bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient Safety Incidents in Primary Care Dentistry in England and Wales: A Mixed-Methods Study
Authors: Ensaldo-Carrasco Eduardo , Sheikh Asiyah , Cresswell Kathrin , Bedi Raman , Carson-Stevens Andrew , Sheikh Aziz
Published: September 2018

Background

In recent decades, there has been considerable international attention aimed at improving the safety of hospital care, and more recently, this attention has broadened to include primary medical care. In contrast, the safety profile of primary care dentistry remains poorly characterized.

Objectives

We aimed to describe the types of primary care dental patient safety incidents reported within a national incident reporting database and understand their contributory factors and consequences.

Methods

We undertook a cross-sectional mixed-methods study, which involved analysis of a weighted randomized sample of the most severe incident reports from primary care dentistry submitted to England and Wales’ National Reporting and Learning System. Drawing on a conceptual literature-derived model of patient safety threats that we previously developed, we developed coding frameworks to describe and conduct thematic analysis of free text incident reports and determine the relationship between incident types, contributory factors, and outcomes.

Results

Of 2000 reports sampled, 1456 were eligible for analysis. Sixty types of incidents were identified and organized across preoperative (40.3%, n = 587), intraoperative (56.1%, n = 817), and postoperative (3.6%, n = 52) stages. The main sources of unsafe care were delays in treatment (344/1456, 23.6%), procedural errors (excluding wrong-tooth extraction) (227/1456; 15.6%), medication-related adverse incidents (161/1456, 11.1%), equipment failure (90/1456, 6.2%) and x-ray related errors (87/1456, 6.0%). Of all incidents that resulted in a harmful outcome (n = 77, 5.3%), more than half were due to wrong tooth extractions (37/77, 48.1%) mainly resulting from distraction of the dentist. As a result of this type of incident, 34 of the 37 patients (91.9%) examined required further unnecessary procedures.

Conclusions

Flaws in administrative processes need improvement because they are the main cause for patients experiencing delays in receiving treatment. Checklists and standardization of clinical procedures have the potential to reduce procedural errors and avoid overuse of services. Wrong-tooth extractions should be addressed through focused research initiatives and encouraging policy development to mandate learning from serious dental errors like never events.
Geometric models reveal behavioral and neural signatures of transforming naturalistic experiences into episodic memories
Authors: Heusser Andrew C. , Fitzpatrick Paxton C. , Manning Jeremy R.
Published: September 2018

The mental contexts in which we interpret experiences are often person-specific, even when the experiences themselves are shared. We developed a geometric framework for mathematically characterizing the subjective conceptual content of dynamic naturalistic experiences. We model experiences and memories as trajectories through word embedding spaces whose coordinates reflect the universe of thoughts under consideration. Memory encoding can then be modeled as geometrically preserving or distorting the shape of the original experience. We applied our approach to data collected as participants watched and verbally recounted a television episode while undergoing functional neuroimaging. Participants’ recountings all preserved coarse spatial properties (essential narrative elements), but not fine spatial scale (low-level) details, of the episode’s trajectory. We also identified networks of brain structures sensitive to these trajectory shapes. Our work provides insights into how we preserve and distort our ongoing experiences when we encode them into episodic memories.
Amplifying the redistribution of somato-dendritic inhibition by the interplay of three interneuron types
Authors: Hertäg Loreen , Sprekeler Henning
Published: September 2018

GABAergic interneurons play an important role in shaping the activity of excitatory pyramidal cells (PCs). How the various inhibitory cell types contribute to neuronal information processing, however, is not resolved. Here, we propose a functional role for a widespread network motif consisting of parvalbumin-(PV), somatostatin-(SOM) and vasoactive intestinal peptide (VIP)-expressing interneurons. Following the idea that PV and SOM interneurons control the distribution of somatic and dendritic inhibition onto PCs, we suggest that mutual inhibition between VIP and SOM cells translates weak inputs to VIP interneurons into large changes of somato-dendritic inhibition of PCs. Using a computational model, we show that the neuronal and synaptic properties of the circuit support this hypothesis. Moreover, we show that the SOM-VIP motif allows transient inputs to persistently switch the circuit between two processing modes, in which top-down inputs onto apical dendrites of PCs are either integrated or canceled.
Wide-field imaging of cortical neuronal activity with red-shifted functional indicators during motor task execution
Authors: Montagni Elena , Resta Francesco , Conti Emilia , Scaglione Alessandro , Pasquini Maria , Micera Silvestro , Allegra Mascaro Anna Letizia , Pavone Francesco Saverio
Published: September 2018

Intracellular concentration of free calcium ions in neuronal populations can be longitudinally evaluated by using fluorescent protein indicators, called genetically encoded calcium indicators (GECIs). GECIs with long emission wavelengths are particularly attractive for deep tissue microscopy in vivo, and have the additional advantage of avoiding spectral overlap with commonly used neuronal actuators like Channelrhodopsin.

