bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron and Iron Technology
Authors: Champion Timothy
Published: March 2018

Iron production began in many parts of Europe during the late Bronze Age. Although initially comparatively rare, production steadily increased in volume and quality, and major centres developed in southern France, Bavaria, Austria, and southern Poland; the discovery of standardized ingots shows the distribution of smelted iron. Blacksmithing techniques improved rapidly, and the processes of cold working, quenching, and annealing were mastered. The transition from bronze to iron for tools and weapons varied regionally, and the role of iron varied from a utilitarian material for tools to an exotic inlay for decoration. By the late Iron Age a full range of tools had been developed, which changed little for many centuries. These harder, sharper, and more durable tools had a major impact on the productive capacity of other industries, including agriculture, but especially woodworking and carpentry. The use of iron nails transformed domestic architecture, the construction of fortifications, and shipbuilding.
Migration
Authors: Fitzpatrick Andrew P.
Published: March 2018

Migration has long been one of the defining themes of the pre-Roman Iron Age in Europe. Classical authors record migrations by Celtic peoples into Italy and Greece in the fourth and third centuries BC and their testimonies are corroborated by archaeological evidence. Much work has focused on these events and on mass migration in particular. As a result the archaeological study of migration and mobility is weakly theorized and the subject has been unfashionable in most recent western European scholarship. However, migration and mobility in the pre-Roman Iron Age took many forms, from individual marriages to the establishment of Greek colonies in western Europe and the mass migration of Germanic peoples in the second and first centuries BC. The reasons for mobility are varied, but the archaeological and historical sources are clear and consistent in showing that migration was a dynamic and important feature of the pre-Roman Iron Age.
The Functional Characterization of Podosphaera xanthii Candidate Effector Genes Reveals Novel Target Functions for Fungal Pathogenicity
Authors: Martínez-Cruz Jesús , Romero Diego , de la Torre Fernando N. , Fernández-Ortuño Dolores , Torés Juan A. , de Vicente Antonio , Pérez-García Alejandro
Published: March 2018

Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits. In a previous study, we determined that P. xanthii expresses approximately 50 Podosphaera effector candidates (PECs), identified based on the presence of a predicted signal peptide and the absence of functional annotation. In this work, we used host-induced gene silencing (HIGS), employing Agrobacterium tumefaciens as a vector for the delivery of the silencing constructs (ATM-HIGS), to identify genes involved in early plant-pathogen interaction. The analysis of seven selected PEC-encoding genes showed that six of them, PEC007, PEC009, PEC019, PEC032, PEC034, and PEC054, are required for P. xanthii pathogenesis, as revealed by reduced fungal growth and increased production of hydrogen peroxide by host cells. In addition, protein models and protein-ligand predictions allowed us to identify putative functions for these candidates. The biochemical activities of PEC019, PEC032, and PEC054 were elucidated using their corresponding proteins expressed in Escherichia coli. These proteins were confirmed as phospholipid-binding protein, α-mannosidase, and cellulose-binding protein. Further, BLAST searches showed that these three effectors are widely distributed in phytopathogenic fungi. These results suggest novel targets for fungal effectors, such as host-cell plasma membrane, host-cell glycosylation, and damage-associated molecular pattern–triggered immunity.
Neuroanesthesiology Update
Authors: Pasternak Jeffrey J. , Lanier William L.
Published: March 2018

We provide a synopsis of innovative research, recurring themes, and novel experimental findings pertinent to the care of neurosurgical patients and critically ill patients with neurological diseases. We cover the following broad topics: general neurosurgery, spine surgery, stroke, traumatic brain injury, monitoring, and anesthetic neurotoxicity.
The “Ideal” Body Weight for Pediatric Gentamicin Dosing in the Era of Obesity: A Population Pharmacokinetic Analysis
Authors: Moffett Brady S. , Kam Charissa , Galati Marianne , Schmees Lindsay , Stitt Gideon A. , Revell Paula A. , Palazzi Debra L.
Published: March 2018

Background:

Obese pediatric patients often require dose reductions when initiating gentamicin therapy. An appropriate method for calculating ideal body weight for dosing gentamicin in pediatric patients has not been validated.

Methods:

A retrospective population pharmacokinetic study was designed and included non-intensive care pediatric patients who received gentamicin and had serum gentamicin concentrations sampled. Actual body weight (ABW), adjusted body weight, and fat-free mass (FFM) were used to describe the pharmacokinetic variables. Descriptive statistical methods were used for the population, and pharmacokinetic analysis occurred with NONMEM (ICON Plc, Dublin, Ireland). Simulation was performed to estimate dosing based on adjustments in body weight.

Results:

A total of 520 patients met inclusion criteria (male 57.3%, mean age 9.6 ± 4.9 years, ABW 38.0 ± 24.3 kg). Obesity was present in 21.3% of the patients and overweight in 15.8%. Gentamicin was administered at 2.17 ± 0.86 mg/kg per dose. A median of 2 (interquartile range, 1–3) gentamicin serum concentrations were sampled at a median 1.8 (interquartile range, 1.1–7.8) hours after a dose. Population pharmacokinetic analysis demonstrated a 2-compartment model with allometrically scaled FFM providing the best fit. Other significant covariates included serum creatinine and age. Simulation demonstrated increased doses per body weight for traditional and once-daily dosing when using FFM for gentamicin dosing.

