyers Juliana L , Esterberg Elizabeth , Candrilli Sean D , Lodise Thomas P
Published: October 2019

AbstractAbstract

Introduction

Complicated urinary tract infections (cUTI) are common infections. Despite their frequency, limited data are available on the incidence and healthcare burden associated with cUTIs. This study details the epidemiology and 30-day health care resource utilization associated with cUTI in the US.

Methods

Retrospective study of PharmMetrics Plus database from 1/1/2013 to 12/31/2017. Inclusion criteria: age ≥ 18 years, ICD-9/10 cUTI diagnosis, and continuous enrollment for ≥ 6 months pre- and ≥ 30 days post-index dates. Two mutually exclusive study cohorts for cUTI patients were identified based on the setting of the first observed cUTI diagnosis (inpatient (IP) and outpatient (OP)).

Results

In total 543,502 adults with cUTI met the inclusion criteria (104,866 IP cohort; 438,636 OP cohort). Mean (SD) age was 48.1 (16.5) years and 68.1% were female. The overall incidence of cUTI was 1.01%, equating to approximately 2,882,195 annual cUTI cases in the US. In the IP cohort, overall median (IQR) 30-day health care costs were $13,028 ($4,855-$26,781). Median (IQR) costs for the initial admission were $9,441 ($2,079-$19,027), with median (IQR) length of stay (LOS) of 4 (3-8) days. Among IP patients, 12,933 (12.3%) had a subsequent readmission. In the OP cohort, median (IQR) 30-day health care costs were $1,531 ($305-$4,998). Of OP patients, 40,457 (9.2%) had a 30-day admission.

Conclusions

This study demonstrates that the economic burden associated with cUTIs is substantial, especially among patients requiring hospitalization. These findings highlight the need for new treatment approaches and antibiotics that avert hospitalization and reduce LOS.
Effects of the Your Family, Your Neighborhood Intervention on Neighborhood Social Processes
Authors: Brisson Daniel , Lechuga Peña Stephanie , Mattocks Nicole , Plassmeyer Mark , McCune Sarah
Published: October 2019

The objective of this study was to ascertain whether participation in the Your Family, Your Neighborhood (YFYN) intervention, an intervention for families living in low-income neighborhoods, leads to improved perceptions of neighborhood social cohesion and informal neighborhood social control. Fifty-two families in three low-income, urban neighborhoods participated in the manualized YFYN intervention. In this quasi-experimental study treatment families (n = 37) in two low-income neighborhoods received YFYN and control families (n = 15) from one separate low-income neighborhood did not. Families receiving YFYN attended 10 two-hour skills-based curriculum sessions during which they gathered for a community dinner and participated in parent- and child-specific skills-based groups. Treatment families reported increases in both neighborhood social cohesion and informal neighborhood social control after receiving YFYN. However, families receiving YFYN did not experience statistically significant improvements in perceptions of neighborhood social cohesion or informal neighborhood social control compared with nontreatment families. In conclusion, the delivery of YFYN in low-income neighborhoods may improve perceptions of neighborhood social cohesion. Further testing, with randomization and a larger sample, should be conducted to provide a more robust understanding of the impact of YFYN.
Comparing Approaches for Capturing Bacterial Assemblages Associated with Symptomatic (Bacterial Blotch) and Asymptomatic Mushroom (Agaricus bisporus) Caps
Authors: Martins Samuel J. , Trexler Ryan V. , Vieira Fabricio R. , Pecchia John A. , Kandel Prem P. , Hockett Kevin L. , Bell Terrence H. , Bull Carolee T.
Published: October 2019

Bacterial blotch is a complex of diseases, caused by Pseudomonas tolaasii and other Pseudomonas spp., whose growth may be influenced by other microorganisms associated with mushroom caps. The objectives of this work were to (i) compare methods for extracting DNA from mushroom caps to assess bacterial composition, and (ii) describe and quantify the composition of bacteria in and on symptomatic and asymptomatic mushroom caps. Symptomatic and asymptomatic mushrooms were collected at an organic farm in Pennsylvania and processed. Bacteria were removed from mushrooms by sonication to target surface-associated bacteria (washate), from whole mushrooms postsonication to target bacteria within or tightly adhering to the mushrooms (post-washate), or from whole macerated mushrooms to target all mushroom-associated bacteria in one sample (whole). Bacterial composition was determined through sequencing the V4 hypervariable region of the 16S rRNA gene on an Illumina MiSeq. Bacterial composition differed significantly based on mushroom health status and community removal method. Regardless of sampling approach, Proteobacteria and Bacteroidetes appeared as the most dominant phyla. In comparing the three extraction methods, higher Shannon diversity and Pielou’s evenness were observed for the washate and post-washate methods compared with whole mushroom sampling. Additionally, higher Shannon diversity, operational taxonomic unit richness, and Pielou’s evenness were found for the asymptomatic mushrooms when compared with symptomatic mushrooms. Pseudomonas spp. were overrepresented on mushroom surfaces (washate method), regardless of health status. This research made strides in describing the mushroom cap microbiome and established sampling methods that will allow researchers to target studies and isolation of specific bacterial taxa.
Weather-Based Predictive Modeling of Orange Rust of Sugarcane in Florida
Authors: Chaulagain Bhim , Small Ian M. , Shine James M. , Fraisse Clyde W. , Raid Richard N. , Rott Philippe
Published: October 2019

