bluuebunny/crossref_metadata_2025 huggingface dataset:
Prototype Ultrahigh-Resolution Computed Tomography for Chest Imaging: Initial Human Experience
Authors: Shanbhag Sujata M. , Schuzer John L. , Steveson Chloe , Rollison Shirley , Bronson Kathie C. , Stagliano Michael S. , Rogalla Patrik , Blum Alain , Prokop Mathias , Chen Marcus Y.
Published: September 2019

Objective

The objective of this study was to evaluate a prototype, ultrahigh-resolution computed tomography offering higher reconstruction matrix (1024 × 1024) and spatial resolution (0.15 mm) for chest imaging.

Methods

Higher (1024) matrix reconstruction enabled by ultrahigh-resolution computed tomography scanner (128-detector rows; detector width, 0.25 mm; spatial resolution, 0.15 mm) was compared with conventional (512) reconstruction with image quality grading on a Likert scale (1, excellent; 5, nondiagnostic) for image noise, artifacts, contrast, small detail, lesion conspicuity, image sharpness, and diagnostic confidence. Image noise and signal-to-noise ratio were quantified.

Results

Diagnostic image quality was achieved for all scans on 101 patients. The 1024 reconstruction demonstrated increased image noise (20.2 ± 4.0 vs 17.2 ± 3.8, P < 0.001) and a worse noise rating (1.98 ± 0.63 vs 1.75 ± 0.61, P < 0.001) but performed significantly better than conventional 512 matrix with fewer artifacts (1.37 ± 0.43 vs 1.50 ± 0.48, P < 0.001), better contrast (1.50 ± 0.56 vs 1.62 ± 0.57, P < 0.001), small detail detection (1.06 ± 0.19 vs 2.02 ± 0.22, P < 0.001), lesion conspicuity (1.08 ± 0.23 vs 2.02 ± 0.24, P < 0.001), sharpness (1.09 ± 0.24 vs 2.02 ± 0.28, P < 0.001), and overall diagnostic confidence (1.09 ± 0.25 vs 1.18 ± 0.34, P < 0.001).

Conclusions

Ultrahigh-resolution computed tomography enabled a higher reconstruction matrix and improved image quality compared with conventional matrix reconstruction, with a minor increase in noise.
Preoperative Computed Tomography Features of Intrahepatic Cholangiocarcinoma for Predicting Lymph Node Metastasis and Overall Survival
Authors: Zhu Yong , Mao Yingfan , Chen Jun , Qiu Yudong , Wang Zhongqiu , He Jian
Published: September 2019

Objectives

The aims of this study were to compare the difference of computed tomography (CT) features between intrahepatic cholangiocarcinomas (ICCs) with and without lymph node metastasis (LNM) and to construct a nomogram to predict LNM and overall survival preoperatively.

Methods

Clinicopathological and contrast-enhanced CT features of 63 patients with ICC were analyzed. Multivariate logistic regression analysis was performed to construct a nomogram to predict LNM preoperatively. Survival curves were drawn with the Kaplan-Meier method, and survival difference was compared.

Results

Intrahepatic cholangiocarcinomas with and without LNM differed significantly in clinical symptoms, tumor location, morphologic classification, arterial phase enhancement degree–mean, arterial phase enhancement degree–max, portal venous phase enhancement degree–max, equilibrium phase (EP) enhancement ratio, EP CT value–max, and EP CT value–max/liver. A nomogram based on morphologic classification, EP CT value–max, and EP enhancement ratio was constructed to predict LNM with an area under curve of 0.814 (P < 0.001). Patients with ICC with LNM risk of 0.20 or greater based on the nomogram showed a significantly poorer overall survival than those with LNM risk less than 0.20 (39.5 ± 5.2 vs 51.1 ± 4.7 months).

Conclusions

Preoperative CT features of ICCs differed significantly between those with and without LNM. Nomogram based on those features could predict LNM and overall survival even better than the N stage.
Evaluating Best Methods for Crisis Resource Management Education
Authors: Saravana-Bawan Bianka B. , Fulton Courtney , Riley Brigitta , Katulka Jeremy , King Sharla , Paton-Gay Damian , Widder Sandy
Published: September 2019

Introduction

Health care training traditionally focuses on medical knowledge; however, this is not the only component of successful patient management. Nontechnical skills, such as crisis resource management (CRM), have significant impact on patient care. This study examines whether there is a difference in CRM skills taught by traditional lecture in comparison with low-fidelity simulation consisting of noncontextual learning through team problem-solving activities.

Methods

Two groups of multidisciplinary preclinical students were taught CRM through lecture or noncontextual active learning. Both groups were given a cardiopulmonary resuscitation simulation and clinical performance assessed by basic life support (BLS) checklist and CRM skills by Ottawa Global Rating Scale. The groups were reassessed at 4 months. A third group, who received no CRM education, served as a control group.

Results

The mean BLS scores after CRM education were 18.9 and 24.9 with mean Ottawa Global Rating Scale (GRS) scores of 22.4 and 29.1 in the didactic teaching and noncontextual groups, respectively. The difference between intervention groups was significant for BLS (P = 0.02) and Ottawa GRS (P = 0.03) score. At 4-month follow-up, there was no statistically significant difference in BLS (P = 1.0) or Ottawa GRS score (P = 0.55) between intervention groups. In comparison with the control group, there was a marginally significant difference in Ottawa GRS score (P = 0.06) at 4-month follow-up.

