bluuebunny/crossref_metadata_2025 huggingface dataset:
Wiener filter improves diagnostic accuracy of CAD SPECT images—comparison to angiography and CT angiography
Authors: Masoomi Michael A. , Al-Shammeri Iman , Kalafallah Khaled , Elrahman Hany M.A. , Ragab Osama , Ahmed Ebba , Al-Shammeri Jehan , Arafat Sharif
Published: January 2019

Many discrepancy in selection of proper filter and its parameters for individual cases exists. The authors investigate the impact of the most common filters on patient NM images with coronary artery disease (CAD), and compare the results with the computerized tomography (CT)-Angio and angiography for accuracy.

The investigation initiated by performing various single photon emission computerized tomography (SPECT)/CT scan of the national electrical manufacturers association chest phantoms having hot and cold inserts. Data acquired on GE 670 PRO SPECT/CT; 360Ø, 64 frames, 60 seconds, low energy high resolution (LEHR) 128, low energy general purpose (LEGP) with CT attenuation (120 kV and 170 mA). The images reconstructed with filtered back projection and ITERATIVE ordered-subset expectation maximization utilizing filters; Hann, Butterworth, Metz, Hamming, and Wiener. The Image contrast was calculated to assess absolute nearness of the inserts. Based on the preliminary results, then scans of 92 patients with CAD; 64 males and 28 females, age 41 to 77 years old, who had been reported earlier reprocessed with the nominated filter and were reported by 2 NM expert. The results compared to the earlier reports and to the CT–Angio and angiography.

The optimization suggested 3 filters; Wiener (Wi), Metz and Butterworth (But) provide the highest contrast (99– 66.4%) and (81– 32%) for the cold and hot inserts respectively, with the (Wi) filter to be the better option. The reprocessed patients scan with the (Wi) presented an elevated diagnostic accuracy, correlated well with the CT-Angio and angiography results (P < .001 and r = 0.79 for [Wi] and P = .004 and r = 0.39 for [But]). The percentage of the false negative for moderate to severe CAD cases reported using Wi filter reduced from 27% to 7% and similarly for mild CAD cases from 7% to 1%.

It appears the Wiener filter could produce results with the highest contrast for phantom imaging of various cold and hot spheres and for the patient data which is more consistent with angiography results, with much-elevated accuracy in intermediate cases (r = 0.79 for Wiener and r = 0.39 for Butterworth vs angiography). However, the optimum parameters obtained for the filters have no relation with the resolution of the imaging system, but the details of the objects could be improved.
Retinal inflammation diagnosed as an idiopathic macular hole with multiple recurrences and spontaneous closures
Authors: Hayashi Isami , Shinoda Hajime , Nagai Norihiro , Tsubota Kazuo , Ozawa Yoko
Published: January 2019

Rationale:

An idiopathic macular hole that causes substantial reduction in central visual acuity is believed to involve no obvious underlying diseases; thus, it is suspected to form due to the presence of idiopathic tractional forces at the vitreoretinal interface. Importantly, it is effectively treated with pars plana vitrectomy (PPV), which removes the mechanical forces. However, while it is exceedingly rare, a macular hole can develop in eyes after PPV; fresh or postoperative macular holes can close spontaneously without surgical removal of traction. Thus, another mechanism might be involved, although it remains obscure.

Patients concerns:

A 67-year-old woman experienced 4 episodes of distorted and/or blurred vision.

Diagnosis:

She was diagnosed with recurrent macular hole formation.

Interventions:

For each episode, she either underwent surgery or was placed under observation.