Here we investigated the performances of selected red-shifted GECIs through an ex vivo characterization and in vivo imaging of cortical mouse activity during motor task execution. Cortical neurons were infected with adeno-associated virus (AAV) expressing one of the red GECI variants (jRCaMP1a, jRCaMP1b, jRGECO1a, jRGECO1b). First we characterized the transfection in terms of extension and intensity using wide-field fluorescence microscopy. Next, we used RCaMP1a to analyse the cortical neuronal activity during motor behaviour. To that end, wide-field fluorescent microscopy and a robotic device for motor control were combined for simultaneous recording of cortical neuronal-activity, force applied and forelimb position during task execution.

Our results show that jRCaMP1a has sufficient sensitivity to monitor in vivo neuronal activity over multiple functional areas, and can be successfully used to perform longitudinal imaging in awake mice.
Characterisation of the HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread
Authors: Nazziwa Jamirah , Faria Nuno , Chaplin Beth , Rawizza Holly , Dakum Patrick , Abimiku Alash’le , Charurat Man , Ndembi Nicaise , Esbjörnsson Joakim
Published: September 2018

Nigeria has been reported to have the highest number of AIDS-related deaths in the world. In this study, we aimed to determine the HIV-1 genetic diversity and phylodynamics in Nigeria. We analysed 1442 HIV-1polsequences collected 1999-2014 from four geopolitical zones in Nigeria. Phylogenetic analysis showed that the main circulating strains was the circulating recombinant strain (CRF) 02_AG (44% of the analysed sequences), subtype G (8%), and CRF43_02G (16%); and that these were introduced in Nigeria in the 1960s, 1970s and 1980s, respectively. The number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. We also found a significant number of unique recombinant forms (22.7%). The majority of those were recombinants between two or three of the main circulating strains. Seven of those recombinants may represent novel CRFs. Finally, phylogeographic analysis suggested multiple occasions of HIV-1 transmissions between Lagos and Abuja (two of the main cities in Nigeria), that HIV-1 epidemic started in these cities, and then dispersed into rural areas.

IMPORTANCE

Nigeria has the second largest HIV-1 epidemic in the world with the highest number of AIDS-related deaths. The few previous reports have focused on local HIV-1 subtype/CRF distributions in different Nigerian regions, and the molecular epidemiology of HIV-1 in Nigeria as a whole is less well characterized. In this study, we describe the HIV-1 spatiotemporal dynamics of the five dominating transmission clusters representing the main characteristics of the epidemiology. Our results may contribute to inform prevention strategies against further spread of HIV-1 in Nigeria.
Uromonitor®as a novel sensitive and specific urine-based test for recurrence surveillance of patients with non-muscle invasive bladder cancer
Authors: Sampaio Cristina , Batista Rui , Peralta Pedro , Conceição Paulo , Sismeiro Amílcar , Prazeres Hugo , Vinagre João , Soares Paula
Published: September 2018

Bladder cancer is the most frequent malignancy of the urinary system and is ranked the seventh most diagnosed cancer in men worldwide. About 70-75% of all newly diagnosed patients with bladder cancer will present disease confined to the mucosa or submucosa, the non-muscle invasive bladder cancer (NMIBC) subtype. Of those, approximately 70% will recur after transurethral resection (TUR). Due to this high rate of recurrence, patients are submitted to an intensive follow-up program that should be maintained throughout many years, or even throughout life, resulting in an expensive follow-up, with cystoscopy being the most cost-effective procedure for NMIBC screening. Currently, the gold standard procedure for detection and follow-up of NMIBC is based on the association of cystoscopy and urine cytology. As cystoscopy is a very invasive approach, over the years, many different non-invasive (both in serum and urine samples) assays have been developed in order to search genetic and protein alterations related to the development, progression and recurrence of bladder cancer.TERTpromoter mutations andFGFR3hotspot mutations are the most frequent somatic alterations in bladder cancer and constitute the most reliable biomarkers for bladder cancer. Based on these findings, an ultra-sensitive assay called Uromonitor®was developed that corresponds to a urine-based assay capable of detecting trace amounts of the two most common alterations in NMIBC,TERTpromoter andFGFR3mutation, in urine samples. The Uromonitor®test was performed in a cohort of 72 patients, firstly diagnosed with bladder cancer and under surveillance for NMIBC, to access its sensitivity and specificity in the detection of NMIBC recurrence. Uromonitor®was shown to be highly sensitive and specific in detecting recurrence of bladder cancer in patients under surveillance of non-muscle invasive bladder cancer.
Improving The Performance Of The Amber Rna Force Field By Tuning The Hydrogen-Bonding Interactions
Authors: Kührová Petra , Mlýnský Vojtěch , Zgarbová Marie , Krepl Miroslav , Bussi Giovanni , Best Robert B. , Otyepka Michal , Šponer Jiří , Banáš Pavel
Published: September 2018

Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields,ffs), RNAffshave persisting deficiencies, which hamper their utilization in quantitatively accurate simulations. Previous studies have shown that at least two salient problems contribute to difficulties in description of free-energy landscapes of small RNA motifs: (i) excessive stabilization of the unfolded single-stranded RNA ensemble by intramolecular base-phosphate and sugar-phosphate interactions, and (ii) destabilization of the native folded state by underestimation of stability of base pairing. Here, we introduce a generalffterm (gHBfix) that can selectively fine-tune non-bonding interaction terms in RNAffs, in particular the H-bonds. gHBfix potential affects the pair-wise interactions between all possible pairs of the specific atom types, while all other interactions remain intact, i.e., it is not a structure-based model. In order to probe the ability of the gHBfix potential to refine theffnon-bonded terms, we performed an extensive set of folding simulations of RNA tetranucleotides and tetraloops. Based on these data we propose particular gHBfix parameters to modify the AMBER RNAff. The suggested parametrization significantly improves the agreement between experimental data and the simulation conformational ensembles, although our currentffversion still remains far from being flawless. While attempts to tune the RNAffsby conventional reparametrizations of dihedral potentials or non-bonded terms can lead to major undesired side effects as we demonstrate for some recently publishedffs, gHBfix has a clear promising potential to improve theffperformance while avoiding introduction of major new imbalances.
Theory of measurement for site-specific evolutionary rates in amino-acid sequences
Authors: Sydykova Dariya K. , Wilke Claus O.
Published: September 2018

In the field of molecular evolution, we commonly calculate site-specific evolutionary rates from alignments of amino-acid sequences. For example, catalytic residues in enzymes and interface regions in protein complexes can be inferred from observed relative rates. While numerous approaches exist to calculate amino-acid rates, it is not entirely clear what physical quantities the inferred rates represent and how these rates relate to the underlying fitness landscape of the evolving proteins. Further, amino-acid rates can be calculated in the context of different amino-acid exchangeability matrices, such as JTT, LG, or WAG, and again it is not well understood how the choice of the matrix influences the physical inter-pretation of the inferred rates. Here, we develop a theory of measurement for site-specific evolutionary rates, by analytically solving the maximum-likelihood equations for rate inference performed on sequences evolved under a mutation–selection model. We demonstrate that for realistic analysis settings the measurement process will recover the true expected rates of the mutation–selection model if rates are measured relative to a naïve exchangeability matrix, in which all exchangeabilities are equal to 1/19. We also show that rate measurements using other matrices are quantitatively close but in general not mathematically equivalent. Our results demonstrate that insights obtained from phylogenetic-tree inference do not necessarily apply to rate inference, and best practices for the former may be deleterious for the latter.

Significance Statement

Maximum likelihood inference is widely used to infer model parameters from sequence data in an evolutionary context. One major challenge in such inference procedures is the problem of having to identify the appropriate model used for inference. Model parameters usually are meaningful only to the extent that the model is appropriately specified and matches the process that generated the data. However, in practice, we don’t know what process generated the data, and most models in actual use are misspecified. To circumvent this problem, we show here that we can employ maximum likelihood inference to make defined and meaningful measurements on arbitrary processes. Our approach uses misspecification as a deliberate strategy, and this strategy results in robust and meaningful parameter inference.
On the post-glacial spread of human commensal Arabidopsis thaliana: journey to the east
Authors: Hsu Che-Wei , Lo Cheng-Yu , Lee Cheng-Ruei
Published: September 2018

With the availability of more sequenced genomes, our understanding of the evolution and demographic history of the model plant Arabidopsis thaliana is rapidly expanding. Here we compile previously published data to investigate global patterns of genetic variation. While the Southeast African accessions were reported to be the most divergent among worldwide populations, we found accessions from Yunnan, China to be genetically close to the sub-Saharan accessions. Our further investigation of worldwide chloroplast genomes identified several deeply diverged haplogroups existing only in Eurasia, and the African populations have lower variation in many haplogroups they shared with the Eurasian populations. Bayesian inferences of chloroplast demography showed that representative haplogroups of Africa exhibited long-term stable population size, suggesting recent selective sweep or bottleneck is not able to explain the lower chloroplast variation in Africa. Taken together, these patterns cannot be easily explained by a single out-of-Africa event. Several Eurasian chloroplast haplogroups had rapid population growth since 10 kya, presumably reflecting the recent expansion of the weedy non-relicts across Eurasia. Our demographic analysis on a chromosomal region un-affected by relict introgression also suggested the European, Central Asian, and Chinese Yangtze populations diverged no earlier than 15 kya, in contrast to previous estimates of 45 kya inferred from whole genome that likely contains relict admixture. The most recent expansion is observed in the Yangtze population of China less than 2000 years ago. Similar to Iberia, the western end of non-relict expansion reported in our previous study, in this eastern end of Eurasia we find clear traces of gene flow between the Yangtze non-relicts and the Yunnan relicts. Genes under strong selection and previously suggested to contribute to adaptation in the Yangtze valley are enriched for traces of relict introgression, especially those related with biotic and immune responses. The results suggest the ability of non-relicts to obtain locally adaptive alleles through admixture with relicts is an important factor contributing to the rapid expansion across the environmental gradients spanning the eastern to the western coast of Eurasia.
Tau filaments from multiple cases of sporadic and inherited Alzheimer’s disease adopt a common fold
Authors: Falcon Benjamin , Zhang Wenjuan , Schweighauser Manuel , Murzin Alexey G. , Vidal Ruben , Garringer Holly J. , Ghetti Bernardino , Scheres Sjors H.W. , Goedert Michel
Published: September 2018