Conclusions

Noncontextual active learning of CRM using low-fidelity simulation results in improved CRM performance in comparison with didactic teaching. The benefits of CRM education do not seem to be sustained after one education session, suggesting the need for continued education and practice of skills to improve retention.
Aftermath of a Midurethral Sling Placed in the First Trimester: A Case Report
Authors: Anglim Breffini , McDermott Colleen D.
Published: September 2019

There are limited data on the management of pregnancy and delivery after midurethral sling (MUS) surgery for stress urinary incontinence (SUI). We report a case of a 39-year-old woman who underwent an MUS in July 2017. She reported a 10-year history of frequency, urgency with rare urge incontinence, nocturia, and occasional SUI when coughing or sneezing. Preoperative assessment did not include a pregnancy test. Two days after MUS placement, she developed complete urinary retention, and it was determined that she was 6 weeks pregnant. She was referred to a tertiary urogynecology unit and was seen at 23 weeks’ gestation with worsening symptoms of urinary frequency and nocturia. She also described difficulty voiding but no incontinence. She was managed with conservative measures initially, but by 35 weeks, she required intermittent self-catherization (ISC). She underwent an elective cesarean delivery at 39 weeks’ gestation. She reported postvoid dribbling, urge incontinence, and recurrent SUI at 10 months postpartum. This case report adds to the body of knowledge around outcomes of MUS during and after pregnancy.
Environmental sensing in dynamic quorum responses
Authors: Chu Eric K. , Groisman Alex , Levchenko Andre
Published: September 2019

Cell communication and coordinated cell behavior are hallmarks of multicellular behavior of living systems. However, in many cases, including the ancient and archetypal example of bacterial quorum sensing, the meaning of the communicated information remains a subject of debate. It is commonly assumed that quorum sensing encodes the information on the current state of the colony, including cell density and physical colony confinement. Here, we show that quorum sensing can also be exquisitely sensitive to dynamic changes in the environment, including fluctuations of the prevailing nutrient source. We propose a new signaling mechanism accounting for this sensory capability. This mechanism combines regulation by the commonly studiedluxoperon-encoded network with the environmentally determined balance of protein synthesis and dilution rates, dependent on the rate of cell proliferation. This regulatory mechanism accounts for observed complex spatial distribution of quorum responses, and emergence of sophisticated processing of dynamic inputs, including temporal thresholds and persistent partial induction following a transient change in the environmental conditions. We further show that, in this context, cell communication in quorum sensing acquires a new meaning: education of cells within a population about the past history of transient exposure to adverse conditions by a subset of induced cells. In combination, these signaling and communication features may endow a cell population with increased fitness in diverse fluctuating environments.
Contralateral Delay Activity is not sensitive to cognitive decline in older adults at risk of Mild Cognitive Impairment
Authors: Farina Francesca R , Pragulbickaitė Gabija , Bennett Marc , Judd Cian , Walsh Kevin , Mitchell Samantha , O’Connell Redmond G , Whelan Robert
Published: September 2019

Contralateral delay activity (CDA) has been proposed as a pre-clinical marker for Mild Cognitive Impairment (MCI). However, existing evidence is limited to one study with a small sample size (n=12 per group). Our aim was to compare CDA amplitudes in a larger sample of low- and high-risk older adult groups (n=35 per group). As expected, behavioural performance decreased as the number of memory items increased, and the low-risk group out-performed the high-risk group. However, we found no differences in CDA amplitudes across groups, indicating that WM capacity increased irrespective of risk-level. These findings suggest that the CDA is not a sensitive marker of MCI risk. More broadly, our results highlight the difficulty in identifying at-risk individuals, particularly as MCI is a heterogeneous, unstable condition. Future research should prioritise longitudinal approaches in order to track the progression of the CDA and its association with cognitive decline in later life.
Metabarcoding for parallel identification of species, sex and diet: an application to the conservation of globally-threatened Gyps vultures
Authors: Ghosh-Harihar Mousumi , Gurung Nehal , Shukla Harsh , Sinha Ishani , Pandit Awadhesh , Prakash Vibhu , Green Rhys E. , Ramakrishnan Uma
Published: September 2019