Outcomes:

The macular hole was twice closed with PPV and twice without. The 2nd PPV procedure, which was performed at the time of 2nd recurrence, confirmed the absence of the epiretinal membrane and internal limiting membrane that cause tractional forces at the vitreoretinal interface in the macular area. At the time of the 3rd recurrence, fluorescein angiographies (FAs) revealed the presence of mild and diffuse inflammation throughout the peripheral retina, although there were no other findings indicative of ocular inflammation during the general eye examination conducted for every episode of macular hole formation. After the initiation of topical steroid treatment, inflammation (as recorded on FA) was reduced, and the macular hole subsequently closed. Development and resolution of perifoveal cystoid change and retinal protrusion were observed in every episode in optical coherence tomography (OCT) images. A bridging element in an OCT image was observed during the 4th closure of the macular hole.

Lessons:

Dynamic changes in FA and OCT images unraveled the pathogenesis of a macular hole that was originally diagnosed as idiopathic; mild inflammation was involved. The FA is typically not used for the diagnosis and management of macular hole formation; however, its use in this case helped determine a new mechanism in an otherwise idiopathic disease.
Diagnostic performance of serum pepsinogen assay for the prediction of atrophic gastritis and gastric neoplasms
Authors: Bang Chang Seok , Lee Jae Jun , Baik Gwang Ho
Published: January 2019

Background:

Serum pepsinogen assay (sPGA) combining concentration of pepsinogen I (PG I), and the ratio of PG I/II is the noninvasive biomarker for predicting chronic atrophic gastritis (CAG) and neoplasms reflecting mucosal secretory status. Although various cut-off values have been suggested, PG I ≤70 ng/mL and PG I/II ≤3 have been widely accepted. However, previous studies for diagnostic test accuracy presented only pooled outcomes, which cannot discriminate the diagnostic validity of sPGA with cut-off of PG I ≤70 ng/mL and PG I/II ≤3.

Methods:

We will search the core databases [MEDLINE (through PubMed), the Cochrane Library, and Embase] from their inception to December 2018 by 2 independent evaluators. The P.I.C.O. is as follows; Patients: who have histologically proven CAG or gastric neoplasms, Intervention: sPGA with cut-off of PG I ≤70 ng/mL and/or PG I/II ≤3, Comparison: none, Outcome: diagnostic performance indices of sPGA for CAG and gastric neoplasms (sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratios) (if, true/false positive, true/false negative values are presented, diagnostic performance indices will be calculated). All types of study design with full text will be sought and included. The risk of bias will be assessed using the QUADAS-2 tool. Descriptive data synthesis is planned and quantitative synthesis (bivariate and HSROC model) will be used if the included studies are sufficiently homogenous. Publication bias will be assessed.

Results:

The results will provide clinical evidence for diagnostic validity of sPGA.

Conclusion:

This study will provide evidence of sPGA for predicting CAG and gastric neoplasms.
The effects of metformin on insulin resistance in overweight or obese children and adolescents: A PRISMA-compliant systematic review and meta-analysis of randomized controlled trials
Authors: Sun Juan , Wang Ya , Zhang Xiaoyi , He Hong
Published: January 2019

Background:

Metformin has shown its effectiveness in reducing body mass index (BMI) in obese children and adolescents, but relevant evidence for improving insulin resistance in overweight or obese children and adolescents is inconclusive.

Objectives:

This study aimed to assess whether metformin could effectively and safely improve homeostasis model assessment insulin resistance index (HOMA-IR) and other related laboratory indicators including fasting glucose, fasting insulin, high-density lipoprotein cholesterol (HDL-C), and low density lipoprotein-cholesterol (LDL-C).

Methods:

Searches were carried out in PubMed, CENTRAL, Web of Science, EMBASE, CBM, Chinese National Knowledge Infrastructure (CNKI), and WanFang from their inception until March 2018. Randomized controlled trials (RCTs) comparing metformin alone with placebo in overweight or obese children and adolescents were included. The Cochrane risk of bias tool was applied to assess the methodological quality of every study and Meta-analysis was carried out with a random effects model or a fixed effects model. Publication bias was evaluated by the Begg and Egger tests.