The ordered assembly of tau protein into abnormal filaments is a defining characteristic of Alzheimer’s disease (AD) and other neurodegenerative disorders. It is not known if the structures of tau filaments vary within, or between, the brains of individuals with AD. We used a combination of electron cryo-microscopy (cryo-EM) and immuno-gold negative-stain electron microscopy (immuno-EM) to determine the structures of paired helical filaments (PHFs) and straight filaments (SFs) from the frontal cortex of 17 cases of typical AD (15 sporadic and 2 inherited) and 2 cases of atypical AD (posterior cortical atrophy). The high-resolution structures of PHFs and SFs from the frontal cortex of 3 cases of typical AD, 2 sporadic and 1 inherited, were determined by cryo-EM. We also used immuno-EM to study the PHFs and SFs from a number of cortical and subcortical brain regions. PHFs outnumbered SFs in all AD cases. By cryo-EM, PHFs and SFs were made of two C-shaped protofilaments with a combined cross-β/β-helix structure, as described previously for a case of AD. The higher resolution structures obtained here showed two additional amino acids at each end of the protofilament structure. The immuno-EM findings, which established the presence of repeats 3 and 4, but not repeats 1 and 2, of tau in the filament cores of all AD cases and brain regions thereof, were consistent with the cryo-EM results. These findings show that there is no significant variation in tau filament structures between individuals with AD. This knowledge will be crucial for understanding the mechanisms that underlie tau filament formation and for developing novel diagnostics and therapies.
Karyopherin Kap114p regulates TATA-binding protein-mediated transcription
Authors: Liao Chung-Chi , Shankar Sahana , Ahmed Golam Rizvee , Hsia Kuo-Chiang
Published: September 2018

Gene expression is regulated by nuclear accessibility of transcription factors controlled by transport receptors and competitive inhibitors. Multiple karyopherin-βs (Kap-βs) facilitate nuclear import of yeast TATA-binding protein (yTBP). However, only Kap114p suppresses temperature-sensitive yTBP mutations, suggesting Kap114p executes undefined non-transport functions. We show that yTBP preferably binds Kap114p with an affinity three orders of magnitude higher than other Kap-βs facilitating yTBP nuclear import. Our crystal structure of Kap114p reveals an extensively negatively-charged concave surface, accounting for high-affinity basic-protein binding. Furthermore, we biochemically demonstrate that two intra-HEAT-repeat inserts act as regulatory TBP-binding domains carried by TBP-associated factor 1 (TAF1-TAND), suppressing binding of yTBP with DNA and the transcription factor IIA. Remarkably, dual-knockout of Kap114 and TAF1-TAND in yeast synergistically suppresses cell growth. Our study reveals that Kap114p has a dual function that modulates the nuclear localization and activity of yTBP, illuminating how the nuclear transport machinery regulates yTBP-mediated transcription.
SCDT: Detecting somatic CNVs of low chimeric ratio in cf-DNA
Authors: Qian Zhaoyang , Wang Xiaofeng , Shi Chang , Han Rui , Wang Yaoshen , Zhu Hongmei
Published: September 2018

Motivation

Sequencing of cell-free DNA (cf-DNA) has enabled Noninvasive Prenatal Testing (NIPT) and”liquid biopsy” of cancers. However, while the aneuploidy and point mutations were focused on by most of NITP and liquid biopsy studies, detecting sub-chromosome CNVs that affect a few to dozens of megabases was rarely reported, likely attributable to the difficulty in accurately identifying them, especially for those present in a small fraction of cf-DNA.

Results

We developed a somatic CNV detection tool (SCDT), for detecting sub-chromosome CNVs in cf-DNA using whole genome sequencing (WGS) data or off-target reads in target sequencing data. Additional to using control samples for correcting genome position specific bias, two GC correction steps were performed, which regressed GC content of DNA fragments and that of genome bins, respectively. After GC correction, the coefficients of variation of copy ratios approximated the lower boundary of theoretical values, suggesting removing of almost all systematic errors. Finally, CNVs were detected by a piecewise least squares fitting based segmentation algorithm, which outperformed other segmentation methods. We applied SCDT on simulated and real maternal plasma samples, and target cf-DNA sequencing of 118 normal individuals and 240 cancer patients, and demonstrated high sensitivity and specificity.

Availability

SCDT is available at https://github.com/Martiantian/Somatic_cnv_detect_tool.