An understanding of the factors affecting the diet composition of critically endangered Gyps vultures in the Indian subcontinent has important applications to the design of effective conservation strategies. After suffering a massive decline (~99%) in numbers caused by veterinary use of the nephrotoxic drug diclofenac, vultures now persist in very low numbers, mostly concentrated within or near National Parks. This spatial association might be attributed to the availability of wild ungulate carcasses free from toxic veterinary drugs. Hence, quantification of vulture diets and the factors affecting them is critical to test this hypothesis. Here, we describe and validate a robust “field-to-benchtop-to-desktop” metabarcoding workflow for assessing the species- and sex-specific diet of these obligate scavengers from non-invasively collected faecal samples. Seven metabarcodes targeting mitochondrial and nuclear genes were used to simultaneously determine the vulture species identity, sex and species consumed. The amplicons were sequenced using an Illumina Miseq platform. We included controls and three replicates per sample to establish a series of non-arbitrary thresholds to filter the sequence data and eliminate cross-contamination, PCR/sequencing errors and false positives. Using this strategy enabled identification of species and sex for all samples. Diet species-specific sequences could be identified with high taxonomic resolution for 93% of samples. Out of the seven metabarcodes, just four were sufficient to meet the objectives. From this preliminary analysis, domestic livestock seem to be the most frequently consumed diet item across samples from inside and outside protected habitats. Our method provides a rapid and reliable tool for describing large-scale variation in consumption of domestic versus wild species in the diet of these species, paving the way for a better understanding of the role protected areas play in persistence and recovery of the remaining Gyps vulture populations in the wild.
Sleep homeostasis reflects temporally integrated local cortical neuronal activity
Authors: Thomas Christopher W. , Guillaumin Mathilde C. C. , McKillop Laura E. , Achermann Peter , Vyazovskiy Vladyslav V.
Published: September 2019

The homeostatic regulation of sleep manifests as a relative constancy of its daily amount and intensity. Theoretical descriptions of this phenomenon define “Process S”, a variable with dynamics dependent only on sleep-wake history, whose levels are reflected in electroencephalogram (EEG) slow wave activity (0.5 – 4 Hz) during sleep. Here we developed novel mathematical models of Process S in mice, assuming that its dynamics are a function of the deviation of cortical neuronal firing rates from a locally defined set-point, crucially without explicit knowledge of sleep-wake state. Our results suggest that Process S tracks global sleep-wake history through an integration of local cortical neuronal activity levels over time. We posit that, instead of reflecting sleep-wake-dependent changes in specific variables and serving their homeostatic regulation, Process S may be a time-keeping mechanism which enables individuals to obtain a species-specific and ecologically-relevant quantity of sleep, even in the absence of external temporal information.
Connecting Histopathology Imaging and Proteomics in Kidney Cancer through Machine Learning
Authors: Azuaje Francisco , Kim Sang-Yoon , Hernandez Daniel Perez , Dittmar Gunnar
Published: September 2019

Proteomics data encode molecular features of diagnostic value and accurately reflect key underlying biological mechanisms in cancers. Histopathology imaging is a well-established clinical approach to cancer diagnosis. The predictive relationship between large-scale proteomics and H&E-stained histopathology images remains largely uncharacterized. Here we investigate such associations through the application of machine learning, including deep neural networks, to proteomics and histology imaging datasets generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) from clear cell renal cell carcinoma patients. We report robust correlations between a set of diagnostic proteins and predictions generated by an imaging-based classification model. Proteins significantly correlated with the histology-based predictions are significantly implicated in immune responses, extracellular matrix reorganization and metabolism. Moreover, we showed that the genes encoding these proteins also reliably recapitulate the biological associations with imaging-derived predictions based on strong gene-protein expression correlations. Our findings offer novel insights into the integrative modeling of histology and omics data through machine learning, as well as the methodological basis for new research opportunities in this and other cancer types.
Multiband acceleration can provide moderate improvements in single-subject voxel-wise statistics in block-design task-based fMRI
Authors: Bhandari Ritu , Gazzola Valeria , Keysers Christian
Published: September 2019

Multiband (MB) acceleration of functional magnetic resonance imaging has become more widely available to neuroscientists. Here we compare MB factors of 1, 2 and 4 while participants view complex hand actions vs. simpler hand movements to localize the action observation network. While in a previous study, we show that MB4 shows moderate improvements in the group-level statistics, here we explore the impact it has on single subject statistics. We find that MB4 provides an increase in p values at the first level that is of medium effect size compared to MB1, providing moderate evidence across a number of voxels that MB4 indeed improves single subject statistics. This effect was localized mostly within regions that belong to the action observation network. In parallel, we find that Cohen’s d at the single subject level actually decreases using MB4 compared to MB1. Intriguingly, we find that subsampling MB4 sequences, by only considering every fourth acquired volume, also leads to increased Cohen’s d values, suggesting that the FAST algorithm we used to correct for temporal auto-correlation may over-penalize sequences with higher temporal autocorrelation, thereby underestimating the potential gains in single subject statistics offered by MB acceleration, and alternative methods should be explored. In summary, considering the moderate gains in statistical values observed both at the group level in our previous study and at the single subject level in this study, we believe that MB technology is now ripe for neuroscientists to start using MB4 acceleration for their studies, be it to accurately map activity in single subjects of interest (e.g. for presurgical planning or to explore rare patients) or for the purpose of group studies.
Urbanization and market-integration have strong, non-linear effects on cardio-metabolic health in the Turkana
Authors: Lea Amanda J. , Martins Dino , Kamau Joseph , Gurven Michael , Ayroles Julien F.
Published: September 2019