Results:

A total of 11 trials with a total of 865 participants met the inclusion criteria. Participants were between 4 and 18 years old. The time span of these studies ranged from 2001 to 2017. The daily dose of metformin was from 1000 mg to 2000 mg and the duration of intervention was 8 weeks to 18 months. Compared with placebo, metformin with lifestyle intervention reduced the level of LDL-C (P = 008, MD = - 4.29, 95% confidence interval [CI]: -7.45, -1.12). However, there was no obvious differences in improving insulin resistance, fasting glucose, and HDL-C.

Conclusion:

Metformin may improve the level of LDL-C, but it has no significant effect on insulin resistance. The use of metformin may be a new approach to lipid metabolism management in overweight or obese children and adolescents.

Registration number:

CRD42018092059.
Optical coherence tomography angiography in unilateral multifocal choroiditis and panuveitis
Authors: Lee Lung-Chi , Huang Ke-Hao , Chen Yi-Hao , Lin Hsin-Ting , Hsu Chia-Chen , Tai Ming-Cheng , Liang Chang-Min , Chen Jiann-Torng , Chen Ching-Long
Published: January 2019

Rationale:

Optical coherence tomography angiography (OCT-A) has the advantage to visualize the microvascular structure of the retina in vivo and was utilized clinically in various neovascular retinal diseases. The OCT-A has also been used to examine the lesion in multifocal choroiditis and panuveitis (MCP). This study aimed to describe a case of MCP and present the disease process of a punched-out lesion in the chorioretina with neovascular activity using OCT-A.

Patients concerns:

A 32-year-old female Caucasian patient presented with a 2-week history of progressive blurred vision in her right eye with photophobia and a diminished temporal visual field. On presentation, her best corrected visual acuity was 6/60 in the right eye with a prominent anterior uveitis seen under slit lamp examination.

Diagnoses:

Dilated fundus examination of the right eye showed vitritis and multiple, punched-out yellowish-white lesions over the peripheral retina. Additional multimodal imaging (MMI) were done including fluorescein angiography (FA), indocyanine green angiography (ICGA) and fundus autofluorescence (FAF), which all revealed characteristic findings of MCP. In general, the diagnosis of unilateral MCP was made. Furthermore, one of the punched-out lesions in the right eye was particularly selected and examined under OCT and OCT-A, which revealed a subretinal elevated lesion with high flow signal under OCT-A.

Interventions:

Treatment with oral prednisolone at 30 mg daily with topical prednisolone acetate 1% every 2 hours were prescribed, which were gradually tapered down within a 2-month course.

Outcomes:

The patient's best corrected visual acuity of the right eye returned to 6/6 at 2 months after the diagnosis. The flow signal in the OCT-A study of the punched-out lesion had also resolved after steroid treatment.

Lessons:

The MCP is an uncommon uveitis with multiple inflammatory chorioretinal lesions. Using multimodal imaging technique, physicians can better differentiate these lesions for diagnosis and for further monitoring. Our results demonstrated that these chorioretinal lesions in MCP may display neovascular activities that might not be seen easily using conventional FA or ICGA study. With OCT-A, ophthalmologists could identify and monitor subtle choroidal neovascularization (CNV) changes over these punched-out lesions.
Intraparenchymal schwannoma with calcification of the temporal lobe
Authors: Chen Fan , Zhao Shuai , Yu Ying , Chen Dawei
Published: January 2019

Rationale:

Intracranial schwannomas most frequently arise from the trigeminal nerve and the vestibular nerve. Schwannomas within the cerebral parenchyma are exceedingly rare. Additionally, calcification is an uncommon histopathological and radiological characteristic in schwannomas.

Patient concerns:

A 46-year-old man presented to us with sudden onset epileptic seizure and a 3-month history of intermittent headache. After admission, the physical and neurological examinations were all normal. Brain CT revealed an irregular, well-defined, hyperdense mass in the right temporal lobe. MRI showed a solid mass appearing iso- to hypointensity on T1-weighted imaging and heterogeneous intensity on T2-weighted imaging in the right temporal lobe; after Gd-DTPA administration, the lesion showed heterogeneous enhancement.