Conclusions:

FFM should be used to adjust ABW for empirically dosing gentamicin in pediatric patients aged 2–18 years.
Perceptions of Global Warming Among the Poorest Counties in the Southeastern United States
Authors: Kearney Gregory D. , Bell Ronny A.
Published: March 2018

The geographic position and high level of poverty in the southeastern United States are significant risk factors that contribute to the region's high vulnerability to climate change. The goal of this study was to evaluate beliefs and perceptions of global warming among those living in poverty in the poorest counties in the southeastern United States. Results from this project may be used to support public health efforts to increase climate-related messaging to vulnerable and underserved communities. This was an ecological study that analyzed public opinion poll estimates from previously gathered national level survey data (2016). Responses to 5 questions related to beliefs, attitudes, and perceptions of global warming were evaluated. Counties below the national average poverty level (13.5%) were identified among 11 southeastern US states (Alabama, Arkansas, Florida, Georgia, Kentucky, Louisiana, Michigan, North Carolina, South Carolina, Tennessee, Virginia). Student t tests were used to compare public perceptions of global warming among the poorest urban and rural counties with national-level public opinion estimates. Overall, counties below the national poverty level in the southeastern US were significantly less likely to believe that global warming was happening compared with national-level estimates. The poorest rural counties were less likely to believe that global warming was happening than the poorest urban counties. Health care providers and public health leaders at regional and local levels are in ideal positions to raise awareness and advocate the health implications of climate change to decision makers for the benefit of helping underserved communities mitigate and adequately adapt to climate-related threats.
Can Statewide Emergency Department, Hospital Discharge, and Violent Death Reporting System Data Be Used to Monitor Burden of Firearm-Related Injury and Death in Rhode Island?
Authors: Jiang Yongwen , Ranney Megan L. , Sullivan Brian , Hilliard Dennis , Viner-Brown Samara , Alexander-Scott Nicole
Published: March 2018

Context:

National data on the epidemiology of firearm injuries and circumstances of firearm deaths are difficult to obtain and often are nonreliable. Since firearm injury and death rates and causes can vary substantially between states, it is critical to consider state-specific data sources.

Objective:

In this study, we illustrate how states can systematically examine demographic characteristics, firearm information, type of wound, toxicology tests, precipitating circumstances, and costs to provide a comprehensive picture of firearm injuries and deaths using data sets from a single state with relatively low rates of firearm injury and death.

Design:

Cross-sectional study.

Setting:

Firearm-related injury data for the period 2005-2014 were obtained from the Rhode Island emergency department and hospital discharge data sets; death data for the same period were obtained from the Rhode Island Violent Death Reporting System.

Main Outcome Measure:

Descriptive statistics were used. Healthcare Cost and Utilization Project cost-to-charge ratios were used to convert total hospital charges to costs.

Results:

Most firearm-related emergency department visits (55.8%) and hospital discharges (79.2%) in Rhode Island were from assaults; however, most firearm-related deaths were suicides (60.1%). The annual cost of firearm-related hospitalizations was more than $830 000. Most decedents who died because of firearms tested positive for illicit substances. Nearly a quarter (23.5%) of firearm-related homicides were due to a conflict between the decedent and suspect. More than half (59%) of firearm suicide decedents were reported to have had current mental or physical problems prior to death.

Conclusions:

Understanding the state-specific magnitude and patterns (who, where, factors, etc) of firearm injury and death may help inform local injury prevention efforts. States with similar data sets may want to adopt our analyses. Surveillance of firearm-related injury and death is essential. Dissemination of surveillance findings to key stakeholders is critical in improving firearm injury prevention. States that are not part of the National Violent Death Reporting System (NVDRS) could work with their other data sources to obtain a better picture of violent injuries and deaths to make the best use of resources.
Validation of SIMPLE Index for Lupus Disease Activity
Authors: Gandhi Nisarg , Arora Shilpa , Sengupta Mondira , Sequeira Winston , Jolly Meenakshi , Block Joel A.
Published: March 2018

Objective

An easy, quick tool requiring minimal training or health care provider input would potentially have greater uptake for clinical use among rheumatologists and primary care physicians for assessment of disease activity in systemic lupus erythematosus (SLE). SIMPLE (SIMple Disease Assessment forPeople withLupusErythematosus) index is a composite numeric tool that is easy and quick to calculate. We prospectively assessed the performance of the SIMPLE index as a disease activity surrogate against physician-based disease activity measures.

Methods

Ninety-nine consenting patients meeting American College of Rheumatology SLE classification criteria were recruited. Safety of Estrogen in Lupus National Assessment–Systemic Lupus Erythematosus Disease Activity Index (SELENA-SLEDAI), physician global assessment, and SIMPLE index were obtained during routine visits. SIMPLE index is a 17-item patient-reported questionnaire that includes 2 laboratory tests. Health care provider input is needed only to provide laboratory results (normal/abnormal) and confirming patient-reported current use and dosing of glucocorticoids. We performed Spearman test to assess correlation of SIMPLE index with SELENA-SLEDAI and physician global assessment.