Epidemics of sugarcane orange rust (caused by Puccinia kuehnii) in Florida are largely influenced by prevailing weather conditions. In this study, we attempted to model the relationship between weather conditions and rust epidemics as a first step toward development of a decision aid for disease management. For this purpose, rust severity data were collected from 2014 through 2016 at the Everglades Research and Education Center, Belle Glade, Florida, by recording percentage of rust-affected area of the top visible dewlap leaf every 2 weeks from three orange rust susceptible cultivars. Hourly weather data for 10- to 40-day periods prior to each orange rust assessment were evaluated as potential predictors of rust severity under field conditions. Correlation and stepwise regression analyses resulted in the identification of nighttime (8 PM to 8 AM) accumulation of hours with average temperature 20 to 22°C as a key predictor explaining orange rust severity. The five best regression models for a 30-day period prior to disease assessment explained 65.3 to 76.2% of variation of orange rust severity. Prediction accuracy of these models was tested using a case control approach with disease observations collected in 2017 and 2018. Based on receiver operator characteristic curve analysis of these two seasons of test data, a single-variable model with the nighttime temperature predictor mentioned above gave the highest prediction accuracy of disease severity. These models have potential for use in quantitative risk assessment of sugarcane rust epidemics.
Development and Application of a Quantitative PCR Detection Method to Quantify Venturia oleaginea in Asymptomatic Olive (Olea europaea) Leaves
Authors: Scibetta Silvia , Agosteo Giovanni E. , Abdelfattah Ahmed , Li Destri Nicosia Maria G. , Cacciola Santa O. , Schena Leonardo
Published: October 2019

Olive leaf spot (OLS), caused by Venturia oleaginea, is one of the most common and serious diseases of olive trees in the Mediterranean region. Understanding the pathogen life cycle is important for the development of effective control strategies. Current knowledge is incomplete owing to a lack of effective detection methods. It is extremely difficult to culture V. oleaginea in vitro, so primers were designed to amplify and sequence the internal transcribed spacer ITS1-5.8S-ITS2 region of the fungus directly from infected olive leaves. Sanger sequencing indicated a unique ITS region present in the European strains screened, confirming the appropriateness of the target region for developing a quantitative PCR (qPCR) assay. Furthermore, high-throughput sequencing of the same region excluded the presence of other Venturia species in the olive phyllosphere. The qPCR assay proved very specific and sensitive, enabling the detection of approximately 26 copies of target DNA. The analysis of symptomless leaves during early stages of the epidemic from the end of winter through spring revealed a similar quantity of pathogen DNA regardless of the leaf growth stage. In contrast, the pathogen titer changed significantly during the season. Data indicated that leaf infections start earlier than expected over the season and very young leaves are as susceptible as adult leaves. These findings have important practical implications and suggest the need for improved scheduling of fungicide treatments. The qPCR assay represents a valuable tool providing quantitative results and enables detection of V. oleaginea in all olive organs, including those in which OLS cannot be studied using previously available methods.
Use of an Infectious cDNA Clone of Pepper Veinal Mottle Virus to Confirm the Etiology of a Disease in Capsicum chinense
Authors: Hu Weiyao , Qin Li , Yan Haixia , Miao Weiguo , Cui Hongguang , Liu Wenbo
Published: October 2019

The pepper cultivar Yellow Lantern, one of the spiciest pepper varieties, is a local germplasm of Capsicum chinense, cultivated exclusively on Hainan Island, China. However, this variety is susceptible to viral diseases that severely affect its production. In this study, we report that pepper veinal mottle virus (PVMV) is associated with foliar chlorosis and rugosity symptoms in Yellow Lantern. To verify this correlation, we constructed a full-length cDNA clone of a PVMV isolate named HNu. The virus progeny derived from the cDNA clone replicated and moved systemically in the pepper, inducing the same symptoms as those induced by PVMV-HNu in Yellow Lantern peppers in the field. The results support that PVMV-HNu is the causal agent of foliar chlorosis and rugosity disease in Yellow Lantern. This knowledge will help in the diagnosis and prevention of disease caused by PVMV. Furthermore, the cDNA clone serves as a reverse genetic tool to study the molecular pathogenesis of PVMV.
Echoes from the past: synaesthetic colour associations reflect childhood gender stereotypes
Authors: Root Nicholas B. , Dobkins Karen , Ramachandran Vilayanur S. , Rouw Romke
Published: October 2019