Diagnosis:

Histopathological examination revealed hyperchromatic nuclei and loose intercellular matrix with calcification. Immunohistochemical analysis demonstrated that the tumor was strongly positive for S100 protein but negative for GFAP and CK, which was consistent with a schwannoma.

Interventions and outcomes:

A surgical resection via the right temporal approach was performed. Intraoperatively, we noticed that the tumor was grayish yellow, capsuled, and located entirely within the temporal parenchyma. A gross total resection was achieved. The postoperative course was uneventful, and there was no epileptic seizure.

Lessons:

Intraparenchymal schwannoma with calcification is an uncommon histopathological and radiological characteristic in schwannomas. Intraparenchymal schwannoma with calcification is extremely rare. The early identification and appropriate surgical treatment should be highlighted.
Micronutrients and Bioactive Compounds in Mushrooms
Authors: Beelman Robert B. , Kalaras Michael D. , Richie John P.
Published: January 2019

Mushrooms have been used both as food and as medicine in many cultures, and their popularity as both is growing in the United States. We have shown that they are inherently, or can easily be made to be, excellent dietary sources of 4 important bioactive compounds that are all known to decease in humans as they age. These are the micronutrients selenium and vitamin D2 and antioxidants glutathione and ergothioneine (Ergo). All of these except for Ergo can be found in significant amounts in other foods; hence, it will be the primary focus of this review. Because Ergo is made in nature primarily by nonyeast fungi, mushrooms are by far the best human dietary source. Humans produce a highly specific transport protein for Ergo that makes it highly bioavailable and avidly retained, leading many to speculate about its potential importance to human health because such specific transporters are rarely present for nonnutrient bioactive compounds. Ergo is found in small amounts throughout the food chain presumably owing to fungi in the soil passing it on to plants and then animals that eat them. We have preliminary evidence that Ergo levels in the American food supply might be compromised because of reduced fungal populations in agricultural soils caused by some cultivation practices. Relationships observed between estimated Ergo consumption and average longevity and reductions in chronic neurodegenerative diseases across different countries supports additional interest in Ergo as a dietary chemopreventive agent for aging-related diseases.
Black Esophagus (Acute Necrotizing Esophagitis) and Wischnewsky Lesions in a Death From Diabetic Ketoacidosis
Authors: McCarthy Sinead , Garland Jack , Hensby-Bennett Sarah , Philcox Winston , Kesha Kilak , Stables Simon , Tse Rexson
Published: January 2019

Acute esophageal necrosis (AEN), also known as black esophagus, is a rare clinical entity. It is recently described to be associated with diabetic ketoacidosis (DKA) in a few case reports. Wischnewsky lesions (WLs) are a classic postmortem finding seen in fatal hypothermia but are recently described to be associated with DKA. Interestingly, the pathogenesis and morphology of AEN and WLs appear to share similar characteristics. Both AEN and WLs are reported to be seen simultaneously in hypothermic deaths and deaths related to alcohol abuse, but not in DKA. We report a death in a 67-year-old woman who died of DKA. At postmortem examination, the esophagus and stomach showed AEN and WLs, respectively. Although not previously reported together, both AEN and WLs have separately been described in cases of DKA. This case raises a possible unifying etiology of AEN and WLs in DKA (and probably also in hypothermic deaths and deaths related to alcohol abuse), manifested in different parts of the gastrointestinal tract.
Does variation in egg structure among five populations of Atlantic salmon (Salmo salar) influence their survival in low oxygen conditions?
Authors: Bloomer Jack , Sear David , Kemp Paul
Published: January 2019