Results

Mean age (SD) was 39.7 (12.3) years. The correlation coefficient between SIMPLE index and SELENA-SLEDAI was 0.56 (P= 0.0001), and that between SIMPLE index and physician global assessment was 0.54 (P= 0.0001). In SLE patients without fibromyalgia (FM), the correlation of SIMPLE index with SELENA-SLEDAI and physician global assessment was 0.58 (P= 0.0001) and 0.57 (P= 0.0001), respectively.

Conclusions

SIMPLE index is strongly correlated with formal physician assessments of disease activity in SLE, and correlation was marginally higher among those without FM. SIMPLE index can be performed easily in places with limited physician and laboratory resources.
Fibrous Dysplasia of the Rib Mimicking a Malignant Bone Tumor at SPECT/CT with 99mTc-MDP
Authors: Fournel Ludovic , Rapicetta Cristian , Fraternali Alessandro , Bellafiore Salvatore , Paci Massimiliano , Lococo Filippo
Published: March 2018

We herein report a case of a 43-year-old man with a right 8th-rib bone tumor exhibiting features of malignancy at CT-scan. Considering that a SPECT/CT with 99mTc-MDP showed solitary intense radio-tracer uptake and the inconclusive results from a fine-needle biopsy, surgical en bloc tumor resection was performed. Pathologic analysis revealed a well-limited benign bone lesion (“fibrous rib dysplasia”) composed by a cellular fibrous proliferation. Since benign osseous diseases may present an intense scintigraphic tracer uptake (as in this case), we suggest a certain caution when interpreting the results of SPECT/CT with 99mTc-MDP in order to avoid misdiagnosis and wrong treatments.
Quantifying the relative effects of environmental and direct transmission of norovirus
Authors: Towers S. , Chen J. , Cruz C. , Melendez J. , Rodriguez J. , Salinas A. , Yu F. , Kang Y.
Published: March 2018

Norovirus is a common cause of outbreaks of acute gastroenteritis in health- and child-care settings, with serial outbreaks also frequently observed aboard cruise ships. The relative contributions of environmental and direct person-to-person transmission of norovirus have hitherto not been quantified. We employ a novel mathematical model of norovirus transmission, and fit the model to daily incidence data from a major norovirus outbreak on a cruise ship, and examine the relative efficacy of potential control strategies aimed at reducing environmental and/or direct transmission. The reproduction number for environmental and direct transmission combined isR0tot=7.2[6.1,9.5], and of environmental transmission alone isR0environ=1.6[0.9,2.6]. Direct transmission is overwhelmingly due to passenger-to-passenger contacts, but crew can act as a reservoir of infection from cruise to cruise. This is the first quantification of the relative roles of environmental and direct transmission of norovirus. While environmental transmission has the potential to maintain a sustained series of outbreaks aboard a cruise ship in the absence of strict sanitation practices, direct transmission dominates. We find that intensive promotion of good hand washing practices may prevent outbreaks. Isolation of ill passengers and cleaning are beneficial, but appear to be less efficacious at outbreak control.
Graphene foam as a biocompatible scaffold for culturing human neurons
Authors: D'Abaco Giovanna M. , Mattei Cristiana , Nasr Babak , Hudson Emma J. , Alshawaf Abdullah J. , Chana Gursharan , Everall Ian P. , Nayagam Bryony , Dottori Mirella , Skafidas Efstratios
Published: March 2018

In this study, we explore the use of electrically active graphene foam as a scaffold for the culture of human-derived neurons. Human embryonic stem cell (hESC)-derived cortical neurons fated as either glutamatergic or GABAergic neuronal phenotypes were cultured on graphene foam. We show that graphene foam is biocompatible for the culture of human neurons, capable of supporting cell viability and differentiation of hESC-derived cortical neurons. Based on the findings, we propose that graphene foam represents a suitable scaffold for engineering neuronal tissue and warrants further investigation as a model for understanding neuronal maturation, function and circuit formation.
The effect of ethylene glycol on pore arrangement of anodic aluminium oxide prepared by hard anodization
Authors: Guo Yang , Zhang Li , Han Mangui , Wang Xin , Xie Jianliang , Deng Longjiang
Published: March 2018

The influence of the addition of ethylene glycol (EG) on the pore self-ordering process in anodic aluminium oxide (AAO) membranes prepared by hard anodization (HA) was investigated. It was illustrated that EG has a substantial effect on the pore arrangement of AAO, and it was found that a smaller pore size can be obtained with an EG concentration reaching 20 wt% in aqueous electrolyte. The number of estimated defects of AAO increases significantly with an increase in EG concentration to 50 wt%. Excellent ordering of pores was realized when the samples were anodized in the 30 wt%-EG-containing aqueous electrolyte.
Comparative limb proportions reveal differential locomotor morphofunctions of alligatoroids and crocodyloids
Authors: Iijima Masaya , Kubo Tai , Kobayashi Yoshitsugu
Published: March 2018