Grapheme–colour synaesthesia is a neurological phenomenon in which linguistic symbols evoke consistent colour sensations. Synaesthesia is believed to be influenced by both genetic and environmental factors, but how these factors interact to create specific associations in specific individuals is poorly understood. In this paper, we show that a grapheme–colour association in adult synaesthetes can be traced to a particular environmental effect at a particular moment in childhood. We propose a model in which specific grapheme–colour associations are ‘locked in’ during development in children predisposed to become synaesthetes, whereas grapheme–colour associations remain flexible in non-synaesthetes. We exploit Western gender–colour stereotypes to test our model: we found that young girls
in general
tend to associate their first initial with the colour pink. Consistent with our model, adult female synaesthetes are influenced by their childhood environment: they associate their first initial with pink. Adult female non-synaesthetes do not show this bias. Instead, in our study, non-synaesthetes tended to associate their first initial with their
current
favourite colour. The results thus support the ‘locking in’ model of synaesthesia, suggesting that synaesthetic associations can be used as a ‘time capsule’, revealing childhood influences on adult linguistic associations. Grapheme–colour synaesthesia may thus offer an extraordinary opportunity to study linguistic development.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Exploring the relationship between grapheme colour-picking consistency and mental imagery
Authors: Spiller Mary Jane , Harkry Lee , McCullagh Fintan , Thoma Volker , Jonas Clare
Published: October 2019

Previous research has indicated a potential link between mental imagery and synaesthesia. However, these findings are mainly based on imagery self-report measures and recruitment of self-selected synaesthetes. To avoid issues of self-selection and demand effects, we recruited participants from the general population, rather than synaesthetes specifically, and used colour-picking consistency tests for letters and numbers to assess a ‘synaesthete-like’ experience. Mental imagery ability and mental rotation ability were assessed using both self-report measures and behavioural assessments. Consistency in colour-picking for letters (but not numbers) was predicted by performance on the visual mental imagery task but not by a mental rotation task or self-report measures. Using the consistency score as a proxy measure of grapheme-colour synaesthesia, we provide more evidence for the suggestion that synaesthetic experience is associated with enhanced mental imagery, even when participants are naive to the research topic.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Cellulosimicrobium cellulans aortic prosthetic valve endocarditis
Authors: Monticelli Jacopo , Gerloni Riccardo , Farina Claudio , Knezevich Anna , Dore Franca , Luzzati Roberto
Published: October 2019

Introduction. Invasive infections due to

Cellulosimicrobium

spp. (a Gram-positive coryneform) are extremely rare. Only a few cases of bloodstream infections and endocarditis have been described, as bacteraemia due to coryneforms is usually discarded as blood culture contamination.

Case presentation. A 66-year-old female, with a history of aortic valve replacement, presented with fever, left leg purpura and acute kidney injury. Multiple repeated blood cultures were positive for

Cellulosimicrobium cellulans

, and targeted therapy was started. At first, endocarditis was excluded by echocardiograms, and the acute nephritis was interpreted as an atypical presentation of Henoch–Shönlein purpura. High-dose prednisone was started, and after 10 weeks the patient presented again with fever, mental confusion and acute left arm ischaemia. A subsequent echocardiogram and radiolabelled leukocyte scintigraphic evaluation revealed aortic prosthetic valve endocarditis with periprosthetic abscess and arterial brachial thrombosis. The patient deceased, and the autoptic examination confirmed an aortic valve periprosthetic abscess and revealed multiple arterial thromboses and septic embolisms in the kidneys, brain, spleen and myocardium.

Conclusion. Isolation of coryneform bacteria on blood culture should not always be discarded as blood culture contamination. In the case of endocarditis due to

Cellulosimicrobium

spp., the removal of any prosthetic material, along with prolonged in vitro active antimicrobial therapy, should be pursued in order to reduce persistence or relapses of infection.
DNA Break-Induced Epigenetic Drift as a Cause of Mammalian Aging
Authors: Hayano Motoshi , Yang Jae-Hyun , Bonkowski Michael S. , Amorim Joao A. , Ross Jaime M. , Coppotelli Giuseppe , Griffin Patrick T. , Chew Yap Ching , Guo Wei , Yang Xiaojing , Vera Daniel L. , Salfati Elias L. , Das Abhirup , Thakur Sachin , Kane Alice E. , Mitchell Sarah J. , Mohri Yasuaki , Nishimura Emi K. , Schaevitz Laura , Garg Neha , Balta Ana-Maria , Rego Meghan A. , Gregory-Ksander Meredith , Jakobs Tatjana C. , Zhong Lei , Wakimoto Hiroko , Mostoslavsky Raul , Wagers Amy J. , Tsubota Kazuo , Bonasera Stephen J. , Palmeira Carlos M. , Seidman Jonathan G. , Seidman Christine E. , Wolf Norman S. , Kreiling Jill A. , Sedivy John M. , Murphy George F. , Oberdoerffer Philipp , Ksander Bruce R. , Rajman Luis A. , Sinclair David A.
Published: October 2019

There are numerous hallmarks of aging in mammals, but no unifying cause has been identified. In budding yeast, aging is associated with a loss of epigenetic information that occurs in response to genome instability, particularly DNA double-strand breaks (DSBs). Mammals also undergo predictable epigenetic changes with age, including alterations to DNA methylation patterns that serve as epigenetic “age” clocks, but what drives these changes is not known. Using a transgenic mouse system called “ICE” (for induciblechanges to theepigenome), we show that a tissue’s response to non-mutagenic DSBs reorganizes the epigenome and accelerates physiological, cognitive, and molecular changes normally seen in older mice, including advancement of the epigenetic clock. These findings implicate DSB-induced epigenetic drift as a conserved cause of aging from yeast to mammals.