Oxygen supply to the salmonid egg surface can be limited by external factors such as sedimentation and groundwater upwelling, while the egg membrane itself can impede diffusion from the egg surface to the embryo. Therefore, the structure of egg membranes could affect the rate at which embryos obtain oxygen from their surroundings. Published field data indicate that oxygen stress experienced by salmonid eggs can vary widely among populations. Therefore, if membrane architecture influences diffusion rate to the embryo, selection for more permeable membranes could occur in oxygen-stressed environments. Using electron microscopy, the membrane structure of eggs obtained from five UK Atlantic salmon (Salmo salar) populations is described. Membrane thickness, porosity and permeability to dissolved oxygen varied among populations. Furthermore, comparison of membranes of eggs that survived laboratory controlled low-oxygen conditions compared to those that died suggested that ova with less permeable membranes were more susceptible to hypoxia-induced mortality. In addition, membrane porosity was lower than previously reported indicating that oxygen requirements during incubation have been underestimated, so models such as the mass transfer theory that predict incubation success could currently overestimate ova survival. Variation in egg membrane structure influences low oxygen tolerance of Atlantic salmon embryos and could represent adaptation to low oxygen stress. Consequently, stock enhancement techniques such as supportive breeding that relieve incubation stress could erode structural adaptations.
Maiden voyage into death: are fisheries affecting seabird juvenile survival during the first days at sea?
Authors: Afán Isabel , Navarro Joan , Grémillet David , Coll Marta , Forero Manuela G.
Published: January 2019

The study of juvenile migration behaviour of seabird species has been limited so far by the inability to track their movements during long time periods. Foraging and flying skills of young individuals are assumed to be inferior to those of adults, making them more vulnerable during long-distance migrations. In addition to natural oceanographic effects and intrinsic conditions, incidental seabird harvest by human fisheries is one of the main causes of worldwide seabird population declines, and it has been hypothesized that juveniles are particularly vulnerable to bycatch during their first weeks at sea after leaving the nest. We used solar-powered satellite tags to track the at-sea movements of adults and juveniles of Scopoli's shearwater (
Calonectris diomedea
) after the autumn departure from their breeding colony in Chafarinas Islands (southwestern Mediterranean Sea). Eighty per cent of juvenile tags stopped transmitting during the first week at sea, within 50 km of their natal colony, in an area with one of the highest concentrations of fishing activities in the Mediterranean Sea. All adult birds tagged and only 20% of juveniles migrated into the Atlantic and southwards along the coast of West Africa. The two age groups showed different habitat preferences, with juveniles travelling farther from the coast, in windier and less productive waters than adults. We conclude that Scopoli's shearwater juveniles are particularly vulnerable to mortality events, and we highlight that fisheries, along with differential age-related behaviour skills between adults and juveniles, are likely causes of this mortality. Overall, our study highlights the importance of conducting tracking studies during the first stages of juvenile migration.
Identification of 12 cancer types through genome deep learning
Authors: Sun Yingshuai , Zhu Sitao , Ma Kailong , Liu Weiqing , Yue Yao , Hu Gang , Lu Huifang , Chen Wenbin
Published: January 2019

Motivation

Cancer is a major cause of death worldwide, and an early diagnosis is required for a favorable prognosis. Histological examination is the gold standard for cancer identification; however, there is a large amount of inter-observer variability in histological diagnosis. Numerous studies have shown that cancer genesis is accompanied by an accumulation of harmful mutations within patients’ genome, potentiating the identification of cancer based on genomic information. We have proposed a method, GDL (genome deep learning), to study the relationship between genomic variations and traits based on deep neural networks with multiple hidden layers and nonlinear transformations.

