bluuebunny/crossref_metadata_2025 huggingface dataset:
Persistence in the fine-scale distribution and spatial aggregation of fishing
Authors: Hintzen Niels T , Aarts Geert , Rijnsdorp Adriaan D
Published: September 2018

High-resolution vessel monitoring (VMS) data have led to detailed estimates of the distribution of fishing in both time and space. While several studies have documented large-scale changes in fishing distribution, fine-scale patterns are still poorly documented, despite VMS data allowing for such analyses. We apply a methodology that can explain and predict effort allocation at fine spatial scales; a scale relevant to assess impact on the benthic ecosystem. This study uses VMS data to quantify the stability of fishing grounds (i.e. aggregated fishing effort) at a microscale (tens of meters). The model links effort registered at a large scale (ICES rectangle; 1° longitude × 0.5° latitude, ˜3600 km2) to fine spatial trawling intensities at a local scale (i.e. scale matching gear width, here 24 m). For the first time in the literature, the method estimates the part of an ICES rectangle that is unfavourable or inaccessible for fisheries, which is shown to be highly stable over time and suggests higher proportions of inaccessible grounds for either extremely muddy or courser substrates. The study furthermore shows high stability in aggregation of fishing, where aggregation shows a positive relationship with depth heterogeneity and a negative relationship with year-on-year variability in fishing intensity.
Atrial fibrillation in immigrants under the age of 45 y in Sweden
Authors: Wändell Per , Carlsson Axel C , Li Xinjun , Gasevic Danijela , Ärnlöv Johan , Holzmann Martin J , Sundquist Jan , Sundquist Kristina
Published: September 2018

Aim

To study association between country of birth and risk of first-onset atrial fibrillation (AF) in first- and second-generation immigrants to Sweden under 45 y of age.

Methods

The study population included all individuals (n = 3 248 457) under the age of 45 y in Sweden, including immigrants (n = 722 249). AF was defined as first registered diagnosis in the National Patient Register. Association between country of birth and risk of AF was assessed by Cox regression, calculating HRs and 95% CIs, using Swedish-born individuals as referents. All models were stratified by sex, and in different models were adjusted for age, area of residence in Sweden, educational level, marital status, neighbourhood socioeconomic status and co-morbidity(ies).

Results

A higher fully adjusted HR of incident AF was found in the total sample of first-generation immigrants, 1.44 (95% CI 1.35 to 1.54), in males born in Denmark, Lebanon and Iraq, and in females born in Turkey and Iraq. Lower HRs were found in male and female immigrants from Latin America and Iran, and female immigrants from Finland. Among second-generation immigrants, the fully adjusted HR was significantly lower, 0.70 (95% CI 0.58 to 0.83).

Conclusions

Clinicians may show a greater awareness of AF in some groups of younger immigrants to enable early diagnosis.
Is the use of Stereotactic Electroencephalography Safe and Effective in Children? A Meta-Analysis of the use of Stereotactic Electroencephalography in Comparison to Subdural Grids for Invasive Epilepsy Monitoring in Pediatric Subjects
Authors: Sacino Matthew F , Huang Sean S , Schreiber John , Gaillard William D , Oluigbo Chima O
Published: September 2018

BACKGROUND

Stereoelectroencephalography (SEEG) is an alternative addition to subdural grids (SDG) in invasive extra-operative monitoring for medically refractory epilepsy. Few studies exist on the clinical efficacy and safety of these techniques in pediatric populations.

OBJECTIVE

To provide a comparative quantitative summary of surgical complications and postoperative seizure freedom associated with invasive extra-operative presurgical techniques in pediatric patients.

METHODS

The systematic review was conducted following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). A literature search was conducted utilizing Ovid Medline, Embase, Pubmed, and the Cochrane database.

RESULTS

Fourteen papers with a total of 697 pediatric patients undergoing invasive SDG monitoring and 9 papers with a total of 277 pediatric patients undergoing SEEG monitoring were utilized in the systemic review. Cerebral spinal fluid (CSF) leaks were the most common adverse event in the SDG studies (pooled prevalence 11.9% 95% confidence interval [CI] 5.7-23.3). There was one case of CSF leak in the SEEG studies. Intracranial hemorrhages (SDG: 10.7%, 95% CI 5.3-20.3; SEEG: 2.9%, 95% CI –0.7 to 10.8) and infection (SDG: 10.8%, 95% CI 6.7-17) were more common in the SDG studies reviewed. At the time of the last postoperative visit, a greater percentage of pediatric patients achieved seizure freedom in the SEEG studies (SEEG: 66.5%, 95% CI 58.8-73.4; SDG: 52.1%, 95% CI 43.0-61.1).