Although two major clades of crocodylians (Alligatoroidea and Crocodyloidea) were split during the Cretaceous period, relatively few morphological and functional differences between them have been known. In addition, interaction of multiple morphofunctional systems that differentiated their ecology has barely been assessed. In this study, we examined the limb proportions of crocodylians to infer the differences of locomotor functions between alligatoroids and crocodyloids, and tested the correlation of locomotor and feeding morphofunctions. Our analyses revealed crocodyloids including
Gavialis
have longer stylopodia (humerus and femur) than alligatoroids, indicating that two groups may differ in locomotor functions. Fossil evidence suggested that alligatoroids have retained short stylopodia since the early stage of their evolution. Furthermore, rostral shape, an indicator of trophic function, is correlated with limb proportions, where slender-snouted piscivorous taxa have relatively long stylopodia and short overall limbs. In combination, trophic and locomotor functions might differently delimit the ecological opportunity of alligatoroids and crocodyloids in the evolution of crocodylians.
Sulfur resistance of Ce-Mn/TiO
2
catalysts for low-temperature NH
3
–SCR
Authors: Xu Quan , Yang Wenjing , Cui Shitong , Street Jason , Luo Yan
Published: March 2018

Ce-Mn/TiO
2
catalyst prepared using a simple impregnation method demonstrated a better low-temperature selective catalytic reduction of NO with NH
3
(NH
3
–SCR) activity in comparison with the sol-gel method. The Ce-Mn/TiO
2
catalyst loading with 20% Ce had the best low-temperature activity and achieved a NO conversion rate higher than 90% at 140–260°C with a 99.7% NO conversion rate at 180°C. The Ce-Mn/TiO
2
catalyst only had a 6% NO conversion rate decrease after 100 ppm of SO
2
was added to the stream. When SO
2
was removed from the stream, the catalyst was able to recover completely. The crystal structure, morphology, textural properties and valence state of the metals involving the novel catalysts were investigated using X-ray diffraction, N
2
adsorption and desorption analysis, X-ray photoelectron spectroscopy, scanning electron microscopy and energy dispersive spectroscopy, respectively. The decrease of NH
3
–SCR performance in the presence of 100 ppm SO
2
was due to the decrease of the surface area, change of the pore structure, the decrease of Ce
4+
and Mn
4+
concentration and the formation of the sulfur phase chemicals which blocked the active sites and changed the valence status of the elements.
A longitudinal study of phenotypic changes in early domestication of house mice
Authors: Geiger Madeleine , Sánchez-Villagra Marcelo R. , Lindholm Anna K.
Published: March 2018

Similar phenotypic changes occur across many species as a result of domestication, e.g. in pigmentation and snout size. Experimental studies of domestication have concentrated on intense and directed selection regimes, while conditions that approximate the commensal and indirect interactions with humans have not been explored. We examine long-term data on a free-living population of wild house mice that have been indirectly selected for tameness by regular exposure to humans. In the course of a decade, this mouse population exhibited significantly increased occurrence of white patches of fur and decreased head length. These phenotypic changes fit to the predictions of the ‘domestication syndrome'.
Investigation of the antibiofilm capacity of peptide-modified stainless steel
Authors: Cao Pan , Li Wen-Wu , Morris Andrew R. , Horrocks Paul D. , Yuan Cheng-Qing , Yang Ying
Published: March 2018

Biofilm formation on surfaces is an important research topic in ship tribology and medical implants. In this study, dopamine and two types of synthetic peptides were designed and attached to 304 stainless steel surfaces, aiming to inhibit the formation of biofilms. A combinatory surface modification procedure was applied in which dopamine was used as a coupling agent, allowing a strong binding ability with the two peptides. X-ray photoelectron spectroscopy (XPS), elemental analysis, contact angle measurement and surface roughness test were used to evaluate the efficiency of the peptide modification. An antibiofilm assay against
Staphylococcus aureus
was conducted to validate the antibiofilm capacity of the peptide-modified stainless steel samples. XPS analysis confirmed that the optimal dopamine concentration was 40 µg ml
−1
in the coupling reaction. Element analysis showed that dopamine and the peptides had bound to the steel surfaces. The robustness assay of the modified surface demonstrated that most peptide molecules had bound on the surface of the stainless steel firmly. The contact angle of the modified surfaces was significantly changed. Modified steel samples exhibited improved antibiofilm properties in comparison to untreated and dopamine-only counterpart, with the peptide 1 modification displaying the best antibiofilm effect. The modified surfaces showed antibacterial capacity. The antibiofilm capacity of the modified surfaces was also surface topography sensitive. The steel sample surfaces polished with 600# sandpaper exhibited stronger antibiofilm capacity than those polished with other types of sandpapers after peptide modification. These findings present valuable information for future antifouling material research.
Extreme fertilization bias towards freshly inseminated sperm in a species exhibiting prolonged female sperm storage
Authors: Gasparini Clelia , Daymond Emma , Evans Jonathan P.
Published: March 2018