Result

We analyzed 6,083 samples from 12 cancer types obtained from the TCGA (The Cancer Genome Atlas) and 1,991 healthy samples from the 1000 Genomes project(Genomes Project, et al., 2010). We constructed 12 specific models to distinguish between certain types of cancers and healthy tissues, a specific model that can identify healthy vs diseased tissues, and a mixture model to distinguish between all 12 types of cancer based on GDL. We present the success obtained with GDL when applied to the challenging problem of cancer based on genomic variations and demonstrate state-of-the-art results (97%, 70.08% and 94.70%) for cancer identification. The mixture model achieved a comparable performance. With the development of new molecular and sequencing technologies, we can now collect circulating tumor DNA (ctDNA) from blood and monitor the cancer risk in real time, and using our model, we can also target cancerous tissue that may develop in the future. We developed a new and efficient method for the identification of cancer based on genomic information that offers a new direction for disease diagnosis while providing a new method to predict traits based on that information.

Contact:

chenwenbin@genomics.cn
Bioshake: a Haskell EDSL for bioinformatics pipelines
Authors: Bedő Justin
Published: January 2019

Background

Typical bioinformatics analysis comprise long running computational pipelines. An important part of producing reproducible research is the management and execution of these computational pipelines to allow robust execution and to minimise errors. Bioshake is an embedded domain specific language embedded in Haskell for specifying and executing computational pipelines in bioinformatics that significantly reduces the possibility of errors occurring.

Results

Unlike other pipeline frameworks, Bioshake raises many properties to the type level to allow the correctness of a pipeline to be statically checked during compilation, catching errors before any lengthy execution process. Bioshake builds on the Shake build tool to provide robust dependency tracking, parallel execution, reporting, and resumption capabilities. Finally, Bioshake abstracts execution so that jobs can either be executed directly or submitted to a cluster.

Conclusions

Bioshake is available at http://github.com/papenfusslab/bioshake.
3.5KJPNv2, An allele frequency panel of 3,552 Japanese Individuals
Authors: Tadaka Shu , Katsuoka Fumiki , Ueki Masao , Kojima Kaname , Makino Satoshi , Saito Sakae , Otsuki Akihito , Gocho Chinatsu , Sakurai-Yageta Mika , Danjoh Inaho , Motoike Ikuko N. , Yamaguchi-Kabata Yumi , Shirota Matsuyuki , Koshiba Seizo , Nagasaki Masao , Minegishi Naoko , Hozawa Atsushi , Kuriyama Shinichi , Shimizu Atsushi , Yasuda Jun , Fuse Nobuo ,   the Tohoku Medical Megabank Project Study Group, Tamiya Gen , Yamamoto Masayuki , Kinoshita Kengo
Published: January 2019

The first step towards realizing personalized healthcare is to catalog the genetic variations in a population. Since the dissemination of individual-level genomic information is strictly controlled, it will be useful to construct population-level allele frequency panels and to provide them through easy-to-use interfaces.

In the Tohoku Medical Megabank Project, we have sequenced nearly 4,000 individuals from a Japanese population, and constructed an allele frequency panel of 3,552 individuals after removing related samples. The panel is called the 3.5KJPNv2. It was constructed by using a standard pipeline including the 1KGP and gnomAD algorithms to reduce technical biases and to allow comparisons to other populations. Our database is the first largescale panel providing the frequencies of variants present on the X chromosome and on the mitochondria in the Japanese population. All the data are available on our original database at https://jmorp.megabank.tohoku.ac.jp.
Huntington’s disease onset is determined by length of uninterrupted CAG, not encoded polyglutamine, and is modified by DNA maintenance mechanisms
Authors:   Genetic Modifiers of Huntington’s Disease (GeM-HD) Consortium, Lee Jong-Min , Correia Kevin , Loupe Jacob , Kim Kyung-Hee , Barker Douglas , Hong Eun Pyo , Chao Michael J , Long Jeffrey D. , Lucente Diane , Vonsattel Jean-Paul , Mouro Pinto Ricardo , Abu Elneel Kawther , Ramos Eliana Marisa , Mysore Jayalakshmi Srinidhi , Gillis Tammy , Wheeler Vanessa C. , MacDonald Marcy E. , Gusella James F , Massey Thomas , McAllister Branduff , Medway Christopher , Stone Timothy C , Hall Lynsey , Jones Lesley , Holmans Peter , Kwak Seung , Ehrhardt Anka , Sampaio Cristina , Ciosi Marc , Maxwell Alastair , Chatzi Afroditi , Monckton Darren G , Orth Michael , Landwehrmeyer G. Bernhard , Paulsen Jane S , Dorsey E. Ray , Shoulson Ira , Myers Richard H
Published: January 2019