Cardio-metabolic disease is a leading cause of death worldwide, with high prevalence in western, industrialized societies relative to developing nations and subsistence-level populations. This stark difference has been attributed to the dietary and lifestyle changes associated with industrialization, but current work has relied on health comparisons between separate, genetically distinct populations to draw conclusions. To more robustly determine how lifestyle impacts health, we collected interview and health biomarker data from a single population undergoing a rapid lifestyle transition. Specifically, we sampled Turkana individuals who practice subsistence-level, nomadic pastoralism (the traditional, ancestral way of life for this group), as well as individuals who no longer practice pastoralism and engage either minimally or strongly with the market economy. Comparisons across this lifestyle gradient revealed clear, non-linear effects of industrialization: only individuals with highly urban, market-integrated lifestyles experience increases in BMI, body fat, blood pressure, and other biomarkers of cardio-metabolic health. These health differences are partially mediated by increased consumption of refined carbohydrates, and more strongly by fine-scale measures of urbanicity. Finally, because many Turkana are transitioning between rural and urban areas within their lifetime, we were able to show that being born in an urban area is associated with worse adult metabolic health, independent of adult lifestyle. Together, these analyses provide comprehensive insight into the timing, magnitude, and causes of health declines in urban, industrialized groups – an area of critical study given the massive public health burden of cardio-metabolic disease and the rate at which developing nations are experiencing lifestyle transitions.

SIGNIFICANCE

The “mismatch” between evolved human physiology and western, industrialized lifestyles is thought to explain to the current epidemic of cardiovascular disease (CVD). However, this hypothesis has been difficult to test in real time. To do so, we studied a traditional pastoralist group—the Turkana—that is currently transitioning from their ancestral way of life to an urban, industrialized lifestyle. We found that Turkana who move to cities exhibit poor cardio-metabolic health, partially because of a shift toward “western diets” high in carbohydrates. We also show that early life urbanicity independently predicts adult health, such that life-long city dwellers will experience the greatest CVD risk. Our work thus uncovers the timing, magnitude, and evolutionary causes of a major health gradient.
Detecting fabrication in large-scale molecular omics data
Authors: Bradshaw Michael S. , Payne Samuel H.
Published: September 2019

Fraud is a pervasive problem and can occur as fabrication, falsification, plagiarism or theft. The scientific community is not exempt from this universal problem and several studies have recently been caught manipulating or fabricating data. Current measures to prevent and deter scientific misconduct come in the form of the peer-review process and on-site clinical trial auditors. As recent advances in high-throughput omics technologies have moved biology into the realm of big-data, fraud detection methods must be updated for sophisticated computational fraud. In the financial sector, machine learning and digit-preference are successfully used to detect fraud. Drawing from these sources, we develop methods of fabrication detection in biomedical research and show that machine learning can be used to detect fraud in large-scale omic experiments. Using the raw data as input, the best machine learning models correctly predicted fraud with 84-95% accuracy. With digit frequency as input features, the best models detected fraud with 98%-100% accuracy. All of the data and analysis scripts used in this project are available at https://github.com/MSBradshaw/FakeData.
Use of Nanosphere Self-Assembly to Pattern Nanoporous Membranes for the Study of Extracellular Vesicles
Authors: Mireles Marcela , Soule Cody W. , Dehghani Mehdi , Gaborski Thomas R.
Published: September 2019

Nanoscale biocomponents naturally released by cells, such as extracellular vesicles (EVs), have recently gained interest due to their therapeutic and diagnostic potential. Membrane based isolation and co-culture systems have been utilized in an effort to study EVs and their effects. Nevertheless, improved platforms for the study of small EVs are still needed. Suitable membranes, for isolation and co-culture systems, require pore sizes to reach into the nanoscale. These pore sizes cannot be achieved through traditional lithographic techniques and conventional thick nanoporous membranes commonly exhibit low permeability. Here we utilized nanospheres, similar in size and shape to the targeted small EVs, as patterning features for the fabrication of freestanding SiN membranes (120 nm thick) released in minutes through a sacrificial ZnO layer. We evaluated the feasibility of separating subpopulation of EVs based on size using these membranes. The membrane used here showed an effective size cut-off of 300 nm with the majority of the EVs ≤200 nm. This work provides a convenient platform with great potential for studying subpopulations of EVs.
Development of a monkey avatar to study social perception in macaques
Authors: Wilson Vanessa A.D. , Kade Carolin , Moeller Sebastian , Treue Stefan , Kagan Igor , Fischer Julia
Published: September 2019