The storage of sperm by females across successive reproductive cycles is well documented in internal fertilizers, yet the fate of stored sperm when they compete with ‘new’ sperm to fertilize a female's eggs has rarely been considered. This gap in our understanding is likely due to the logistical difficulties of controlling behavioural interactions during or after mating, which in turn may influence how many sperm are inseminated and how stored sperm are ultimately used during successive bouts of sperm competition with freshly inseminated sperm. Here, we use artificial insemination (AI) in guppies (
Poecilia reticulata
), a polyandrous live-bearing poeciliid fish exhibiting prolonged sperm storage by females, to overcome these challenges. The use of AI enables us to control potential differential maternal effects (e.g. behaviourally mediated cryptic female choice) and specifically test for post-copulatory paternity biases that favour either stored or fresh sperm when they compete to fertilize eggs. Our paternity analyses revealed the almost complete dominance of freshly inseminated sperm over stored sperm, supporting previous studies reporting similar patterns following natural matings across successive brood cycles. However, our use of AI, which excluded behavioural interactions between males and females, most likely generated a far stronger pattern of fresh sperm precedence compared with those reported in previous studies, possibly implicating ‘cryptic' forms of selection by females that may sometimes bolster the success of stored sperm.
A networked voting rule for democratic representation
Authors: Hernández Alexis R. , Gracia-Lázaro Carlos , Brigatti Edgardo , Moreno Yamir
Published: March 2018

We introduce a general framework for exploring the problem of selecting a committee of representatives with the aim of studying a networked voting rule based on a decentralized large-scale platform, which can assure a strong accountability of the elected. The results of our simulations suggest that this algorithm-based approach is able to obtain a high representativeness for relatively small committees, performing even better than a classical voting rule based on a closed list of candidates. We show that a general relation between committee size and representatives exists in the form of an inverse square root law and that the normalized committee size approximately scales with the inverse of the community size, allowing the scalability to very large populations. These findings are not strongly influenced by the different networks used to describe the individuals’ interactions, except for the presence of few individuals with very high connectivity which can have a marginal negative effect in the committee selection process.
Inferring forest fate from demographic data: from vital rates to population dynamic models
Authors: Needham Jessica , Merow Cory , Chang-Yang Chia-Hao , Caswell Hal , McMahon Sean M.
Published: March 2018

As population-level patterns of interest in forests emerge from individual vital rates, modelling forest dynamics requires making the link between the scales at which data are collected (individual stems) and the scales at which questions are asked (e.g. populations and communities). Structured population models (e.g. integral projection models (IPMs)) are useful tools for linking vital rates to population dynamics. However, the application of such models to forest trees remains challenging owing to features of tree life cycles, such as slow growth, long lifespan and lack of data on crucial ontogenic stages. We developed a survival model that accounts for size-dependent mortality and a growth model that characterizes individual heterogeneity. We integrated vital rate models into two types of population model; an analytically tractable form of IPM and an individual-based model (IBM) that is applied with stochastic simulations. We calculated longevities, passage times to, and occupancy time in, different life cycle stages, important metrics for understanding how demographic rates translate into patterns of forest turnover and carbon residence times. Here, we illustrate the methods for three tropical forest species with varying life-forms. Population dynamics from IPMs and IBMs matched a 34 year time series of data (albeit a snapshot of the life cycle for canopy trees) and highlight differences in life-history strategies between species. Specifically, the greater variation in growth rates within the two canopy species suggests an ability to respond to available resources, which in turn manifests as faster passage times and greater occupancy times in larger size classes. The framework presented here offers a novel and accessible approach to modelling the population dynamics of forest trees.
The enemy of my enemy is my friend: native pine marten recovery reverses the decline of the red squirrel by suppressing grey squirrel populations
Authors: Sheehy Emma , Sutherland Chris , O'Reilly Catherine , Lambin Xavier
Published: March 2018

Shared enemies may instigate or modify competitive interactions between species. The dis-equilibrium caused by non-native species introductions has revealed that the outcome of such indirect interactions can often be dramatic. However, studies of enemy-mediated competition mostly consider the impact of a single enemy, despite species being embedded in complex networks of interactions. Here, we demonstrate that native red and invasive grey squirrels in Britain, two terrestrial species linked by resource and disease-mediated apparent competition, are also now linked by a second enemy-mediated relationship involving a shared native predator recovering from historical persecution, the European pine marten. Through combining spatial capture–recapture techniques to estimate pine marten density, and squirrel site-occupancy data, we find that the impact of exposure to predation is highly asymmetrical, with non-native grey squirrel occupancy strongly negatively affected by exposure to pine martens. By contrast, exposure to pine marten predation has an indirect positive effect on red squirrel populations. Pine marten predation thus reverses the well-documented outcome of resource and apparent competition between red and grey squirrels.
Assessment of cognitive reserve using near infrared spectroscopy
Authors: Medvedev Andrei V.
Published: March 2018

Cognitive reserve (CR) is the ability to preserve cognitive functions in the presence of brain pathology. One commonly used proxy measure of CR is IQ. In the context of Alzheimer’s disease (AD), patients with higher CR show better cognitive performance relative to brain damage therefore higher CR reduces the risk of dementia. There is a strong need to develop a reliable biomarker of CR given the growing interest in understanding protective brain mechanisms in AD. Recent fMRI studies indicate that frontoparietal network may play an important role in the maintenance of cognitive reserve. The goal of this study was to measure functional connectivity (FC) of the prefrontal cortex using near infrared spectroscopy (NIRS) and to study the relationship of prefrontal FC with cognitive abilities and motoric skills.