One Sentence Summary

DNA breaks induce epigenomic changes that accelerate the aging clock in mammals
Correlating STED and synchrotron XRF nano-imaging unveils the co-segregation of metals and cytoskeleton proteins in dendrites
Authors: Domart Florelle , Cloetens Peter , Roudeau Stéphane , Carmona Asuncion , Verdier Emeline , Choquet Daniel , Ortega Richard
Published: October 2019

Zinc and copper are involved in neuronal differentiation and synaptic plasticity but the molecular mechanisms behind these processes are still elusive due in part to the difficulty of imaging trace metals together with proteins at the synaptic level. We correlate stimulated emission depletion (STED) microscopy of proteins and synchrotron X-ray fluorescence (SXRF) imaging of trace metals, both performed with 40 nm spatial resolution, on primary rat hippocampal neurons. We achieve a detection limit for zinc of 14 zeptogram (10-21 g) per pixel. We reveal the co-localization at the nanoscale of zinc and tubulin in dendrites with a molecular ratio of about one zinc atom per tubulin-αβ dimer. We observe the co-segregation of copper and F-actin within the nano-architecture of dendritic protrusions. In addition, zinc chelation causes a decrease in the expression of cytoskeleton proteins in dendrites and spines. Overall, these results indicate new functions for zinc and copper in the modulation of the cytoskeleton morphology in dendrites, a mechanism associated to neuronal plasticity and memory formation.
Rapid multicomponent bioluminescence imaging via substrate unmixing
Authors: Rathbun Colin M. , Ionkina Anastasia A. , Yao Zi , Jones Krysten A. , Porterfield William B. , Prescher Jennifer A.
Published: October 2019

Engineered luciferases and luciferins have dramatically expanded the scope of bioluminescence imaging in recent years. Multicomponent tracking remains challenging, though, due to a lack of streamlined methods to visualize combinations of bioluminescent reporters. Here we report a strategy for rapid, multiplexed imaging with a wide range of luciferases and luciferins. Sequential addition of orthogonal luciferins, followed by substrate unmixing, enabled facile detection of multiple luciferases in vitro and in vivo. Multicomponent imaging in mice was also achieved on the minutes-to-hours time scale, a vast improvement over conventional protocols.
Inhibitory signaling in mammalian olfactory transduction potentially mediated by Gαo
Authors: Corey Elizabeth A. , Ukhanov Kirill , Bobkov Yuriy V. , McIntyre Jeremy C. , Martens Jeffrey R. , Ache Barry W.
Published: October 2019

Olfactory GPCRs (ORs) in mammalian olfactory receptor neurons (ORNs) mediate excitation through the Gαsfamily member Gαolf. Here we tentatively associate a second G protein, Gαo, with inhibitory signalling in mammalian olfactory transduction by first showing that odor evoked phosphoinositide 3-kinase (PI3K)-dependent inhibition of signal transduction is absent in the native ORNs of mice carrying a conditional OMP-Cre based knockout of Gαo. We then identify an OR from native rat ORNs that are activated by octanol through cyclic nucleotide signaling and inhibited by citral in a PI3K-dependent manner. We show that the OR activates cyclic nucleotide signaling and PI3K signaling in a manner that reflects its functionality in native ORNs. Our findings lay the groundwork to explore the interesting possibility that ORs can interact with two different G proteins in a functionally identified, ligand-dependent manner to mediate opponent signaling in mature mammalian ORNs.
Multiple ribonuclease A family members cleave transfer RNAs in response to stress
Authors: Akiyama Yasutoshi , Lyons Shawn , Fay Marta M. , Abe Takaaki , Anderson Paul , Ivanov Pavel
Published: October 2019

During stress, changes in gene expression are critical for cell survival. Stress-induced tRNA cleavage has been implicated in various cellular processes, where tRNA fragments play diverse regulatory roles. Angiogenin (ANG), a member of the RNase A superfamily, induces cleavage of tRNAs resulting in the formation of tRNA-derived stress-induced RNAs (tiRNAs) that contribute to translational reprogramming aiming at cell survival. The role of other stress-induced RNases in tRNA cleavage is poorly understood. Using gene editing and biochemical approaches, we show that other members of the RNase A family are capable of targeting tRNAs in stress-responsive manner. We show that in the absence of ANG, these RNases also promote the production of tiRNAs. Moreover, specific stresses (such as treatment with sodium arsenite) activate cleavage of universal 3’-CCA termini of tRNAs in ANG-independent fashion in living cells. We conclude that multiple RNase A family members are capable of targeting tRNAs in a stress-specific mannerin vivo.
Amygdalostriatal coupling underpins positive but not negative coloring of ambiguous affect
Authors: Kim M. Justin , Mattek Alison M. , Shin Jin
Published: October 2019