The effects of variable, glutamine-encoding, CAA interruptions indicate that a property of the uninterrupted HTT CAG repeat sequence, distinct from huntingtin’s polyglutamine segment, dictates the rate at which HD develops. The timing of onset shows no significant association with HTT cis-eQTLs but is influenced, sometimes in a sex-specific manner, by polymorphic variation at multiple DNA maintenance genes, suggesting that the special onset-determining property of the uninterrupted CAG repeat is a propensity for length instability that leads to its somatic expansion. Additional naturally-occurring genetic modifier loci, defined by GWAS, may influence HD pathogenesis through other mechanisms. These findings have profound implications for the pathogenesis of HD and other repeat diseases and question a fundamental premise of the “polyglutamine disorders”.
Excess neuronal branching allows for innervation of specific dendritic compartments in cortex
Authors: Bird A D , Deters L H , Cuntz H
Published: January 2019

The connectivity of cortical microcircuits is a major determinant of brain function; defining how activity propagates between different cell types is key to scaling our understanding of individual neuronal behaviour to encompass functional networks. Furthermore, the integration of synaptic currents within a dendrite depends on the spatial organisation of inputs, both excitatory and inhibitory. We identify a simple equation to estimate the number of potential anatomical contacts between neurons; finding a linear increase in potential connectivity with cable length and maximum spine length, and a decrease with overlapping volume. This enables us to predict the mean number of candidate synapses for reconstructed cells, including those realistically arranged. We identify an excess of putative connections in cortical data, with densities of neurite higher than is necessary to reliably ensure the possible implementation of any given connection. We show that potential contacts allow the particular implementation of connectivity at a subcellular level.
RNA interactions with CTCF are essential for its proper function
Authors: Saldaña-Meyer Ricardo , Rodriguez-Hernaez Javier , Nishana Mayilaadumveettil , Jácome-López Karina , Nora Elphege P. , Bruneau Benoit G. , Furlan-Magaril Mayra , Skok Jane , Reinberg Danny
Published: January 2019

The function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms of how CTCF dynamically contributes to genome organization is not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs; promoting its oligomerization. Here we found that inhibition of transcription or interfering with CTCF ability to bind RNA through mutations of two of its 11 zinc fingers that are not involved with CTCF binding to its cognate site in vitro, zinc finger-1 (ZF1) or −10 (ZF10), disrupt CTCF association to chromatin. These mutations alter gene expression profiles as CTCF mutants lose their ability to promote local insulation. Our results highlight the importance of RNA as a structural component of the genome, in part by affecting the association of CTCF with chromatin and likely its interaction with other factors.

Transcriptional inhibition disrupts CTCF binding to chromatin

RNA-binding regions (RBR) in CTCF are found within ZF1 and ZF10

Local insulation is markedly decreased in ZF1∆ and ZF10∆ mutant rescues

Gene expression and chromatin organization are disrupted by RBR mutants
Potential involvement of root auxins in drought tolerance by modulating nocturnal and daytime water use in wheat
Authors: Sadok Walid , Schoppach Rémy
Published: January 2019