Following the expanding use and applications of virtual reality in every-day life, dynamic virtual stimuli are of increasing interest in cognitive studies. They allow for control of features such as gaze, expression and movement, which may help to overcome limitations of using either static or poorly controlled real stimuli. In using virtual stimuli however, one must be careful to avoid the uncanny valley effect - where realistic stimuli can be perceived as eerie, and induce an aversion response. At the same time, it is important to establish whether responses to virtual stimuli mirror responses to depictions of a real conspecific. In the current study, we describe the development of a new avatar with realistic features for nonhuman primates, the ‘primatar’. As a first step towards validation, we assessed how monkeys respond to images of this avatar compared to images of real monkeys, and an unrealistic avatar. We also compared responses between original images and scrambled as well as obfuscated versions of these images. We measured looking time to images in six free moving long-tailed macaques (Macaca fascicularis) and eye movement exploration behaviour in three rhesus macaques (Macaca mulatta). Both groups showed more of such signs of overt attention to original images than scrambled or obfuscated images. In addition, we assessed whether the realistic avatar created an uncanny valley effect through decreased looking time, finding that in both groups, monkeys did not differentiate between real, realistic or unrealistic images. These results provide support for further development of our avatar for use in social cognition studies, and more generally for cognitive research with virtual stimuli in nonhuman primates. Future research needs to shed light on the source of the inconsistent findings for the uncanny valley effect in macaques, to elucidate the roots of this mechanism in humans.
Selective activation of estrogen receptors α and β: Implications for depressive-like phenotypes in female mice exposed to chronic unpredictable stress
Authors: Eid Rand S. , Lieblich Stephanie E. , Duarte-Guterman Paula , Chaiton Jessica A. , Mah Amanda G. , Wong Sarah J. , Wen Yanhua , Galea Liisa A.M.
Published: September 2019

The estrogen receptor (ER) mechanisms by which 17β-estradiol influences depressive-like behaviour have primarily been investigated acutely and not within an animal model of depression. Therefore, the current study aimed to dissect the contribution of ERα and ERβ to the effects of 17β-estradiol under non-stress and chronic stress conditions. Ovariectomized (OVX) or sham-operated mice were treated chronically (47 days) with 17β-estradiol (E2), the ERβ agonist diarylpropionitrile (DPN), the ERα agonist propylpyrazole-triol (PPT), or vehicle. On day 15 of treatment, mice from each group were assigned to Chronic Unpredictable Stress (CUS; 28 days) or non-CUS conditions. Mice were assessed for anxiety- and depressive-like behaviour and hypothalamic-pituitary-adrenal (HPA) axis function. Cytokine and chemokine levels, and postsynaptic density protein 95 were measured in the hippocampus and frontal cortex, and adult hippocampal neurogenesis was assessed. Overall, the effects of CUS were more robust that those of estrogenic treatments, as seen by increased immobility in the tail suspension test (TST), reduced PSD-95 expression, reduced neurogenesis in the ventral hippocampus, and HPA axis negative feedback dysregulation. However, we also observe CUS-dependent and -independent effects of ovarian status and estrogenic treatments. The effects of CUS on PSD-95 expression, the cytokine milieu, and in TST were largely driven by PPT and DPN, indicating that these treatments were not protective. Independent of CUS, estradiol increased neurogenesis in the dorsal hippocampus, blunted the corticosterone response to an acute stressor, but increased anxiety-like behaviour. These findings provide insights into the complexities of estrogen signaling in modulating depressive-like phenotypes under non-stress and chronic stress conditions.
The inverse relationship between fibronectin and neuroligins in the embryonic rat colon
Authors: Gao Ni , Hou Peimin , Zhang Qiangye , Mu Weijing , Wang Jian , Wang Dongming , Li Aiwu
Published: September 2019

Our previous study identified that the abnormal expression of fibronectin (FN), neuroligin-1 (NL1) and neuroligin-2 (NL2) in the colons of children with Hirschsprung disease (HSCR), but the correlated relationship between the three in the development of the enteric nervous system (ENS) remains unclear. Colons of Wistar rats and PC12 neurons were used to investigate the relationship between FN and the neuroligins (NLs). Colon tissues from thirty healthy embryonic rats, including fifteen at embryonic day 16 (E16), eight at E18, seven at E20, and fifteen newborn rats within 24 hours (Ep0) were analyzed to determine the correlated expression of FN and NLs using Western blot (WB) analysis and real-time fluorescence quantitative PCR (qRT-PCR) methods. Small interfering ribonucleic acid (siRNA) targeting and gene plasmids were used to explore the functional interaction between FN and NLs by using PC12 neuron cells. Furthermore, we used recombinant FN and NL proteins to confirm their interactions. Our studies showed that there were downregulatory effects between FN and the NLs in the embryonic rat colon and different cell lines, indicating that FN and NLs could directly regulate each other, and there is a negative linear correlation between them. The imbalanced interaction between extracellular matrix and synapse-related genes may provide a new perspective for the pathogenesis and treatment of HSCR and neuronal intestinal malformations (NIMs).
Ubiquitylated H2A.Z nucleosomes are associated with nuclear architectural proteins and global transcriptional silencing
Authors: Ng Marlee K. , Braunschweig Ulrich , Blencowe Benjamin J. , Cheung Peter
Published: September 2019