Humans routinely integrate affective information from multiple sources. For example, we rarely interpret an emotional facial expression devoid of context. Here, we describe the neural correlates of an affective computation that involves integrating multiple sources, by leveraging the ambiguity and subtle feature-based valence signals found in surprised faces. Using functional magnetic resonance imaging, participants reported the valence of surprised faces modulated by positive or negative sentences. Amygdala activity corresponded to the valence value assigned to each contextually modulated face, with greater activity reflecting more negative ratings. Amygdala activity did not track the valence of the faces or sentences per se. Moreover, the amygdala was functionally coupled with the nucleus accumbens only during face trials preceded by positive contextual cues. These data suggest 1) valence-related amygdala activity reflects the integrated valence values rather than the valence values of each individual component, and 2) amygdalostriatal coupling underpins positive but not negative coloring of ambiguous affect.
Low-dimensional learned feature spaces quantify individual and group differences in vocal repertoires
Authors: Goffinet Jack , Brudner Samuel , Mooney Richard , Pearson John
Published: October 2019

Increases in the scale and complexity of behavioral data pose an increasing challenge for data analysis. A common strategy involves replacing entire behaviors with small numbers of handpicked, domain-specific features, but this approach suffers from several crucial limitations. For example, handpicked features may miss important dimensions of variability, and correlations among them complicate statistical testing. Here, by contrast, we apply the variational autoencoder (VAE), an unsupervised learning method, to learn features directly from data and quantify the vocal behavior of two model species: the laboratory mouse and the zebra finch. The VAE converges on a parsimonious representation that outperforms handpicked features on a variety of common analysis tasks, enables the measurement of moment-by-moment vocal variability on the timescale of tens of milliseconds in the zebra finch, provides strong evidence that mouse ultrasonic vocalizations do not cluster as is commonly believed, and captures the similarity of tutor and pupil birdsong with qualitatively higher fidelity than previous approaches. In all, we demonstrate the utility of modern unsupervised learning approaches to the quantification of complex and high-dimensional vocal behavior.
Among-individual diet variation within a lake trout ecotype: lack of stability of niche use
Authors: Chavarie L. , Howland K.L. , Harris L.N. , Gallagher C.P. , Hansen M.J. , Tonn W.M. , Muir A.M. , Krueger C.C.
Published: October 2019

In a polymorphic species, stable differences in resource use are expected among ecotypes, and homogeneity in resource use is predicted within an ecotype. Yet, using a broad resource spectrum has been identified as a strategy for fishes living in unproductive northern environments, where food is patchily distributed and ephemeral. We investigated whether individual specialization of trophic resources occurred within the generalist piscivore ecotype of lake trout from Great Bear Lake, Canada, reflective of a form of diversity. Four distinct dietary patterns of resource use within the lake trout ecotype were detected from fatty acid composition, with some variation linked to spatial patterns within Great Bear Lake. Feeding habits of different groups within the ecotype were not associated with detectable morphological or genetic differentiation, suggesting that behavioral plasticity caused the trophic differences. A low level of genetic differentiation was detected between exceptionally large-sized individuals and other individuals. Investigating a geologically young system that displays high levels of intraspecific diversity and focusing on individual variation in diet suggested that individual trophic specialization can occur within an ecotype. The characterization of niche use among individuals, as done in this study, is necessary to understand the role that individual variation can play at the beginning of differentiation processes.
CellProfiler: A fit tool for image analysis in droplet microfluidics
Authors: Bartkova Simona , Vendelin Marko , Sanka Immanuel , Pata Pille , Scheler Ott
Published: October 2019

Droplet microfluidic assays are rapidly gaining popularity as the result of the ability to manipulate and monitor single biological molecules, individual cells or small populations of bacteria in pico- and nanoliter droplets, with high sensitivity, precision and accuracy in a high-throughput manner. Nonetheless, there is a demand for user-friendly and low-cost droplet analysis technology. In this article we meet this demand with free open-source software CellProfiler (CP). To illustrate the competence of CP as a droplet analysis tool, we show droplet digital quantification of viable fluorescent bacteria.
Population coding of strategic variables during foraging in freely-moving macaques
Authors: Shahidi Neda , Parajuli Arun , Franch Melissa , Schrater Paul , Wright Anthony , Pitkow Xaq , Dragoi Valentin
Published: October 2019