CONCLUSION

SEEG is a safe alternative to SDG and should be considered on an individual basis for selected pediatric patients.
Increased 30-Day Mortality Associated With Carbapenem-Resistant Enterobacteriaceae in Children
Authors: Chiotos Kathleen , Tamma Pranita D , Flett Kelly B , Karandikar Manjiree V , Nemati Koorosh , Bilker Warren B , Zaoutis Theoklis , Han Jennifer H
Published: September 2018

In this multicenter study, we identified an increased risk of 30-day mortality among hospitalized children with carbapenem-resistant Enterobacteriaceae (CRE) isolated from clinical cultures compared with those with carbapenem-susceptible Enterobacteriaceae. We additionally report significant variation in antibiotic treatment for children with CRE infections with infrequent use of combination therapy.
Effects of two equine digestive aid supplements on hindgut health1
Authors: Johnson Alexa C B , Rossow Heidi A
Published: September 2018

Gastrointestinal disease is the number one killer of horses. Little is known about the maintenance of microbes in the equine hindgut and how to distinguish a healthy gut in a live horse. Utilization of internal and external digestibility markers and starch fermentation has been extensively studied in ruminants and is the basis for research conducted on horses. The aims of this study were to investigate the effects of two equine feed digestive aid supplements on hindgut health (HGH) as reflected in fecal pH and digestibility and to compare and validate DM digestibility measurements through the use of internal and external markers such as chromium oxide (CR), lignin (Lig), indigestible ADF (iADF), indigestible NDF (iNDF), and indigestible lignin (iLig). Nine mature Quarter horses (six geldings, three mares) were used in a crossover design, three feeding periods of 17 d (51 d total), using three treatments: control, no feed additive (CON), Smartpak (SP; Plymouth, MA), or Platinum Performance (PP; Buellton, CA). Both SP and PP contained a strain of Lactobacillus, whereas SP further supplied mannanoligosaccharides (MOS) and fructooligosaccharides (FOS) and PP supplied Saccharomyces boulardii. Within the 17-d period, horses were offered orchard grass hay and sweet cob grain and the assigned treatment daily and four CR cookies to deliver 8 g/d of CR for the last 7 d of each period. Total feces were collected from 15 to 17 d. Feed and fecal samples were dried, ground, and sent to ANALAB (Fulton, IL) for nutrient analysis. Duplicate samples of feed and feces were placed in ruminally cannulated cows for in situ determination of iADF, iNDF, and iLig to estimate digestibility. Estimated CR fecal output, CR DMI, and DM digestibilities were evaluated using the root mean square prediction error percentage of the observed mean (RMSPE), concordance correlation coefficient (CCC), and Nash–Sutcliffe efficiency methods. Marker predictive ability tests showed iADF to have the least amount of bias with the smallest RMSPE (4%), largest CCC (0.43), and the largest amount of random bias (error of dispersion = 0.45). Supplementation of PP decreased CR DM digestibility (P < 0.02). Smartpak increased fecal pH (P < 0.09), but PP had no effect on fecal pH. Therefore, SP had a beneficial effect on HGH that is believed to be due to MOS and FOS.
Single Sided Deaf Cochlear Implant Users in the Difficult Listening Situation: Speech Perception and Subjective Benefit
Authors: Prejban David A. , Hamzavi Jafar-Sasan , Arnoldner Christoph , Liepins Rudolfs , Honeder Clemens , Kaider Alexandra , Gstöttner Wolfgang , Baumgartner Wolf-Dieter , Riss Dominik
Published: September 2018

Objectives:

Patients with single-sided deafness (SSD) have great difficulties in listening situations which rely on binaural auditory processing. The purpose of this study was to examine to which extent a cochlear implant (CI) can improve speech perception outcomes in various noisy listening environments. Additionally, the ability to use interaural level differences for sound localization and subjective benefit with the CI were assessed.

Methods:

Ten single-sided deaf patients with CI were tested in different loudspeaker configurations with and without the CI. A multi-source noise field (MSNF) with uncorrelated noise from four different directions was used in addition to a setup with the signal from the CI side and noise from the normal-hearing side (SCINNH, azimuth of ±45 degrees). Ten normal-hearing subjects were used as a control for the setup. Speech understanding was measured by an adaptive sentence test (Oldenburg Sentence Test, OLSA) in stationary speech shaped noise and temporally modulated noise to assess the benefit in each listening situation. Sensitivity to interaural level differences was measured in a lateralization experiment. Furthermore, patients completed the Bern Benefit in Single-Sided Deafness (BBSS) questionnaire to assess subjective benefit with the CI.

Results:

An overall average benefit in speech reception threshold (SRT) of 1.6 dB (±0.6 dB standard error of the mean [SEM]) was observed in the binaural listening condition (with CI) in all conditions. In the MSNF setup thresholds improved by 0.4 dB (±0.5 dB SEM) and in the SCINNH configuration by 2.7 dB (±0.7 dB SEM). The choice of masking noise effect also had a significant effect on the SRT outcome. The lateralization performance of the SSD users was on a par with the normal hearing group. BBSS scores reflect the overall benefit with the CI apparent in the speech test results.