Contact

zhuhongmei@genomics.cn

Supplementary Information

Supplementary data are available at Bioinformatics online
Computational mechanisms of curiosity and goal-directed exploration
Authors: Schwartenbeck Philipp , Passecker Johannes , Hauser Tobias U , FitzGerald Thomas H B , Kronbichler Martin , Friston Karl
Published: September 2018

Successful behaviour depends on the right balance between maximising reward and soliciting information about the world. Here, we show how different types of information-gain emerge when casting behaviour as surprise minimisation. We present two distinct mechanisms for goal-directed exploration that express separable profiles of active sampling to reduce uncertainty. ‘Hidden state’ exploration motivates agents to sample unambiguous observations to accurately infer the (hidden) state of the world. Conversely, ‘model parameter’ exploration, compels agents to sample outcomes associated with high uncertainty, if they are informative for their representation of the task structure. We illustrate the emergence of these types of information-gain, termed active inference and active learning, and show how these forms of exploration induce distinct patterns of ‘Bayes-optimal’ behaviour. Our findings provide a computational framework to understand how distinct levels of uncertainty induce different modes of information-gain in decision-making.
Tissue self-organization based on collective cell migration by contact activation of locomotion and chemotaxis
Authors: Fujimori Taihei , Nakajima Akihiko , Shimada Nao , Sawai Satoshi
Published: September 2018

Despite their central role in multicellular organization, navigation rules that dictate cell rearrangement remain much to be elucidated. Contact between neighboring cells and diffusive attractant molecules are two of the major determinants of tissue-level patterning, however in most cases, molecular and developmental complexity hinders one from decoding the exact governing rules of individual cell movement. A primordial example of tissue patterning by cell rearrangement is found in the social amoebaDictyostelium discoideumwhere the organizing center or the ‘tip’ self-organize as a result of sorting of differentiating prestalk and prespore cells. Due to its relatively simple and conditional multicellularity, the system provides a rare case where the process can be fully dissected into individual cell behavior. By employing microfluidics and microsphere-based manipulation of navigational cues at the single-cell level, here we uncovered a previously overlooked mode ofDictyosteliumcell migration that is strictly directed by cell-cell contact. The cell-cell contact signal is mediated by E-set Ig-like domain containing heterophilic adhesion molecules TgrB1/TgrC1 that act in trans to induce plasma membrane recruitment of SCAR complex and formation of dendritic actin networks, and the resulting cell protrusion competes with those induced by chemoattractant cAMP. Furthermore, we demonstrate that both prestalk and prespore cells can protrude towards the contact signal as well as to chemotax towards cAMP, however when given both signals, prestalk cells orient towards the chemoattractant whereas prespore cells choose the contact signal. These data suggest a new model of cell sorting by competing juxtacrine and diffusive cues each with potential to drive its own mode of collective cell migration. The present findings not only resolve the long standing question of how cells sort inDictyosteliumbut also cast light on the remarkable parallels in collective cell migration that evolved independently in metazoa and amoebozoa.
Influenza incidence prediction for the United States: an update for the 2018-2019 season
Authors: Du Xiangjun , Peng Yousong , Liu Mi , Pascual Mercedes
Published: September 2018

Introduction:

Seasonal influenza causes a high disease burden every year in the United States and worldwide. Anticipating epidemic size ahead of season can contribute to preparedness and more targetted control and prevention of seasonal influenza.

Methods:

A recently developed process-based epidemiological model that incorporates evolutionary change of the virus and generates incidence forecasts for the H3N2 subtype ahead of the season, was previously validated by several statistical criteria, including an accurate real-time prediction for the 2016-2017 influenza season. With this model, a new forecast is generated here for the upcoming 2018-2019 season. The accuracy of predictions published for the 2017-2018 season is also retrospectively evaluated.

Results:

For 2017-2018, the model correctly predicted the dominance of the H3N2 subtype and its higher than average incidence. Based on surveillance and sequence data up to June 2018, the new forecast for the upcoming 2018-2019 season indicates low levels for H3N2, and suggests an H1N1 dominant season with low incidence of influenza B.

Discussion:

Real-time forecasts, those generated with a model that was parameterized based on data preceding the predicted season, allows valuable evaluation of the approach. Anticipating the dominant subtype and the size of the upcoming epidemic ahead of season informs disease control. Further studies are needed to promote more accurate ahead-of-season forecasts and extend the approach to multiple subtypes.
Systematically improved in vitro culture conditions reveal new insights into the reproductive biology of the human parasite Schistosoma mansoni
Authors: Wang Jipeng , Chen Rui , Collins James J.
Published: September 2018

Schistosomes infect over 200 million people. The prodigious egg output of these parasites is the sole driver of pathology due to infection, yet our understanding of their sexual reproduction is limited because egg production is not sustained for more than a few days in vitro. Here, we describe culture conditions that support schistosome sexual development and sustained egg production in vitro. Female schistosomes rely on continuous pairing with male worms to fuel the maturation of their reproductive organs. Exploiting these new culture conditions, we explore the process of male-stimulated female maturation and demonstrate that physical contact with a male worm, and not insemination, is sufficient to induce female development and the production of viable parthenogenetic haploid embryos. We further report the characterization of a novel nuclear receptor, that we call vitellogenic factor 1, that is essential for female sexual development following pairing with a male worm. Taken together, these results provide a platform to study the fascinating sexual biology of these parasites on a molecular level, illuminating new strategies to control schistosome egg production.
Neuroanatomical correlates of food addiction and obesity in the general population
Authors: Beyer F. , García-García I. , Heinrich M. , Scholz M. , Schroeter ML , Sacher J. , Luck T. , Riedel-Heller S.G. , Stumvoll M. , Villringer A. , Witte A.V.
Published: September 2018