We analyzed resting state optical data recorded from prefrontal cortex in 13 healthy individuals who were also assessed by Wechsler Abbreviated Scale of Intelligence (WASI) test and the Purdue Pegboard test (PPT). For each participant, activity of each prefrontal channel was correlated with all other channels and positive correlation coefficients were Fisher-transformed and averaged over all PFC channels giving the Global Functional Connectivity (GFC) of PFC. The resulting GFC number for each individual was then correlated with the corresponding IQ (WASI full score) and the PPT scores.

Prefrontal connectivity was found to positively correlate with IQ while showing the lack of or negative correlation with the Purdue Pegboard subtests. These results demonstrate that the cost-effective and noninvasive NIRS technology can be used to evaluate prefrontal functional connectivity thus providing a neurophysiological measure of cognitive reserve.

E-mail address for correspondence:

am236@georgetown.edu
Comparative analysis of
1.688
satellite DNA on
D. melanogaster
species
subgroup
provides new insights of its pervasive presence throughout both chromatin domains and reveals a recent horizontal transfer event.
Authors: De Lima Leonardo Gomes , Kuhn Gustavo C. S.
Published: March 2018

The
1.688
satellite DNA is present in the genome of
Drosophila
species from the
melanogaster
subgroup and has never been detected in species outside this subgroup. We investigated the presence and evolution of the
1.688
satDNA in all
Drosophila
genomes sequenced so far. Blast searches showed that
1.688
repeats are virtually confined to species from the
melanogaster
subgroup. Phylogenetic analysis of ~6,500 repeats extracted from
D. melanogaster
,
D. simulans
,
D. sechellia
,
D. yakuba
and
D. erecta
revealed the presence of
1.688
family on heterochromatin and euchromatin of all five species. Heterochromatic copies revealed a concerted mode of evolution and a species-specific pattern. Oppositely, euchromatic copies lack species-specific or array-specific pattern. Euchromatic arrays also showed a high number of insertions on 5Kb upstream/downstream of genes and in intronic regions. Unexpectedly, we found an array with at least three full
1.688
tandem repeats in the genome of
D. willistoni
. These repeats were highly similar to the ones present in the chromosome X of
D. melanogaster
, although both species have diverged from each other more than 35Mya, suggesting that
1.688
repeats from the X chromosome of
D. melanogaster
moved to
D. willistoni
by a recent horizontal transfer event.
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
Authors: Liu Qian , Georgieva Daniela C. , Egli Dieter , Wang Kai
Published: March 2018

Background

Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analysis of raw signals. These DNA modifications include naturally occurring modifications such as DNA methylations, as well as modifications that are introduced by DNA damage or through synthetic modifications to one of the four standard nucleotides.

Methods

To improve the performance of detecting DNA modifications, especially synthetically introduced modifications, we developed a novel computational tool called NanoMod. NanoMod takes raw signal data on a pair of DNA samples with and without modified bases, extracts signal intensities, performs base error correction based on a reference sequence, and then identifies bases with modifications by comparing the distribution of raw signals between two samples, while taking into account of the effects of neighboring bases on modified bases (“neighborhood effects”).

Results

We evaluated NanoMod on simulation data sets, based on different types of modifications and different magnitudes of neighborhood effects, and found that NanoMod outperformed other methods in identifying known modified bases. Additionally, we demonstrated superior performance of NanoMod on an E. coli data set with 5mC (5-methylcytosine) modifications.

Conclusions

In summary, NanoMod is a flexible tool to detect DNA modifications with single-base resolution from raw signals in Nanopore sequencing, and will greatly facilitate large-scale functional genomics experiments in the future that use modified nucleotides.
Distance-dependent changes in courtship song amplitude reflect song state changes
Authors: Suri Harini , Rajan Raghav
Published: March 2018

Many animals increase the amplitude of their vocalizations as distance from a receiver increases. However, behavioral mechanisms underlying this increase remain unclear. Here, we addressed this using head-attached microphones to accurately record song amplitude in male zebra finches while presenting a female at difference distances. We show that individual courtship song syllables either increased (5/13) or decreased their amplitude (4/13) as distance from the female increased. Both increases and decreases were part of more general acoustic changes that resulted in properties more similar to those of “undirected” songs typically produced in the absence of a female. Increasing distance also reduced female responses to songs and absence of female responses reduced courtship song amplitude and number of songs per bout. These data suggest a simple behavioral mechanism where distance-dependent song amplitude changes reflect song state changes. Such state changes may be a general mechanism underlying distance-dependent amplitude changes in other organisms.
Dual roles of electrostatic-steering and conformational dynamics in the binding of calcineurin’s intrinsically-disordered recognition domain to calmodulin
Authors: Sun Bin , Cook Eric C. , Creamer Trevor P. , Kekenes-Huskey Peter M.
Published: March 2018