H2A.Z mono-ubiquitylation has been linked to transcriptional repression, but the mechanisms involved are not well understood. To address this, we developed a biotinylation-based approach to purify ubiquitylated H2A.Z (H2A.Zub) mononucleosomes for biochemical and genome-wide analyses. We observe that H2A.Zub nucleosomes are enriched for the repressive histone post-translational modification H3K27me3, but depleted of H3K4 methylation and other modifications associated with active transcription. ChIP-Seq analyses reveal that H2A.Zub-nucleosomes are enriched over non-expressed genes, and suggest that it is the relative ratio of ubiquitylated to non-ubiquitylated H2A.Z, rather than absolute presence or absence of H2A.Z ubiquitylation, that correlates with gene silencing. Finally, we observe that H2A.Zub-eniched mononucleosomes preferentially co-purify with transcriptional silencing factors as well as proteins involved in higher order chromatin organization such as CTCF and cohesin. Collectively, these results suggest an important role for H2A.Z ubiquitylation in mediating global transcriptional repression through its recruitment of silencing factors and nuclear architectural proteins.
Odorant Receptor Inhibition is Fundamental to Odor Encoding
Authors: Pfister Patrick , Smith Benjamin C. , Evans Barry J. , Brann Jessica H. , Trimmer Casey , Sheikh Mushhood , Arroyave Randy , Reddy Gautam , Jeong Hyo-Young , Raps Daniel A. , Peterlin Zita , Vergassola Massimo , Rogers Matthew E.
Published: September 2019

Most natural odors are complex mixtures of many volatile components, competing to bind odorant receptors (ORs) expressed in olfactory sensory neurons (OSNs) of the nose. To date surprisingly little is known about how OR antagonism shapes neuronal representations in the periphery of the olfactory system. Here, we investigated its prevalence, the degree to which it disrupts OR ensemble activity, and its conservation across related ORs. Calcium imaging microscopy of dissociated OSNs revealed significant inhibition, often complete attenuation, of responses to indole, a commonly occurring volatile associated with both floral and fecal odors, by a set of 36 tested odorants. To confirm an OR mechanism for the observed inhibition, we performed single-cell transcriptomics on OSNs that exhibited specific response profiles to a diagnostic panel of odorants and identified the receptor Olfr743 which, when tested in vitro, recapitulated ex vivo responses. We screened ten ORs from the Olfr743 clade with 800 perfumery-related odorants spanning a range of chemical scaffolds and functional groups, over half of which (430) antagonized at least one of the ten ORs. Furthermore, OR activity outcomes were divergent rather than redundant, even for the most closely related paralogs. OR activity fitted a mathematical model of competitive receptor binding and suggests that normalization of OSN ensemble responses to odorant mixtures is the rule rather than the exception. In summary, we observed OR antagonism, inverse agonism and partial agonism occurring frequently and in a combinatorial manner. Thus, extensive receptor-mediated computation of mixture information appears to occur in the olfactory epithelium prior to transmission of odor information to the olfactory bulb.
Unravelling the strain relaxation processes in silicon nanowire arrays by X-ray diffraction
Authors: Romanitan Cosmin , Kusko Mihaela , Popescu Marian , Varasteanu Pericle , Radoi Antonio , Pachiu Cristina
Published: September 2019

Investigations performed on silicon nanowires of different lengths by scanning electron microscopy revealed coalescence processes in longer nanowires. Using X-ray diffraction (XRD), it was found that the shape of the pole figure in reciprocal space is ellipsoidal. This is the signature of lattice defects generated by the relaxation of the strain concentrated in the coalescence regions. This observation is strengthened by the deviation of the XRD peaks from Gaussianity and the appearance of the acoustic phonon mode in the Raman spectrum. It implies that bending, torsion and structural defects coexist in the longer nanowires. To separate these effects, a grazing-incidence XRD technique was conceived which allows the nanowire to be scanned along its entire length. Both ω and φ rocking curves were recorded, and their shapes were used to extract the bending and torsion profiles, respectively, along the nanowire length. Dips were found in both profiles of longer nanowires, while they are absent from shorter ones, and these dips correspond to the regions where both bending and torsion relax. The energy dissipated in the nanowires, which tracks the bending and torsion profiles, has been used to estimate the emergent dislocation density in nanowire arrays.
The optics of focusing bent-crystal monochromators on X-ray powder diffractometers with application to lattice parameter determination and microstructure analysis
Authors: Mendenhall Marcus H. , Black David , Cline James P.
Published: September 2019

The use of an incident-beam monochromator (IBM) in an X-ray powder diffractometer modifies both the shape of the spectrum from the X-ray source and the relation between the apparent diffracted angle and the actual wavelength of the X-rays. For high-accuracy work, the traditional assumption of a narrow line of typically Gaussian shape does not suffice. Both the shape of the tails of peaks and their width can be described by a new model which couples the dispersion from the optic to the dispersion from the powder sample, and to its transport to a detector. This work presents such a model, and demonstrates that it produces excellent fits via the fundamental parameters approach and requires few free parameters to achieve this. Furthermore, the parameters used are directly relatable to physical characteristics of the diffractometer optics. This agreement is critical for the evaluation of high-precision lattice parameters and crystal microstructural parameters by powder diffraction.
A simple correction for the parallax effect in X-ray pair distribution function measurements
Authors: Marlton Frederick , Ivashko Oleh , Zimmerman Martin v. , Gutowski Olof , Dippel Ann-Christin , Jørgensen Mads Ry Vogel
Published: September 2019