The food addiction model suggests neurobiological similarities between substance-related and addictive disorders and obesity. While structural brain differences have been consistently reported in these conditions, little is known about the neuroanatomical correlates of food addiction. We therefore assessed whether food addiction, assessed with the Yale Food Addiction Scale (YFAS), related to obesity, personality and brain structure in a large population-based sample (n=625; 20-59 years old, 45% women). A higher YFAS symptom score correlated with obesity and disinhibited eating. In a whole-brain analysis, YFAS symptom score was not associated with cortical thickness nor subcortical gray matter volumes. Higher body mass index (BMI) correlated with reduced thickness of (pre)frontal, temporal and occipital cortex. Bayes factor analysis suggested that BMI and - to a smaller extent - YFAS symptom score contributed independently to right lateral orbitofrontal cortex thickness. Our study shows that food addiction is not associated with neuroanatomical differences in a large population-based sample, and does not account for the major part of obesity-associated gray matter alterations. Yet, food addiction might explain additional variance in orbitofrontal cortex, a hub area of the reward network. Longitudinal studies implementing both anatomical and functional MRI could further disentangle the neural mechanisms of addictive eating behaviors.
Enhancing the cell-free expression of native membrane proteins by in-silico optimization of the coding sequence – an experimental study of the human voltage-dependent anion channel
Authors: Zayni Sonja , Damiati Samar , Moreno-Flores Susana , Amman Fabian , Hofacker Ivo , Ehmoser Eva-Kathrin
Published: September 2018

The investigation of membrane proteins, key constituents of cells, is hampered by the difficulty and complexity of their in vitro synthesis, of unpredictable yield. Cell-free synthesis is herein employed to unravel the impact of the expression construct on gene transcription and translation, without the complex regulatory mechanisms of cellular systems. Through the systematic design of plasmids in the immediacy of the start of the target gene, it was possible to identify translation initiation and the conformation of mRNA as the main factors governing the cell-free expression efficiency of the human voltage dependent anion channel (VDAC), a relevant membrane protein in drug-based therapy. A simple translation initiation model was developed to quantitatively assess the expression potential for the designed constructs. A scoring function is proposed that quantifies the feasibility of formation of the translation initiation complex through the ribosome-mRNA hybridization energy and the accessibility of the mRNA segment binding to the ribosome. The scoring function enables to optimize plasmid sequences and semi-quantitatively predict protein expression efficiencies.
Rodent-borne bacterial infections in Gwangju, Korea
Authors: Bang Mi Seon , Kim Choon-Mee , Kim Dong-Min , Yun Na Ra
Published: September 2018

Background

This study investigated the prevalence ofOrientia tsutsugamushi, Anaplasma phagocytophilum,andLeptospira interroganin wild rodents through molecular detection in organ samples collected from two distinct sites in Gwangju Metropolitan City, Republic of Korea.

Methodology/Principal Findings

A total of 47 wild rodents, identified asApodemus agrarius (A. agrarius), were captured from June to August 2016. The seroprevalence of antibodies against bacterial pathogens in rodent sera was analyzed; 17.4% (8/46) were identified asO. tsutsugamushithrough indirect immunofluorescence assay and 2.2% (1/46) were identified asLeptospiraspp. through passive hemagglutination assay. Using molecular methods, the spleen, kidney, and blood samples were evaluated for the presence ofO. tsutsugamushi, A. phagocytophilum, andL. interrogans. Out of 47 wild rodents, 25.5% (12/47) were positive for bacterial pathogens by PCR, where 19.1% (9/47) were positive forA. phagocytophilumand 6.4% (3/47) were positive forL. interrogans, while none were positive forO. tsutsugamushi. In addition, testing for bacterial infection in different tissues indicated that 8.7% (4/46) were positive forA. phagocytophilumin the blood, 13.3% (6/45) were positive forA. phagocytophilumin the spleen, and 6.4% (3/47) and 2.1% (1/47) were positive forL.interrogansandA. phagocytophilum, respectively, in the kidney.

Conclusions/Significance

In this study, tropisms forA. phagocytophilumin the spleen andL. interrogansin the kidney were identified. Notably,A. phagocytophilumandL. interroganswere detected in wild rodents living in close proximity to humans in the metropolitan suburban areas. Results of the present study indicate that rodent-borne bacteria may be present in wild rodents in the metropolitan suburban area of Republic of Korea.