calcineurin (CaN) is a serine/threonine phosphatase that regulates a variety of physiological and pathophysiological processes in mammalian tissue. The CaN regulatory domain (RD) is responsible for regulating the enzyme’s phosphatase activity, and is believed to be highly-disordered when inhibiting CaN, but undergoes a disorderto-order transition upon diffusion-limited binding with the regulatory protein calmodulin (CaM). The prevalence of polar and charged amino acids in the regulatory domain (RD) suggests electrostatic interactions are involved in mediating CaM binding, yet the lack of atomistic-resolution data for the bound complex has stymied efforts to probe how the RD sequence controls its conformational ensemble and long-range attractions contribute to target protein binding. In the present study, we investigated via computational modeling the extent to which electrostatics and structural disorder cofacilitate or hinder CaM/CaN association kinetics. Specifically, we examined several RD constructs that contain the CaM binding region (CAMBR) to characterize the roles of electrostatics versus conformational diversity in controlling diffusion-limited association rates, via microsecond-scale molecular dynamics (MD) and Brownian dynamic (BD) simulations. Our results indicate that the RD amino acid composition and sequence length influence both the dynamic availability of conformations amenable to CaM binding, as well as long-range electrostatic interactions to steer association. These findings provide intriguing insight into the interplay between conformational diversity and electrostatically-driven protein-protein association involving CaN, which are likely to extend to wide-ranging diffusion-limited processes regulated by intrinsically-disordered proteins.
The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
Authors: Choudhary Kumari Sonal , Mih Nathan , Monk Jonathan , Kavvas Erol , Yurkovich James T. , Sakoulas George , Palsson Bernhard O.
Published: March 2018

Two-component systems (TCSs) consist of a histidine kinase and a response regulator. Here, we evaluated the conservation of the AgrAC TCS among 149 completely sequenced S. aureus strains. It is composed of four genes: agrBDCA. We found that: i) AgrAC system (agr) was found in all but one of the 149 strains; ii) The agr positive strains were further classified into four agr types based on AgrD protein sequences, iii) the four agr types not only specified the chromosomal arrangement of the agr genes but also the sequence divergence of AgrC histidine kinase protein, which confers signal specificity, iv) the sequence divergence was reflected in distinct structural properties especially in the transmembrane region and second extracellular binding domain, and v) there was a strong correlation between the agr type and the virulence genomic profile of the organism. Taken together, these results demonstrate that bioinformatic analysis of the agr locus leads to a classification system that correlates with the presence of virulence factors and protein structural properties.
Deficiency of the E3 Ubiquitin Ligase RBCK1 Causes Diffuse Brain Polyglucosan Accumulation and Neurodegeneration
Authors: Sullivan Mitchell A. , Nitschke Felix , Chown Erin E. , DiGiovanni Laura F. , Chown Mackenzie , Perri Ami M. , Mitra Sharmistha , Zhao Xiaochu , Ackerley Cameron A. , Israelian Lori , Ahonen Saija , Wang Peixiang , Minassian Berge A.
Published: March 2018

Glycogen synthesis is vital, malstructure resulting in precipitation and accumulation into neurotoxic polyglucosan bodies (PBs). One well-understood mechanism of PB generation is glycogen branching enzyme deficiency (GBED). Less understood is Lafora disease (LD), resulting from absence of the glycogen phosphatase laforin or the E3 ubiquitin ligase malin, and accumulation of hyperphosphorylated PBs. LD afforded first insight that glycogen sphericity depends on more than adequate branching activity. Unexpectedly, deficiencies of the Linear Ubiquitin Chain Assembly Complex (LUBAC) components RBCK1 and HOIP result in PBs in muscle tissues. Here we analyzed nervous system phenotypes of mice lacking RBCK1 and find profuse PB accumulations in brain and spinal cord with extensive neurodegeneration and neurobehavioral deficits. Brain glycogen in these mice is characterized by long chains and hyperphosphorylation, similar to LD. Like in LD, glycogen synthase and branching enzyme are unaltered. Regional PB distribution mirrors LD and not GBED. Perisynaptic PB localization is unlike LD or GBED. The results indicate that RBCK1 is part of a system supplementing laforin-malin in regulating glycogen architecture including in unique neuronal locales.
Pyridine 1:1 adducts of urea (Z′ = 1) and thiourea (Z′ = 8)
Authors: Strey Mark , Jones Peter G.
Published: March 2018

During our studies of urea and thiourea adducts, we noticed that no adducts with unsubstituted pyridine had been structurally investigated. The 1:1 adduct of pyridine and urea, C5H5N·CH4N2O, crystallizes in the P21/c space group with Z = 4. The structure is of a standard type for urea adducts, whereby the urea molecules form a ribbon, parallel to the a axis, consisting of linked R
2
2(8) rings, and the pyridine molecules are attached to the periphery of the ribbon by bifurcated (N—H...)2N hydrogen bonds. The 1:1 adduct of pyridine and thiourea, C5H5N·CH4N2S, crystallizes in the P21/n space group, with Z = 32 (Z′ = 8). The structure displays similar ribbons to those of the urea adduct. There are two independent ribbons parallel to the b axis at z ≃ 0 and 1 \over 2, and three at z ≃ 1 \over 4 and 3 \over 4; the latter are crosslinked to form a layer structure by additional long N—H...S interactions, which each formally replace one branch of a bifurcated hydrogen-bond system.
A three-dimensional twofold interpenetrated cobalt(II) MOF containing a flexible carboxylate-based ligand: synthesis, structure and magnetic properties
Authors: An Yan-Yan , Lu Li-Ping , Zhu Miao-Li
Published: March 2018