Until now it has been difficult to examine the neural bases of foraging in naturalistic environments because previous approaches have relied on restrained animals performing trial-based foraging tasks. Here, we allowed unrestrained monkeys to freely interact with concurrent reward options while we wirelessly recorded population activity in dorsolateral prefrontal cortex (dlPFC). The animals decided when and where to forage, based on whether their prediction of reward was fulfilled or violated. This prediction was not solely based on a history of reward delivery, but also on the understanding that waiting longer improves the chance of reward. The decoded reward dynamics were continuously represented in a subspace of the high-dimensional population activity, and predicted animal’s subsequent choice better than the true experimental variables and as well as the raw neural activity. Our results indicate that monkeys’ foraging strategy is based on a cortical model of reward dynamics as animals freely explore their environment.
Neto-α controls synapse organization and homeostasis at the Drosophila neuromuscular junction
Authors: Han Tae Hee , Vicidomini Rosario , Ramos Cathy Isaura , Wang Qi , Nguyen Peter , Jarnik Michal , Li Moyi , Stawarski Michal , Hernandez Roberto X. , Macleod Gregory T. , Serpe Mihaela
Published: October 2019

Glutamate receptor auxiliary proteins control receptor distribution and function, ultimately controlling synapse assembly, maturation and plasticity. At the Drosophila neuromuscular junction (NMJ), a synapse with both pre- and post-synaptic kainate-type glutamate receptors (KARs), we show that the auxiliary protein Neto evolved functionally distinct isoforms to modulate synapse development and homeostasis. Using genetics, cell biology and electrophysiology we demonstrate that Neto-α functions on both sides of the NMJ. In muscle, Neto-α limits the size of the postsynaptic receptors field. In motor neurons, Neto-α controls neurotransmitter release in a KAR-dependent manner. Furthermore, Neto-α is both required and sufficient for the presynaptic increase in neurotransmitter release in response to reduced postsynaptic sensitivity. This KAR-independent function of Neto-α is involved in activity-induced cytomatrix remodeling. We propose that Drosophila ensured NMJ functionality by acquiring two Neto isoforms with differential expression patterns and activities.
AutoTuner: High fidelity, robust, and rapid parameter selection for metabolomics data processing
Authors: McLean Craig , Kujawinski Elizabeth B.
Published: October 2019

Untargeted metabolomics experiments provide a snapshot of cellular metabolism, but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly-used parameter selection tool, and compared the resulting parameters’ influence on the quality of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection, and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100-1000X speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.
Neuropeptide Y expression defines a novel class of GABAergic projection neuron in the inferior colliculus
Authors: Silveira Marina A. , Anair Justin D. , Beebe Nichole L. , Mirjalili Pooyan , Schofield Brett R. , Roberts Michael T.
Published: October 2019

Located in the midbrain, the inferior colliculus (IC) integrates information from numerous auditory nuclei and is an important hub for sound processing. Despite its importance, little is known about the molecular identity and functional roles of defined neuron types in the IC. Using a multifaceted approach in mice, we found that neuropeptide Y (NPY) expression identifies a major class of inhibitory neurons, accounting for approximately one-third of GABAergic neurons in the IC. Retrograde tracing showed that NPY neurons are principal neurons that can project to the medial geniculate nucleus. In brain slice recordings, many NPY neurons fired spontaneously, suggesting that NPY neurons may drive tonic inhibition onto postsynaptic targets. Morphological reconstructions showed that NPY neurons are stellate cells, and the dendrites of NPY neurons in the tonotopically-organized central nucleus of the IC cross isofrequency laminae. Immunostaining confirmed that NPY neurons express NPY, and we therefore hypothesized that NPY signaling regulates activity in the IC. In crosses between Npy1rcreand Ai14 Cre-reporter mice, we found that NPY Y1receptor (Y1R)-expressing neurons are glutamatergic and were broadly distributed throughout the rostro-caudal extent of the IC. In whole-cell recordings, application of a high affinity Y1R agonist led to hyperpolarization in most Y1R-expressing IC neurons. Thus, NPY neurons represent a novel class of inhibitory principal neurons that are well poised to use GABAergic and NPY signaling to regulate the excitability of circuits in the IC and auditory thalamus.
New analysis framework incorporating mixed mutual information and scalable Bayesian networks for multimodal high dimensional genomic and epigenomic cancer data
Authors: Wang Xichun , Branciamore Sergio , Gogoshin Grigoriy , Ding Shuyu , Rodin Andrei S
Published: October 2019

We propose a novel two-stage analysis strategy to discover candidate genes associated with the particular cancer outcomes in large multimodal genomic cancers databases, such as The Cancer Genome Atlas (TCGA). During the first stage, we use mixed mutual information to perform variable selection; during the second stage, we use scalable Bayesian network (BN) modeling to identify candidate genes and their interactions. Two crucial features of the proposed approach are (i) the ability to handle mixed data types (continuous and discrete, genomic, epigenomic, etc.), and (ii) a flexible boundary between the variable selection and network modeling stages --- the boundary that can be adjusted in accordance with the investigators’ BN software scalability and hardware implementation. These two aspects result in high generalizability of the proposed analytical framework. We apply the above strategy to three different TCGA datasets (LGG, Brain Lower Grade Glioma; HNSC, Head and Neck Squamous Cell Carcinoma; STES, Stomach and Esophageal Carcinoma), linking multimodal molecular information (SNPs, mRNA expression, DNA methylation) to two clinical outcome variables (tumor status and patient survival). We identify 11 candidate genes, of which 6 have already been directly implicated in the cancer literature. One novel LGG prognostic factor suggested by our analysis, methylation of TMPRSS11F type II transmembrane serine protease, presents intriguing direction for the follow-up studies.
Tubulin recycling limits cold tolerance
Authors: Li Gabriella , Moore Jeffrey K.
Published: October 2019