Author Summary

Many zoonotic diseases are spreading not only in the Republic of Korea (ROK), but also worldwide. Scrub typhus, anaplasmosis, and leptospirosis are well known diseases that are considered common, widespread rodent-borne infectious diseases. Rodents serve as important reservoirs for zoonotic pathogens such asO. tsutsugamushi, A. phagocytophilum, andL. interrogans,which may be fatal to humans. Our study demonstrated the prevalence of these pathogens in wild rodents, through molecular assays and seroprevalence in organ samples. We captured 47 wild rodents in the Gwangju metropolitan city area of ROK. All were identified asA. agrarius. The prevalence of rodent-borne bacteria was 17.4% in the sera, where 25.5% was positively detected as bacterial pathogens via polymerase chain reaction. Our results indicate the importance of detecting rodent-borne bacteria in wild rodents living close to humans in suburban areas of ROK. Our data was limited to only a few samples of rodents in two regions. More samples may have to be collected over longer periods of time, to investigate the infectious nature of these pathogens in detail.
Gene regulation underlies environmental adaptation in house mice
Authors: Mack Katya L. , Ballinger Mallory A. , Phifer-Rixey Megan , Nachman Michael W.
Published: September 2018

Changes in cis-regulatory regions are thought to play a major role in the genetic basis of adaptation. However, few studies have linked cis-regulatory variation with adaptation in natural populations. Here, using a combination of exome and RNA-seq data, we performed expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses to study the genetic architecture of regulatory variation in wild house mice (Mus musculus domesticus) using individuals from five populations collected along a latitudinal cline in eastern North America. Mice in this transect showed clinal patterns of variation in several traits, including body mass. Mice were larger in more northern latitudes, in accordance with Bergmann's rule. We identified 17 genes where cis-eQTLs were clinal outliers and for which expression level was correlated with latitude. Among these clinal outliers, we identified two genes (Adam17 and Bcat2) with cis-eQTLs that were associated with adaptive body mass variation and for which expression is correlated with body mass both within and between populations. Finally, we performed a weighted gene co-expression network analysis (WGCNA) to identify expression modules associated with measures of body size variation in these mice. These findings demonstrate the power of combining gene expression data with scans for selection to identify genes involved in adaptive phenotypic evolution, and also provide strong evidence for cis-regulatory elements as essential loci of environmental adaptation in natural populations.
Role of weak C—H...O and strong N—H...O intermolecular interactions on the high-symmetry molecular packing oftrans-cyclohexane-1,4-dicarboxamide
Authors: García-Reyes Fernando , Fantoni Adolfo C. , Barón Máximo , Romano Rosana M. , Punte Graciela M. , Echeverría Gustavo A.
Published: September 2018

An unpredicted fourfold screw N—H...O hydrogen bondC(4) motif in a primary dicarboxamide (trans-cyclohexane-1,4-dicarboxamide, C8H14N2O2) was investigated by single-crystal X-ray diffraction and IR and Raman spectroscopies. Electron-density topology and intermolecular energy analyses determined fromab initiocalculations were employed to examine the influence of weak C—H...O hydrogen-bond interactions on the peculiar arrangement of molecules in the tetragonalP43212 space group. In addition, the way in which the co-operative effects of those weak bonds might modify their relative influence on molecular packing was estimated from cluster calculations. Based on the results, a structural model is proposed which helps to rationalize the unusual fourfold screw molecular arrangement.
Synthesis of FeN4at 180 GPa and its crystal structure from a submicron-sized grain
Authors: Bykov Maxim , Khandarkhaeva Saiana , Fedotenko Timofey , Sedmak Pavel , Dubrovinskaia Natalia , Dubrovinsky Leonid
Published: September 2018

Iron tetranitride, FeN4, was synthesized from the elements in a laser-heated diamond anvil cell at 180 (5) GPa and 2700 (200) K. Its crystal structure was determined based on single-crystal X-ray diffraction data collected from a submicron-sized grain at the synchrotron beamline ID11 of ESRF. The compound crystallizes in the triclinic space groupP\overline{1}. In the asymmetric unit, the Fe atom occupies an inversion centre (Wyckoff position 1d), while two N atoms occupy general positions (2i). The structure is made up from edge-sharing [FeN6] octahedra forming chains along [100] and being interconnected through N—N bridges. N atoms formcatena-poly[tetraz-1-ene-1,4-diyl] anions [–N=N—N—N–]∞2−running along [001]. In comparison with the previously reported structure of FeN4at 135 GPa [Bykovet al.(2018).Nat. Commun.9, 2756], the crystal structure of FeN4at 180 GPa is similar but the structural model is significantly improved in terms of the precision of the bond lengths and angles.
Crystal structure of (η4-cyclooctadiene)(3,3′-dimesityl-1,1′-methylenediimidazoline-2,2′-diylidene)nickel(0) tetrahydrofuran monosolvate
Authors: Yamamoto Carlos D. , Zhang Zijie , Stieber Sabine Chantal E.
Published: September 2018

The crystal structure of the title compound, [Ni(C25H28N4)(C8H12)]·C4H8O or (MesNHC2Me)Ni(COD), which contains a bidentate N-heterocyclic carbene (NHC) ligand with mesityl aryl groups is reported. The complex at 100 K has monoclinic (P21/c) symmetry and a distorted tetrahedral geometry around the nickel center, with the cyclooctadiene ligand coordinated in a κ2,η2 fashion. The bidentate NHC ligand is not planar, with a C(carbene)—Ni—C(carbene) angle of 91.51 (12)°, resulting in the mesityl groups being on the same side of the cyclooctadiene (COD) ligand. One molecule of tetrahydrofuran (THF) is co-crystallized with the nickel complex and has positional disorder.
Impact of agricultural credit on farm income under the Savanna and Transitional zones of Ghana
Authors: Abdallah Abdul-Hanan , Ayamga Micheal , Awuni Joseph A.
Published: September 2018

Purpose

The purpose of this paper is twofold: to determine the factors contributing to farm income in the Transitional and Savanna zones of Ghana and to ascertain variations between in the same and across the two locations; and to determine the impact of credit on farm income in each of the two zones and to ascertain the variation in impact of credit across the two locations.