Conclusion:

Patients with single-sided deafness do benefit from a CI in difficult listening environments and are able to localize sound based on interaural level differences. Considering these outcomes, cochlear implantation represents a promising treatment option for patients with single-sided deafness.
Superior Canal Dehiscence Involving the Superior Petrosal Sinus: A Novel Classification Scheme
Authors: Sweeney Alex D. , O’Connell Brendan P. , Patel Neil S. , Tombers Nicole M. , Wanna George B. , Lane John I. , Carlson Matthew L.
Published: September 2018

Objectives:

To highlight superior semicircular canal dehiscence (SSCD) involving the superior petrosal sinus (SPS), and to propose a novel classification system for SPS associated SSCD with potential surgical implications.

Study Design:

Multicenter retrospective review.

Setting:

Three tertiary referral centers.

Patients:

All patients diagnosed with SPS associated SSCD (1/2000 to 8/2016). Radiographic findings and clinical symptoms were analyzed.

Intervention:

Surgical repair or observation.

Main Outcome Measure:

Radiographic findings and clinical symptoms were analyzed.

Results:

Thirty-three dehiscences (30 patients) involving the SPS were identified. The average age at the time of presentation was 52.5 years (median, 56.9; range, 4.9–75.3 yr), and 53.3% of patients were men. Three patients had bilateral SPS associated SSCD. The most common associated symptoms at presentation were episodic vertigo (63.6%), subjective hearing loss (60.6%), and aural fullness (57.6%). Four distinct types of dehiscence were identified: class Ia. SSCD involving a single dehiscence into an otherwise normal appearing SPS; class Ib. SSCD involving a single dehiscence into an apparent venous anomaly of the SPS; class IIa. SSCD involving two distinct dehiscences into the middle cranial fossa and the SPS; class IIb. SSCD involving a single confluent dehiscence into the middle cranial fossa and the SPS.

Conclusions:

SSCD involving the SPS represents a small but distinct subset of SSCD cases. This scenario can create a unique set of symptoms and surgical challenges when intervention is sought. Clinical findings and considerations for surgical intervention are provided to facilitate effective diagnosis and management.
Clues to basis of exploratory behaviour of theC. eleganssnout from head somatotropy
Authors: White John
Published: September 2018

Wave propagation during locomotory movements ofCaenorhabditis elegansis constrained to a single dorso/ventral plane. By contrast, the tip of the head (snout) can make rapid exploratory movements in all directions relative to the body axis. These extra degrees of freedom are probably important for animals to seek and identify desirable passages in the interstices of the three-dimensional matrix of soil particles, their usual habitat. The differences in degrees of freedom of movement between snout and body are reflected in the innervation of the musculature. Along the length of the body, the two quadrants of dorsal muscle receive common innervation as do the two quadrants of ventral muscle. By contrast, muscles in the snout have an octagonal arrangement of innervation. It is likely that the exploratory behaviour of the snout is mediated by octant-specific motor and sensory neurons, together with their associated interneurons. The well-defined anatomical structure and neural circuitry of the snout together with behavioural observations should facilitate the implementation of models of the neural basis of exploratory movements, which could lead to an understanding of the basis of this relatively complex behaviour, a behaviour that has similarities to foraging in some vertebrates.

This article is part of a discussion meeting issue ‘Connectome to behaviour: modellingC. elegansat cellular resolution’.
The CD56bright CD62L+ NKG2A+ immature cell subset is dominantly expanded in human cytokine-induced memory-like NK cells
Authors: Jin Juhyun , Ahn Yong-Oon , Kim Tae Min , Keam Bhumsuk , Kim Dong-Wan , Heo Dae Seog
Published: September 2018

Recent studies have revealed immunological memory of NK cells. Short-term in vitro cytokine stimulation also induces NK cell memory, but heterogeneous cell subsets within the cytokine-induced memory-like (CIML) NK cells has not been elucidated. Here we found that the dominant cell subset in human CIML NK cells are immature CD56bright CD62L+cells, and they were selectively expanded CD56bright CD16- CD62L+ NK cells. Although these cells acquired KIR expression after the cytokine stimulation, sustained NKG2A expression inhibits cytotoxicity against HLA-E+ target cells. In contrast, another checkpoint molecule LAG-3 is induced mainly on KIR+ NKG2C+ minor CIML NK cells. Our findings imply targeting NKG2A and LAG-3 should be considered for CIML NK cell-based immunotherapy.
Modular reconfiguration of an auditory-control brain network supports adaptive listening behavior
Authors: Alavash Mohsen , Tune Sarah , Obleser Jonas
Published: September 2018