Although cold temperatures have long been used to depolymerize microtubules, how temperature specifically affects the polymerization and depolymerization activities of tubulin proteins and how these lead to changes in microtubule networks in cells has not been established. We investigated these questions in budding yeast, an organism found in diverse environments and therefore predicted to exhibit dynamic microtubules across a broad range of temperatures. We measured the dynamics of GFP-labeled microtubules in living cells and found that lowering the temperature from 37°C to 10°C decreased the rates of both polymerization and depolymerization, decreased the amount of polymer assembled before catastrophes and decreased the frequency of microtubule emergence from nucleation sites. Lowering to 4°C caused rapid loss of almost all microtubule polymer. We provide evidence that these effects on microtubule dynamics may be explained in part by changes in the co-factor-dependent conformational dynamics of tubulin proteins. Ablation of tubulin-binding co-factors further sensitizes cells and their microtubules to low temperatures, and we highlight a specific role for TBCB/Alf1 in microtubule maintenance at low temperatures. Finally, we show that inhibiting the maturation cycle of tubulin by using a point mutant in β-tubulin confers hyper-stable microtubules at low temperatures, rescues the requirement for TBCB/Alf1, and improves the cold tolerance of the yeast. Together, these results reveal an unappreciated step in the tubulin cycle in cells and suggest that this step may be a key limiting factor in the thermal tolerance of organisms.
Loan officer rotation and credit access: evidence from Madagascar
Authors: Sarfo Yaw , Musshoff Oliver , Weber Ron
Published: October 2019

Purpose

With exclusive data from a commercial microfinance institution (MFI) in Madagascar, the purpose of this paper is to investigate if loan officer rotation (change of loan officer) has an effect on credit access (loan approval) in rural and in urban areas. The authors further analyze how the frequency of loan officer rotation affects credit access in rural and in urban areas.

Design/methodology/approach

The authors apply propensity score matching to compare credit access between loan applicants who experienced loan officer rotation and loan applicants who experienced no loan officer rotation in rural and in urban areas.

Findings

Results show that loan officer rotation has a positive and statistically significant effect on credit access. The authors observe further that loan officer rotation has a different effect on credit access in rural and in urban areas. Whilst rural loan applicants who experienced loan officer rotation are more likely to have credit access, urban loan applicants show no statistically significant effect of loan officer rotation on credit access. For the frequency effect on credit access, the authors observe that one loan officer rotation has a positive and statistically significant effect on credit access whereas results are mixed for two loan officer rotations.

Research limitations/implications

Even though the authors can show that loan officer rotation can improve credit access to loan applicants, especially in rural areas, the conditions in Madagascar are unique. Therefore, results need to be verified in other countries and institutional contexts.

Practical implications

From the perspective of MFI, the authors recommend that the management of MFI needs to provide better tools to loan officers to improve on the evaluation of agricultural loan products or standardize the assessment of agricultural loan products to improve on lending decisions. Further, if applicable, the authors recommend that MFI should consider using credit worthiness assessment procedures which rely less on loan officer’s judgment for loan evaluation, such as automated systems. From the perspective of loan applicants, the authors recommend that loan applicants should request for a change of loan officer if they experience successive loan applications rejection.

Originality/value

To the authors’ knowledge, this paper is the first to provide empirical evidence on the effect and frequency of loan officer rotation on credit access in Sub-Sahara Africa, and Madagascar, in particular.
Factors and their relationships in measuring the progress of open government
Authors: Park Eun G. , Oh Wankeun
Published: October 2019

Purpose

The purpose of this paper is to examine the main factors influencing government openness, develop a global government openness index (GGOI) for assessing the progress of government openness and investigate how the factors contribute to the advancement of open government by individual countries and country groups by income.

Design/methodology/approach

This study identifies the four factors and adopts them into four variables for making GGOI: accountability (ACC), citizen participation and freedom (CPF), transparency (TRA) and information and communication technology (ICT). To calculate GGOI, panel data for 134 countries from 2006 to 2015 were used.

Findings

GGOI scores constantly improved with an annual growth rate of 2.09 percent. Countries with high ACC values tend to have high TRA scores, resulting in high GGOI scores. While the differences in ACC and TRA were steady over the period, ICT increased the most in all groups. To boost ICT performance as a channel to support other variables, middle-income countries should make further effort for citizens to use ICT capabilities toward enhancing the levels of CPF and TRA.

Research limitations/implications

This study presents a global picture of the advancement of open government and provides insights into specific areas that can be diagonalized.