Total scattering and pair distribution function (PDF) analysis has created new insights that traditional powder diffraction methods have been unable to achieve in understanding the local structures of materials exhibiting disorder or complex nanostructures. Care must be taken in such analyses as subtle and discrete features in the PDF can easily be artefacts generated in the measurement process, which can result in unphysical models and interpretation. The focus of this study is an artefact called the parallax effect, which can occur in area detectors with thick detection layers during the collection of X-ray PDF data. This effect results in high-Qpeak offsets, which subsequently cause anr-dependent shift in the PDF peak positions in real space. Such effects should be accounted for if a truly accurate model is to be achieved, and a simple correction that can be conducted via a Rietveld refinement against the reference data is proposed.
Diversifying molecular and topological space via a supramolecular solid-state synthesis: a purely organic mok net sustained by hydrogen bonds
Authors: Oburn Shalisa M. , Sinnwell Michael A. , Ericson Devin P. , Reinheimer Eric W. , Proserpio Davide M. , Groeneman Ryan H. , MacGillivray Leonard
Published: September 2019

A three-dimensional hydrogen-bonded network based on a rare mok topology has been constructed using an organic molecule synthesized in the solid state. The molecule is obtained using a supramolecular protecting-group strategy that is applied to a solid-state [2+2] photodimerization. The photodimerization affords a novel head-to-head cyclobutane product. The cyclobutane possesses tetrahedrally disposed cis-hydrogen-bond donor (phenolic) and cis-hydrogen-bond acceptor (pyridyl) groups. The product self-assembles in the solid state to form a mok network that exhibits twofold interpenetration. The cyclobutane adopts different conformations to provide combinations of hydrogen-bond donor and acceptor sites to conform to the structural requirements of the mok net.
Syntheses and characterization of dinuclear and tetranuclear AgIsupramolecular complexes generated from symmetric and asymmetric molecular clips containing oxadiazole rings
Authors: Jin Guoxia , Ji Yuqi , Wang Teng , Sun Yanyan , Li Yulong , Zhu Guiying , Ma Jianping
Published: September 2019

A new asymmetric ligand, 5-{3-[5-(4-methylphenyl)-1,3,4-oxadiazol-2-yl]phenyl}-2-(pyridin-3-yl)-1,3,4-oxadiazole (L5), which contains two oxadiazole rings, was synthesized and characterized. The assembly of symmetric 2,5-bis(pyridin-3-yl)-1,3,4-oxadiazole (L1) and asymmetricL5with AgCO2CF3in solution yielded two novel AgIcomplexes, namelycatena-poly[[di-μ-trifluoroacetato-disilver(I)]-bis[μ-2,5-bis(pyridin-3-yl)-1,3,4-oxadiazole]], [Ag2(C2F3O2)2(C12H8N4O)2]nor [Ag2(μ2-O2CCF3)2(L1)2]n(1), and bis(μ3-5-{3-[5-(4-methylphenyl)-1,3,4-oxadiazol-2-yl]phenyl}-2-(pyridin-3-yl)-1,3,4-oxadiazole)tetra-μ3-trifluoroacetato-tetrasilver(I) dichloromethane monosolvate, [Ag4(C2F3O2)4(C22H15N5O2)2]·CH2Cl2or [Ag2(μ3-O2CCF3)2(L5)]2·CH2Cl2(2). Complex1displays a one-dimensional ring–chain motif, where dinuclear Ag2(CF3CO2)2units alternate with Ag2(L1)2macrocycles. This structure is different from previously reported Ag–L1complexes with different anions. Complex2features a tetranuclear supramolecular macrocycle, in which each ligand adopts a tridentate coordination mode with the oxadiazole ring next to thep-tolyl ring coordinated and that next to the pyridyl ring free. TwoL5ligands are bound to two Ag1 centres through two oxadiazole N and two pyridyl N atoms to form a macrocycle. The other two oxadiazole N atoms coordinate to the two Ag2 centres of the Ag2(O2CCF3)4dimer. Each CF3CO2−anion adopts a μ3-coordination mode, bridging the Ag1 and Ag2 centres to form a tetranuclear silver(I) complex. This study indicates that the donor ability of the bridging oxadiazole rings can be tuned by electron-withdrawing and -donating substituents. The emission properties of ligandsL1andL5and complexes1and2were also investigated in the solid state.
Tolerance factor and phase stability of the garnet structure
Authors: Song Zhen , Zhou Dandan , Liu Quanlin
Published: September 2019

We introduce a structural descriptor, the tolerance factor, for the prediction and systematic description of the phase stability with the garnet structure. Like the tolerance factor widely adopted for the perovskite structure, it is a compositional parameter derived from the geometrical relationship between multi-type polyhedra in the garnet structure, and the calculation only needs the information of the ionic radius. A survey of the tolerance factor over 130 garnet-type compounds reveals that the data points are scattered in a narrow range. The tolerance factor is helpful in understanding the crystal chemistry of some garnet-type compounds and could serve as a guide for predicting the stability of the garnet phase. The correlation between the tolerance factor and the garnet-phase stability could be utilized by machine learning or high-throughput screening methods in material design and discovery.
3-(3,5-Dichlorophenyl)benzene-1,2-diol
Authors: Dhakal Ram , Parkin Sean , Lehmler Hans-Joachim
Published: September 2019

The title structure, C12H8Cl2O2, is a putative metabolite of 3,5-dichlorobiphenyl (PCB 14). The dihedral angle between the two benzene rings of the title compounds is 58.86 (4)°. In the crystal, it displays intra- and intermolecular O—H...O hydrogen bonding and intermolecular O—H...Cl hydrogen...chlorine interactions. The intermolecular interactions form a two-dimensional network parallel to (010).
Employers’ attitudes to HOU postgraduates’ qualities and skills
Authors: Hoang Minh Tuyet
Published: September 2019

Purpose

The purpose of this paper is to investigate employers’ attitudes towards qualities and skills for the twenty-first century of Hanoi Open University (HOU) postgraduates. More specifically, it is to find out employers’ assessment and satisfaction on five sets of skills: foundation skills, professional competencies, personal attributes, organizational skills and technical knowledge and skills.