Speech comprehension in noisy, multi-talker situations poses a challenge. Human listeners differ substantially in the degree to which they adapt behaviorally and can listen successfully under such circumstances. How cortical networks embody this adaptation, particularly at the individual level, is currently unknown. We here explain this adaptation from reconfiguration of brain networks for a challenging listening task (i.e., a novel linguistic variant of the Posner paradigm with concurrent speech) in an age-varying sample of N = 49 healthy adults undergoing resting-state and task fMRI. We here provide evidence for the hypothesis that more successful listeners exhibit stronger task-specific reconfiguration, hence better adaptation, of brain networks. From rest to task, brain networks become reconfigured towards more localized cortical processing characterized by higher topological segregation. This reconfiguration is dominated by the functional division of an auditory and a cingulo-opercular module, and the emergence of a conjoined auditory and ventral attention module along bilateral middle and posterior temporal cortices. Supporting our hypothesis, the degree to which modularity of this fronto-temporal auditory-control network is increased relative to resting state predicts individuals’ listening success in states of divided and selective attention. Our findings elucidate how fine-tuned cortical communication dynamics shape selection and comprehension of speech. Our results highlight modularity of the auditory-control network as a key organizational principle in cortical implementation of auditory spatial attention in challenging listening situations.

Significance Statement

How do brain networks shape our listening behavior? We here develop and test the hypothesis that, during challenging listening situations, intrinsic brain networks are reconfigured to adapt to the listening demands, and thus to enable successful listening. We find that, relative to a task-free resting state, networks of the listening brain show higher segregation of temporal auditory, ventral attention, and frontal control regions known to be involved in speech processing, sound localization, and effortful listening. Importantly, the relative change in modularity of this auditory-control network predicts individuals’ listening success. Our findings shed light on how cortical communication dynamics tune selection and comprehension of speech in challenging listening situations, and suggest modularity as the network principle of auditory spatial attention.
Automated EEG mega-analysis II: Cognitive aspects of event related features
Authors: Bigdely-Shamlo Nima , Touryan Jonathan , Ojeda Alejandro , Kothe Christian , Mullen Tim , Robbins Kay
Published: September 2018

In this paper, we present the results of a large-scale analysis of event-related responses based on raw EEG data from 17 studies performed at six experimental sites associated with four different institutions. The analysis corpus represents 1,155 recordings containing approximately 7.8 million event instances acquired under several different experimental paradigms. Such large-scale analysis is predicated on consistent data organization and event annotation as well as an effective automated pre-processing pipeline to transform raw EEG into a form suitable for comparative analysis. A key component of this analysis is the annotation of study-specific event codes using a common vocabulary to describe relevant event features. We demonstrate that Hierarchical Event Descriptors (HED tags) capture statistically significant cognitive aspects of EEG events common across multiple recordings, subjects, studies, paradigms, headset configurations, and experimental sites. We use representational similarity analysis (RSA) to show that EEG responses annotated with the same cognitive aspect are significantly more similar than those that do not share that cognitive aspect. These RSA similarity results are supported by visualizations that exploit the non-linear similarities of these associations. We apply temporal overlap regression to reduce confounds caused by adjacent events instances and extract time and time-frequency EEG features (regressed ERPs and ERSPs) that are comparable across studies and replicate findings from prior, individual studies. Likewise, we use second-level linear regression to separate effects of different cognitive aspects on these features, across all studies. This work demonstrates that EEG mega-analysis (pooling of raw data across studies) can enable investigations of brain dynamics in a more generalized fashion than single studies afford. A companion paper complements this event-based analysis by addressing commonality of the time and frequency statistical properties of EEG across studies at the channel and dipole level.
Hybrid Automata Library: A modular platform for efficient hybrid modeling with real-time visualization
Authors: Bravo Rafael , Baratchart Etienne , West Jeffrey , Schenck Ryan O. , Miller Anna K. , Gallaher Jill , Gatenbee Chandler D. , Basanta David , Robertson-Tessi Mark , Anderson Alexander R. A.
Published: September 2018

The Hybrid Automata Library (HAL) is a Java Library developed for use in mathematical oncology modeling. It is made of simple, efficient, generic components that can be used to model complex spatial systems. HAL’s components can broadly be classified into: on- and off-lattice agent containers, finite difference diffusion fields, a GUI building system, and additional tools and utilities for computation and data collection. These components are designed to operate independently and are standardized to make them easy to interface with one another. As a demonstration of how modeling can be simplified using our approach, we have included a complete example of a hybrid model (a spatial model with interacting agent-based and PDE components). HAL is a useful asset for researchers who wish to build efficient 1D, 2D and 3D hybrid models in Java, while not starting entirely from scratch. It is available on github at https://github.com/MathOnco/HAL under the MIT License. HAL requires at least Java 8 or later to run, and the Java JDK version 1.8 or later to compile the source code.