Practical implications

The GGOI could be used as a useful assessment tool to measure the progress of government openness in countries and implement policies and action plans for improving government openness.

Originality/value

The GGOI covers the areas related to legal, administrative, participatory and technological factors and provides the factors’ inter-relationships for the composition of GGOI.
Cross-border cooperation and urban change in the Trinational Agglomeration Basel
Authors: Fernández Marín Silvia
Published: October 2019

Purpose

The geographic space of the old Trinational Agglomeration Basel is a complex area where municipalities (and urban systems) belonging to three different countries meet, and part of a paradigmatic scenario where former and recent cross-border cooperation structures and practices are opening opportunities for joint development. The purpose of this paper is to analyse how organisation and spatial relations are being transformed in this context and if there exist barriers, focusing on Weil am Rhein (Germany), Basel (Switzerland) and Saint-Louis and Huningue (France), which converge in the heart of the Agglomeration.

Design/methodology/approach

The paper is structured in two parts. The first one is a theoretical exploration of the evolution and extent of cross-border cooperation structures and practices affecting the area. The second one focuses on urban transformation and intertwining resulting from this environment, exploring it through analytical work and cartographies for the 1985–2010 period. In this study, three categories are considered: transport networks, morphology and land use.

Findings

Results suggest that cooperation structures are bringing opportunities for the interweaving of neighbouring border urban spaces. However, significant limitations due to regulatory and spatial inheritances and economic constraints, among others, persist. The analysed space continued evidencing barriers and over-simplified areas at the end of the period studied.

Originality/value

The research offers a not-so-frequent, but necessary, perspective of border urban systems as complex scenarios: not only nodes of interaction but also inhabited spaces. It provides insights into border urban development and original cross-border cartography, giving clues on planning in singular environments.
Barriers vs potentials
Authors: Hegazy Iman El-Sayed Hossam , Hegazy Ossama El-Sayed Hossam
Published: October 2019

Purpose

In 2017, 50 percent of Syrian refugee applications in Egypt were submitted by females. However, a suitable integration strategy for this target group remains obscure since the available approaches focus mainly on male integration. That is due to the assumption that women refugees are mere followers to men who socially and economically dominate the families in the Middle East. Accordingly, the integration of the Syrian women refugees in society, as well as in the market, proceeds spontaneously without clear visions and therefore with delays. The paper aims to discuss this issue.

Design/methodology/approach

To methodologically understand the circumstances of the aforementioned group expert, focused and narrative “episode interviews” have been conducted. Alexandria, Egypt’s second capital, is the research case study as well as the researchers’ hometown. Thus, it allows following a “descriptive comparative analysis” process between the three Alexandrian districts, with different urban fabric: “Al-Nkhil Agamy” gated community, “El-Asafra/Sidi Becher” informal settlement and “New Borg El-Arab” new city.

Findings

Yet, it is unknown what criteria the Syrian women refugees set for choosing their accommodation. Similarly, the obstacles they encounter, especially the ones preventing their integration, are ambiguous. Even their daily life, which might give insights into the barriers they face, due to their status, is unclear. These are the gaps this paper tackles, in addition to the refugees’ immaterial cultural impact in the host society.

Originality/value

Finally, but also importantly, the topic has been seldom researched in Alexandria, in comparison with Cairo. Therefore, this paper aims at qualitatively hearing of the Syrian refugees’ voices in order to enhance their societal interaction and coexistence in Alexandria.
Risk and benefit perceptions related to wine consumption and how it influences consumers’ attitude and behavioural intentions in India
Authors: Gupta Vikas , Sajnani Manohar
Published: October 2019

Purpose

The purpose of this paper is to discover the numerous risk and benefit perceptions involved in the patrons’ purchase and consumption decisions related to wine in India. It will also recognise and find out the motives behind the consumers’ drinking patterns and attitude towards wine, which affect their overall behavioural intentions (word of mouth and repurchase intentions).

Design/methodology/approach

Data were collected using a structured survey questionnaire from the 375 wine patrons in Delhi. Exploratory factor analysis was used in which the risk (five) and benefit (two) factors related to wine consumption were verified on a factor model using 25 constructs. It was a two-phase process in which the measurement model, with six constructs and 18 measurement items, were measured, trailed by the structural model. A conceptual framework was used to illustrate the relationships amongst the variables and was empirically verified.

Findings

The findings revealed that the risk and benefit perceptions of the wine patrons are not only interlinked but are also accountable for their fluctuations in attitudes. In the factorial analysis, it was discovered that perceived benefit factors, i.e. value for money and convenience, are accountable for positively affecting the attitudes of patrons towards the wines. The results also specify that an increase in benefit perception or decrease in risk perception will positively transform the patrons’ attitude towards wine.

Originality/value

Although a few studies have been done to find out the risk/benefit perceptions of wine consumers in the developed countries (i.e. USA, France, UK, etc.) but this will be the first attempt to find out how the consumption patterns and purchase decisions of wine consumers are affected in developing countries like India. Moreover, it will help the stakeholders to align their wine products as per the needs and demands of the patrons.