Design/methodology/approach

In order to address endogeneity and sample selection bias, the authors draw from the theory of impact evaluation in nonrandom experiment, employing the endogenous switching regression (ESR) while using the propensity score matching (PSM) to check for robustness of the results.

Findings

The results show significant mean differences between some characteristics of households that have access to credit and those that did not have access. Further, the results revealed farm size, labor; gender, age, literacy, wealth and group membership as the significant determinants of both credit access and income in the two zones. With the ESR, credit access increases households farm income by GH¢206.56/ha and GH¢39.74/ha in the Transitional and Savanna zones, respectively, but with the PSM, credit increases farm income by GH¢201.50 and GH¢45.69 and in the Transitional and Savanna, respectively.

Research limitations/implications

The mean differences in characteristics of the households revealed the presence of selection bias in the distribution of household’s covariates in the two zones. The results further indicate the importance of productive resources, information and household characteristics in improved access to credit and farm income. Also, the results from both methods indicate that credit access leads to significant gains in farm income for households in both zones. However, differences exist in the results of PSM and that of the ESR results.

Practical implications

The presence of selection bias in the samples suggests that the use of ESR and PSM techniques is appropriate. Further, the results suggesting that enhanced credit access and farm income could be attained through improved access to household resources and information. The results also suggest the need for establishing and expanding credit programs to cover more households in both zones. The differential impact of credit between the two methods employed in each zone revealed the weakness of each model. The low values from PSM could indicate the presence of selection bias resulting from unobservable factors whiles the high values from the ESR could stem from the restrictive assumption of the model. This reinforces the importance of combining mixed methods to check robustness of results and to explore the weakness of each method employed.

Originality/value

The novelty of this study lies in the use of a very extensive and unique data set to decompose the determinants of credit access and farm income and as well as the impacts of credit into zones.
Procurement of low carbon municipal solid waste infrastructure in India through public-private partnerships
Authors: Dolla Tharun , Laishram Boeing Singh
Published: September 2018

Purpose

The Low carbon (LC) agenda has captured interest across governments and research communities. But such focus is not addressed so far in the operation of municipal solid waste (MSW) infrastructure in India. The purpose of this paper is to draw focus on the promotion of low carbon infrastructure by improving the procurement process of the public–private partnership (PPP) approach.

Design/methodology/approach

The current study employed a case study methodology. This paper develops and validates a “five-fold framework,” comprising of selection, financial, operational, standards and targets measures, for integrating LC principles in the procurement of infrastructure projects.

Findings

The public sector fails to understand the importance of the need to incorporate climate change mitigation strategies due to poor procurement competencies. With respect to the operationalization of the framework, funding of viability gap in operations instead of construction, allowing renegotiation clauses to cater possible future LC technological improvements and incorporating emission reduction targets at the local and national levels were highlighted.

Research limitations/implications

LC principles presented in this paper are not exhaustive and are verified using a single Indian PPP case. Future research endeavor can focus on the relevancy and operationalization of these principles using a more elaborate set of indicators and extend the study to other sectors and countries.

Originality/value

This paper seeks to act as guidelines for governments on how to create and improve LC MSW PPP infrastructure projects to facilitate simultaneous achievement of both climate change mitigation and infrastructure delivery goals. The current study could add value to the current emphasis on LC transitions by policymakers, government agencies and regulators.
Reviewing corporate social responsibility communication: a legitimacy perspective
Authors: Ellerup Nielsen Anne , Thomsen Christa
Published: September 2018

Purpose

The purpose of this paper is to answer the call for CSR communication research to develop and substantiate outcomes that may better explain CSR communication strategies and practices. The paper takes the research a step further, exploring the role of legitimacy in CSR communication research.

Design/methodology/approach

A literature collection methodology, combined with directed content analysis, was used to identify central themes in the literature.

Findings

The following categories of studies were identified: perception, impact and promotion studies; image and reputation studies; performance studies; and conceptual/rhetorical studies. Addressed from a legitimacy perspective, the study found that the most important types of legitimizing communicative practices articulated in the four types of studies were related to: seeking knowledge about stakeholders through perception, impact and promotion activities; monitoring and controlling the environment through image and reputation activities; creating stakeholder value through collaboration and engagement; and persuading and convincing stakeholders through rhetorics, CSR models and concepts. The study also found that practices and activities related to perceiving stakeholders’ expectations, needs and requirements are assumed to be most effective for corporations aiming at building or maintaining legitimacy.

Originality/value

The key contribution of the paper lies in exploring how corporate legitimacy is anticipated and extrapolated in the CSR communication literature, including which pinpointed CSR communication strategies and practices are assumed to be more effective than others in bridging stakeholders’ perceptions of corporations’ social and environmental actions. Until date, no reviews exist of the role of legitimacy in CSR communication research.