Design/methodology/approach

The study used a survey questionnaire as a tool to collect data. The survey was conducted on employers of HOU postgraduates who graduated during the academic years 2015–2016 from five faculties at HOU.

Findings

The findings of the study show that employers highly appreciated HOU postgraduates in numeracy skills, ICT literacy skills and information literacy within foundation skills; critical thinking and problem solving skills, collaboration skills and conceptual skills within professional competencies; responsible, integrity and interpersonal skills within organization skills; productivity, organization and planning and time management within organizational skills; knowledge-related regulations and policies at workplace, capacity to use knowledge and skills at workplace and lifelong learning within technical knowledge and skills.

Originality/value

The values of the study are that the employer attitudes identified can be used to evaluate educational programs and can be used as a quality assurance measure. The study helps to indicate the gap between the expectation and the satisfaction of employers on HOU postgraduates. Thereby, suggestions can be given to HOU’s management to improve the services at the university in general and the services to postgraduate students in particular to upgrade their qualities and skills to meet social demands.
Financial performance assessment using Grey relational analysis (GRA)
Authors: Suvvari Anandarao , S. Raja Sethu Durai , Goyari Phanindra
Published: September 2019

Purpose

Traditional statistical methods to study the financial performance of any industry have many barriers and limitations in terms of the statistical distribution of the financial ratios, and, in particular, it considers only its positive values of it. The purpose of this paper is to estimate the financial performance of 24 Indian life insurance companies for the period from 2013 to 2016 using Grey relational analysis (GRA) proposed by Deng (1982) that accommodates the negative values in the analysis.

Design/methodology/approach

Financial performance of 24 Indian life insurance companies for the years from 2013–2014 to 2015–2016 is examined using a total of 14 indicators from capital adequacy ratios, liquidity ratios, operating ratios and profitability ratios (PR). The methodology used is GRA to obtain the Grey grades to rank the performance indicators, where higher relational grade shows better financial performance, and a lower score depicts the scope for improving the performance.

Findings

The results rank the insurance companies according to their financial performance in which Shriram insurance stands first with higher relational grade score, followed by the companies like IDBI Insurance, Sahara Insurance and Life Insurance Corporation of India. The main finding is that PR which have negative values are playing a crucial role in determining the financial performance of Indian life insurance companies.

Practical implications

This study has far-reaching practical implications in twofold: first, for the Indian life insurance industry, they have to concentrate more on PR for better financial health and, second, for any financial performance analysis, ignoring negative value ratios produce biased inference and GRA can be used for better inference.

Originality/value

This study is the first attempt to evaluate the financial performance of Indian life insurance using the GRA methodology. The advantage of GRA is that there is no restrictions on the statistical distribution of the data and it also accommodates the negative values, whereas all the other traditional methods insist on the statistical distribution of data, and, more importantly, they cannot handle negative values in the performance analysis.
Women housing right, affordable housing for female-headed households, case study
Authors: Ghaedrahmati Safar , SHahsavari Foad
Published: September 2019

Purpose

This paper aims to address housing right for female-headed households in Iran housing plans.

Design/methodology/approach

This research was conducted on female-headed households by a demographic attribute’s analysis. This paper tries to address housing right for female-headed households in housing plans. The analysis is done in the following three steps: (1) demographic variables analysis of female-headed households. Demographic variables include economic, social and health attributes. The statistical information related to the female-headed households in Tehran used in this step is based on the statistics of the Statistical Center of Iran; (2) share of female-headed households in Tehran in proportion to the total households. Also, the activity of female-headed households in Tehran; and (3) share of housing right for female-headed households in Iran Housing Plans. In this step, a questionnaire has been developed for 30 experts in which housing right for female-headed households have been asked for Iran housing plans.

Findings

The results show that with the increase in female-headed households in Tehran, they spend about 49 per cent of their income on housing, which influences the quality and quantity of other essential requirements of them such as food, clothing, health and education. The lack of adequate housing and increased housing rentals have forced them to live in informal settlements and low-quality homes. Based on Women Housing Right, adequate and affordable housing for them has not been considered in Iran’s housing plans.

Social implications

In spite of the emphasis on strengthening the position of female-headed households in the fourth, fifth and sixth development plans of Iran, this has not practically happened. The unfavorable status of female-headed households in the housing system is not due to their lack of problem-solving susceptibility, but their systematic exclusion in housing policy and practice in Tehran.

Originality/value

This paper has not been published in any journal.