The design and synthesis of coordination polymers (CPs) have attracted much interest due to the intriguing diversity of their architectures and topologies. The functional solid catena-poly[μ2-aqua-triaqua{μ4-5-[4-carboxyphenoxy)methyl]benzene-1,3-dicarboxylato}{μ3-5-[4-carboxyphenoxy)methyl]benzene-1,3-dicarboxylato}dicobalt(II)], [Co2(C16H10O7)2(H2O)4]
n
or [Co2(HL)2(μ2-H2O)(H2O)3]
n
, was synthesized successfully by self-assembly of CoII ions with 5-[(4-carboxyphenoxy)methyl]isophthalic acid (H3
L). The title compound was obtained under hydrothermal conditions and exhibits a twofold interpenetrated three-dimensional skeleton with hms 3,5-conn topology according to the cluster representation for valence-bonded metal–organic frameworks (MOFs). It has been characterized by single-crystal X-ray diffraction, IR spectroscopy, powder X-ray diffraction (PXRD), thermogravimetric analysis and susceptibility measurements. The antiferromagnetic coupling between adjacent CoII centres occurs via superexchange through the ligands.
[1-(Pyrazin-2-yl)ethylidene]hydrazine: a new multitopic ligand for the design of hybrid molecular frameworks
Authors: Kassim Muhammad Arif , Yassin Ubaidullah H. M. , Tan Ai Ling , Usman Anwar , Hamid Malai Haniti S. A.
Published: March 2018

Hydrazones and their derivatives are closely related to imine compounds and are potential antimicrobial agents. They have also found application in supramolecular chemistry as multitopic ligands to link multiple metal centres for the design of hybrid molecular frameworks. The molecule of the title compound, C6H8N4, consists of an imine linkage with an N—N bond length of 1.3540 (14) Å. This asymmetric compound is nearly planar and adopts an E configuration about the azomethine C=N double bond. In the solid state, there are two intermolecular N—H...N interactions that interconnect the molecules into a two-dimensional network. The three-dimensional arrangement of the crystal packing is further stabilized by intermolecular π–π interactions interconnecting the centroids of the heterocyclic rings.
Involvement of conformational isomerism in the complexity of the crystal network of 1-(4-nitrophenyl)-1H-1,3-benzimidazole derivatives driven by C—H...A (A = NO2, Npy and π) and orthogonal Npy...NO2 and ONO...Csp
2 interactions
Authors: García-Aranda Mónica I. , Gómez-Castro Carlos Z. , García-Báez Efrén V. , Gómez Yolanda Gómez y , Castrejón-Flores José L. , Padilla-Martínez Itzia I.
Published: March 2018

A detailed structural analysis of the benzimidazole nitroarenes 1-(4-nitrophenyl)-1H-1,3-benzimidazole, C13H9N3O2, (I), 1-(4-nitrophenyl)-2-phenyl-1H-1,3-benzimidazole, C19H13N3O2, (II), and 2-(3-methylphenyl)-1-(4-nitrophenyl)-1H-1,3-benzimidazole, C20H15N3O2, (III), has been performed. They are nonplanar structures whose crystal arrangement is governed by Csp
2—H...A (A = NO2, Npy and π) hydrogen bonding. The inherent complexity of the supramolecular arrangements of compounds (I) (Z′ = 2) and (II) (Z′ = 4) into tapes, helices and sheets is the result of the additional participation of π–{\pi}_{{\rm NO}_2}} and n–π* (n = O and Npy; π* = Csp
2 and {\rm N}_{{\rm NO}_2}}) interactions that contribute to the stabilization of the equi-energetic conformations adopted by each of the independent molecules in the asymmetric unit. In contrast, compound (III) (Z′ = 1) is self-paired, probably due to the effect of the steric demand of the methyl group on the crystal packing. Theoretical ab initio calculations confirmed that the presence of the arene ring at the benzimidazole 2-position increases the rotational barrier of the nitrobenzene ring and also supports the electrostatic nature of the orthogonal ONO...Csp
2 and Npy...NO2 interactions.
A need to help: stories of emergent behaviour from the scene of accident
Authors: Kvarnlöf Linda
Published: March 2018

Purpose

The purpose of this paper is to investigate how spontaneous volunteers make sense of their actions at the scene of accident. More specifically, this paper focusses on the moral aspects of this sense-making process in terms of how spontaneous volunteers justify their own and others actions at the scene of accident through moral positioning.

Design/methodology/approach

This is done through a narrative analysis of volunteers’ retrospective stories from the scene of accident. The empirical material consists of interviews with 12 witnesses to traffic accidents.

Findings

The narrative analysis identifies two central storylines: the interviewees frame their own and others’ actions through norms of how one should act, and the interviewees frame their own actions by presenting themselves as a person of a certain type, sometimes positioned against an real or imaginative “other”.

Originality/value

Disaster sociologists have long argued that emergent behaviours and norms are one of the phenomena distinguishing disasters from everyday emergencies. However, as this paper shows, emergent behaviours and norms are also present at everyday emergencies such as traffic accidents where spontaneous volunteers can play an important role by filling the void before the arrival of emergency services.