1

Author Summary

In this paper we introduce the Hybrid Automata Library (HAL) with the purpose of simplifying the implementation and sharing of hybrid models for use in mathematical oncology. Hybrid modeling is used in oncology to create spatial models of tissue, typically by modeling cells using agent-based techniques, and by modeling diffusible chemicals using partial differential equations (PDEs). HAL’s key components are designed to run agent-based models, PDEs, and visualization. The components are standardized and are completely decoupled, so models can be built with any combination of them. We first explore the philosophy behind HAL, then summarize the components. Lastly we demonstrate how the components work together with an example of a hybrid model, and a walk-through of the code used to construct it. HAL is open-source and will produce identical results on any machine that supports Java 8 and above, making it highly portable. We recommend HAL to modelers interested in spatial dynamics, even those outside of mathematical oncology, as the components are general enough to facilitate a variety of model types. A community page that provides a download link and online documentation can be found at https://halloworld.org [1].
Diversity and composition of methanotroph communities in caves
Authors: Webster Kevin D. , Schimmelmann Arndt , Drobniak Agnieszka , Mastalerz Maria , Lagarde Laura Rosales , Boston Penelope J. , Lennon Jay T.
Published: September 2018

Methane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated that methanotrophs are abundant and contribute to CH4dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98 %) of the samples, including cave sites where CH4concentrations were at or below detection limits (≤ 0.3 ppmv). We identified a core methanotroph community among caves that was comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4concentrations varied. We also observed that methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Last, the relative abundance of methanotrophs was positively correlated with cave-air CH4concentrations suggesting that these microorganisms contribute to CH4flux in subterranean ecosystems.

IMPORTANCE

Recent observations have shown that the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14 % of Earth’s land surface area, and therefore may represent a potentially important, but overlooked CH4sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show that the members of the USC-γclade are dominant in cave communities and can easily disperse through the environment, that methanotroph relative abundance was correlated with local scale mineralogy of soils, and that the relative abundance of methanotrophs was positively correlated with CH4concentrations in cave air.
A tale of two species: human and peafowl interactions in human dominated landscape influence each other’s behaviour
Authors: Paranjpe Dhanashree , Dange Priyanka
Published: September 2018

Wild life is increasingly coming in contact with humans in many parts of the world. Human perception of wild life may be an important factor in population management and conservation practices in urban and semi-urban areas. Human attitude towards bird species may vary from non-violent coexistence to a perception of birds as pests. Based on the data collected from survey interviews, we studied the perceptions of local communities in Rajasthan, India towards Indian Peafowl. Local communities in Rajasthan reported Indian Peafowl as crop pest and this perception varied across seasons. The crop loss incurred due to Indian Peafowl also varied across seasons according to the respondents. Despite reporting peafowls as a crop pest, locals regularly offered grains for them as a traditional practice. Thus, at our study sites locals have mostly positive perception about Indian peafowl around them.

Food provisioning by local human population influenced diet composition and time-budget of Indian Peafowls at food provision and non-provision sites. Sites at which food provisioning was less or absent, peafowl spent more time in walking in search of food and more than half of their diet consisted of natural food. In contrast, the sites at which plenty of grains were available, time spent in walking was significantly less, while time spent in feeding was significantly more; and over 70% of their diet consisted of carbohydrate and protein-rich provisioned grains. Food provisioning changed the benefit: cost ratio (measured as time spent in feeding to time spent in all other behaviours) between provision and non-provision sites. Thus, food provisioning by humans can change feeding ecology of native Indian peafowl populations, while the presence of peafowl in human dominated landscape changes how humans interact with wild life around them.
Genetic correlation between sea age at maturity and iteroparity in Atlantic salmon
Authors: Aykanat Tutku , Ozerov Mikhail , Vähä Juha-Pekka , Orell Panu , Niemelä Eero , Erkinaro Jaakko , Primmer Craig R.
Published: September 2018

Genetic correlations in life history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around thevgll3gene, and we used this opportunity demonstrate that the two traits are genetically correlated around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturingvgll3genotype (EE) compared to fish with the late-maturing genotype(LL). The association had a dominance architecture, although the dominant allele was reversed in the late-maturing group compared to younger groups that stayed only one year at sea before maturation.Post hocanalysis indicated that iteroparous fish with theEEgenotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, while this effect was not detected in fish with theLLgenotype. These results broaden the functional link around thevgll3genome region and help us understand constraints in the evolution of life history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.
The true size of placebo analgesia: Concordant neural and behavioural measures of placebo analgesia during experimental acute pain
Authors: Valentini E , Aglioti SM , Chakrabarti B
Published: September 2018

‘Placebo analgesia’ refers to the reduction of pain following the administration of an inactive treatment. While most clinical trials compare a drug treatment against a placebo to determine the efficacy of the analgesic, most experimental studies of placebo analgesia do not include a real analgesic condition. A direct comparison of placebo against a real analgesic can inform us about the true size of the placebo effect. To this end, we aimed to provide a robust estimate of placebo analgesia by contrasting the effect of pain relief expectation from an inert cream (vaseline) against a real topical analgesic agent (lidocaine) applied on two different limbs and their respective control conditions. Pain reports and electroencephalography (EEG) responses triggered by laser nociceptive stimulation were collected. Forty typical healthy adults were enrolled in a double-blind randomized within-subject study where a standard placebo induction script of verbal suggestions in a sham medical setting was used to enhance the expectation on treatment outcome. In line with the earliest studies of placebo analgesia, majority (30 of 40) of participants was placebo responders, i.e. they reported lower pain to the placebo treatment. Placebo responders reported low pain and displayed low laser evoked potentials (LEPs) amplitude for both the analgesic and placebo treatment limbs compared to the respective control limbs. Placebo analgesia correlated positively with the amplitude of the LEPs, thus establishing convergent validity of the findings. This study provides a robust estimate of the neural and behavioural measures of placebo analgesia, in comparison to a real analgesic. These estimates can help inform the quantitative criteria for similar neural and behavioural measures in assessing the effectiveness of a real drug in placebo controlled trials.
Distance-dependent consistency thresholds for generating group-representative structural brain networks
Authors: Betzel Richard F. , Griffa Alessandra , Hagmann Patric , Mišić Bratislav
Published: September 2018

Large-scale structural brain networks encode white-matter connectivity patterns among distributed brain areas. These connection patterns are believed to support cognitive processes and, when compromised, can lead to neurocognitive deficits and maladaptive behavior. A powerful approach for studying the organizing principles of brain networks is to construct group-representative networks from multi-subject cohorts. Doing so amplifies signal to noise ratios and provides a clearer picture of brain network organization. Here, we show that current approaches for generating grouprepresentative networks over-estimate the proportion of short-range connections present in a network and, as a result, fail to match subject-level networks along a wide range of network statistics. We present an alternative approach that preserves the connection-length distribution of individual subjects. Due to this simple modification, the networks generated using this novel approach successfully recapitulate subject-level properties, outperforming all existing approaches by better preserving features that promote integrative brain function rather than segregative. The method developed here holds promise for future studies investigating basic organizational principles and features of largescale structural brain networks.
Chemical signatures of honey bee group membership develop via a socially-modulated innate process
Authors: Vernier Cassondra L. , Krupp Joshua J. , Marcus Katelyn , Hefetz Abraham , Levine Joel D. , Ben-Shahar Yehuda
Published: September 2018

Large social insect colonies exhibit a remarkable ability for recognizing group members via colony-specific cuticular hydrocarbon (CHC) pheromonal signatures. Previous work suggested that in some ant species colony-specific signatures are generated through a “gestalt” mechanism via the passive transfer and homogenization of CHCs across all individual members of the colony. In contrast, we demonstrate that nestmate recognition cues of worker honey bees (Apis mellifera) mature in foragers via a sequence of stereotypic age-dependent quantitative and qualitative chemical transitions, which are driven by intrinsic biosynthetic pathways. Therefore, in contrast to predictions of the “Gestalt” model, nestmate recognition cues in honey bee colonies do not represent a passive “average” signature that is carried and recognized by all colony members. Instead, specific colony members develop the relevant cues via an innately-determined developmental program that can be modulated by colony-specific social environmental factors.
Reduced Medial Frontal Positivity During the Stimulus-Response Interval Precedes Action Errors and Explains Task Deficits in Attention-Deficit Hyperactivity Disorder
Authors: Burwell Scott J. , Makeig Scott , Iacono William G. , Malone Stephen M.
Published: September 2018

Brain mechanisms responsible for errors during cognitive tasks are poorly understood, particularly in adolescents with attention-deficit hyperactivity disorder (ADHD). Using subject-specific multimodal imaging (EEG, MRI, behavior) during flanker task performance by a sample of 94 human adolescents (mean age = 15.5 years, 50% female) with varying degrees of ADHD symptomatology, we examined the degree to which amplitudes of source-resolved event-related potentials (ERPs) from brain independent components within a critical (but often ignored) period in the action selection process, the stimulus-response interval, predicted motor response errors (across trials) and error rates (across individuals). Reduced amplitudes of Frontocentral P3 (peaking at approximately 390 milliseconds in stimulus-locked ERPs) and Pre-Movement Positivity (PMP, peaking at approximately 110 milliseconds pre-response in response-locked ERPs) in projections from posterior medial frontal cortex (pMFC) predicted erroneous responses, and reduced amplitude of PMP predicted a larger participant error rate. After regressing stimulus-from response-locked ERPs, we concluded that errors primarily depended upon response selection processes reflected in PMP amplitude. Finally, mediation analyses showed that smaller PMPs on correct response trials was associated with the higher frequency of errors committed by adolescents with more ADHD symptoms. These results bolster the importance of pMFC in action selection and support the possible value of using PMP as an intervention target to remediate performance deficits in ADHD.
Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity
Authors: Li Pan , Wei Yifan , Mei Miao , Tang Lei , Sun Lei , Huang Wenze , Zhou Jianyu , Zou Chunlin , Zhang Shaojun , Qin Cheng-feng , Jiang Tao , Dai Jianfeng , Tan Xu , Zhang Qiangfeng Cliff
Published: September 2018

Since its outbreak in 2007, Zika virus (ZIKV) has become a global health threat that causes severe neurological conditions. Here we perform a comparativein vivostructural analysis of the RNA genomes of two ZIKV strains to decipher the regulation of their infection at the RNA level. Our analysis identified both known and novel functional RNA structural elements. We discovered a functional long-range intramolecular interaction specific for the Asian epidemic strains, which contributes to their infectivity. Our findings illuminate the structural basis of ZIKV regulation and provide a rich resource for the discovery of RNA structural elements that are important for ZIKV infection.
Embryonic Exposure to Valproic Acid impairs Social Predispositions for Dynamic Cues of Animate Motion in Newly-Hatched Chicks
Authors: Lorenzi Elena , Pross Alessandra , Rosa-Salva Orsola , Versace Elisabetta , Sgadò Paola , Vallortigara Giorgio
Published: September 2018

Predispositions to preferentially orient towards cues associated with social partners, such as face-like stimuli or biological and animate motion, appear to guide social behavior from the onset of life. These predispositions have been documented in several vertebrate species including human neonates, young monkeys and newly-hatched domestic chicks. Human newborns at high familiar risk of Autism Spectrum Disorder (ASD) show a remarkable deficit in their attention toward these predisposed stimuli, either static and dynamic, compared to newborns at low risk. A previous study showed that prenatal exposure to valproic acid (VPA) (that in humans increases the risk of developing ASD) impairs the chicks’ predisposition to approach naturalistic social stimuli that convey static configurations of features (a stuffed hen), without impairing general cognitive and learning abilities. Here we investigated the effect of VPA exposure on another class of social predispositions, i.e. the spontaneous preference to approach self-propelled objects, namely objects that display autonomous changes in speed. We observed that the preference for stimuli displaying autonomous changes in speed was impaired in VPA-compared to vehicle-injected chicks. Our results indicate an effect of VPA on the development of predisposed orienting mechanisms towards dynamic stimuli, that could be used to investigate the molecular and neurobiological mechanisms underlying ASD early symptoms.
Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing
Authors: Rzechorzek Nina M. , Saunders Olivia M. , Hisco Lucy , Schwarz Tobias , Marioni-Henry Katia , Argyle David J. , Schoenebeck Jeffery J. , Freeman Tom C.
Published: September 2018

Background

Structural ‘brain age’ is a valuable but complex biomarker for several brain disorders. The dog is an unrivalled comparator for neurological disease modeling, however brain phenotypic diversity among pedigrees creates computational and statistical challenges.

Methods

We applied unbiased network correlation analysis in dogs to explore complex interactions between brain morphometrics, patient metadata, and neurological disease. Twenty-four parameters measured from each of 286 brain magnetic resonance imaging scans generated 9,438 data points that were used to cluster canine patients according to their brain morphometry profiles. The network was then explored for statistically significant enrichments within breed, sex, age, and diagnostic categories.

Findings

Morphometric comparisons revealed an advanced ‘aged-brain’ profile in the Boxer breed, consisting of a small brain length, width, and volume, combined with ventriculomegaly. Key features of this profile were paralleled in neutered female dogs which, relative to un-neutered females, had an 11-fold greater risk of developing primary brain tumours. Enrichment analysis confirmed that Boxers and geriatric individuals were enriched for brain tumour diagnoses, despite a lack of geriatric Boxers within the cohort.

Interpretation

These findings suggest that accelerated brain ageing might contribute to tumour risk in Boxers and may be influenced by oestrogen deficiency — a risk factor for dementia and brain tumours in humans. We propose that morphometric features of brain ageing in dogs, like humans, might better predict neurological disease risk than a patient’s chronological age.

Funding

Wellcome Trust Integrated Training Fellowship for Veterinarians (096409/Z/11/Z to N.M.R) and an MSD Animal Health Connect Bursary (to O.M.S.).
Revealing the critical regulators of cell identity in the mouse cell atlas
Authors: Suo Shengbao , Zhu Qian , Saadatpour Assieh , Fei Lijiang , Guo Guoji , Yuan Guo-Cheng
Published: September 2018

Recent progress in single-cell technologies has enabled the identification of all major cell types in mouse. However, for most cell types, the regulatory mechanism underlying their identity remains poorly understood. By computational analysis of the recently published mouse cell atlas data, we have identified 202 gene regulatory networks whose activities are highly variable across different cell types, and more importantly, predicted a small set of essential regulators for each of over 800 cell types in mouse for the first time. Systematic validation by automated literature- and data-mining provides strong additional support for our predictions. Thus, these predictions serve as a valuable resource that would be useful for the broad biological community. Finally, we have built a user-friendly, interactive, web-portal to enable users to navigate this mouse cell network atlas.
FitHiChIP: Identification of significant chromatin contacts from HiChIP data
Authors: Bhattacharyya Sourya , Chandra Vivek , Vijayanand Pandurangan , Ay Ferhat
Published: September 2018

Here we describeFitHiChIP(github.com/ay-lab/FitHiChIP), a computational method for identifying chromatin contacts among regulatory regions such as en-hancers and promoters from HiChIP/PLAC-seq data. FitHiChIP jointly models the non-uniform coverage and genomic distance scaling of HiChIP data, captures previously validated enhancer interactions for several genes includingMYCandTP53, and recovers contacts genome-wide that are supported by ChIA-PET, pro-moter capture Hi-C and Hi-C data. FitHiChIP also provides a framework for differential contact analysis as showcased in a comparison of HiChIP data we have generated for two distinct immune cell types.
Heterogeneity of Sonic Hedgehog response dynamics and fate specification in single neural progenitors
Authors: Xiong Fengzhu , Tentner Andrea R. , Nandagopal Sandy , Hiscock Tom W. , Huang Peng , Megason Sean G.
Published: September 2018

During neural tube patterning, a gradient of Sonic hedgehog (Shh) signaling specifies ventral progenitor fates. The cellular response to Shh is processed through a genetic regulatory network (GRN) to specify distinct fate decisions. This process integrates Shh response level, duration and other inputs and is affected by noise in signaling and cell position. How reliably Shh response profile predicts the fate choice of a single cell is unclear. Here we use live imaging to track neural progenitors in developing zebrafish and quantify both Shh and fate reporters in single cells over time. We found that there is significant heterogeneity between Shh response and fate choice in single cells. We quantitatively modeled reporter intensities to obtain single cell response levels over time and systematically evaluated their correlation with cell fate specification. Motor neuron progenitors (pMN) exhibit a high degree of variability in their Shh responses, which is particularly prominent in the posterior neural tube where the Shh response dynamics are similar to those of the more ventrally fated lateral floor plate cells (LFPs). Our results highlight the precision limit of morphogen-interpretation GRNs in small and dynamic target cell fields.
Cell type-specific complement expression from healthy and diseased retinae
Authors: Pauly Diana , Schäfer Nicole , Grassmann Felix , Pfaller Anna M. , Straub Tobias , Weber Bernhard H. F. , Hauck Stefanie M. , Grosche Antje
Published: September 2018

Retinal degeneration is associated with complement system activation, but retinal sources of complement are unknown. Here, we describe the human and murine complement transcriptomes of Müller cells, microglia/macrophages, vascular cells, neurons and retinal pigment epithelium (RPE) in health and disease. All cell populations expressedc1s, c3, cfb, cfp, cfhandcfi. Murine Müller cells contributed the highest amount of complement activators (c1s, c3, cfb). RPE mainly expressedcfh,whilecfiandcfptranscripts were most abundant in neurons. The main complement negative regulator in the human retina wascfi, whilecfhdominated in the murine retina. Importantly, the expression ofc1s, cfb, cfp, cfiincreased and that ofcfhdecreased with aging. Impaired photoreceptor recycling led to an enhancedc3expression in RPE and to a reducedcfiexpression in microglia/macrophages. Expression of complement components was massively upregulated after transient retinal ischemia in murine microglia, Müller cells and RPE. The individual signature of complement expression in distinct murine and human retinal cell types indicates a local, well-orchestrated regulation of the complement system in both species.
Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in non-model species
Authors: Plese Bruna , Rossi Maria Eleonora , Kenny Nathan James , Taboada Sergi , Koutsouveli Vasiliki , Riesgo Ana
Published: September 2018

Mitochondrial resources are of known utility to many fields of phylogenetic, population and molecular biology. Their combination of faster and slower-evolving regions and high copy number enables them to be used in many situations where other loci are unsuitable, with degraded samples and after recent speciation events.

The advent of next-generation sequencing technologies (and notably the Illumina platform) has led to an explosion in the number of samples that can be studied at transcriptomic level, at relatively low cost. Here we describe a robust pipeline for the recovery of mitochondrial genomes from these RNA-seq resources. This pipeline can be used on sequencing of a variety of depths, and reliably recovers the protein coding and ribosomal gene complements of mitochondria from almost any transcriptomic sequencing experiment. The complete sequence of the mitochondrial genome can also be recovered when sequencing is performed in sufficient depth. We evidence the efficacy of our pipeline using data from a number of non-model invertebrates of four disparate phyla, namely Porifera, Nemertea, Mollusca and Annelida. Interestingly, among our poriferan data, where microbiological symbionts are known empirically to make mitochondrial assembly difficult, this pipeline proved especially useful.

Our pipeline will allow the recovery of mitochondrial data from a variety of previously-sequenced samples, and add an additional angle of enquiry to future RNA-seq efforts, simplifying the process of mitochondrial genome assembly for even the most recalcitrant clades and adding this data to the scientific record for a range of future uses.