The ability of wheat genotypes to save water by reducing their transpiration rate (TR) under times of the day with high vapour pressure deficit (VPD) has been linked to increasing yields in terminal drought environments. Further, recent evidence shows that reducing nocturnal transpiration (TRN) could amplify water-saving. Previous research indicates that such traits involve a root-based hydraulic limitation, but the contribution of hormones, particularly auxin and abscisic acid (ABA) has not been explored to explain the shoot-root link. In this investigation, based on physiological, genetic and molecular evidence gathered on a mapping population, we hypothesized that root auxin accumulation regulates whole-plant water use during both times of the day. Eight double-haploid lines were selected from a mapping population descending from two parents with contrasted water-saving strategies and root hydraulic properties. These spanned the entire range of slopes of TR responses to VPD and TRN encountered in the population. On those lines, we examined daytime/night-time auxin and ABA contents in the roots and the leaves in relation to hydraulic traits that included whole-plant TR, plant hydraulic conductance (KPlant), slopes of TR responses to VPD and leaf-level anatomical traits. Root auxin levels were consistently genotype-dependent in this group irrespective of experiments and times of the day. Daytime root auxin concentrations were found to be strongly and negatively correlated with daytime TR, KPlant and the slope of TR response to VPD. Night-time root auxin levels significantly and negatively correlated with TRN. In addition, daytime and night-time leaf auxin and ABA concentrations did not correlate with any of the examined traits. The above results indicate that accumulation of auxin in the root system reduces daytime and night-time water use and modulates plant hydraulic properties to enable the expression of water-saving traits that have been associated with enhanced yields under drought.
Gametic specialization of centromeric histone paralogs inDrosophila virilis
Authors: Kursel Lisa E. , Malik Harmit S.
Published: January 2019

In most eukaryotes, centromeric histone (CenH3) proteins mediate the highly conserved process of chromosome segregation as the foundational kinetochore assembly factor. However, in multicellular organisms, CenH3 proteins have to perform their essential functions in different chromatin environments. CenH3 proteins not only mediate mitosis and meiosis but also ensure epigenetic inheritance of centromere identity on sperm chromatin, which is highly compact and almost completely stripped of histones during spermiogenesis. We hypothesized that such disparate chromatin environments might impose different functional constraints on CenH3. If so, gene duplications could ameliorate the difficulty of encoding divergent and even potentially incompatible centromeric functions in the same gene. Here, we analyzed the cytological localization of two recently identified CenH3 paralogs, Cid1 and Cid5, inD. virilisusing specific antibodies and epitope-tagged transgenic strains. We find that only ancestral Cid1 is present in somatic cells, whereas both Cid1 and Cid5 are expressed in testes and ovaries. However, Cid1 and Cid5 are alternately retained in male and female gametes; Cid1 is lost in male meiosis but retained throughout oogenesis, whereas Cid5 is lost during female meiosis but retained in mature sperm. Following fertilization, maternally deposited Cid1 rapidly replaces paternal Cid5 during the protamine-to-histone transition. Our studies reveal mutually exclusive gametic specialization of two divergent CenH3 paralogs. We suggest that centromeric histone duplication and divergence may allow essential genes involved in chromosome segregation to specialize and thereby resolve an intralocus conflict between maternal and paternal centromeric histone requirements in many animal species.
The role of π–π stacking and hydrogen-bonding interactions in the assembly of a series of isostructural group IIB coordination compounds
Authors: Hajiashrafi Taraneh , Zekriazadeh Roghayeh , Flanagan Keith J. , Kia Farnoush , Bauzá Antonio , Frontera Antonio , Senge Mathias O.
Published: January 2019

The supramolecular chemistry of coordination compounds has become an important research domain of modern inorganic chemistry. Herein, six isostructural group IIB coordination compounds containing a 2-{[(2-methoxyphenyl)imino]methyl}phenol ligand, namely dichloridobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)zinc(II), [ZnCl2(C28H26N2O4)], 1, diiodidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)zinc(II), [ZnI2(C28H26N2O4)], 2, dibromidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)cadmium(II), [CdBr2(C28H26N2O4)], 3, diiodidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)cadmium(II), [CdI2(C28H26N2O4)], 4, dichloridobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)mercury(II), [HgCl2(C28H26N2O4)], 5, and diiodidobis(2-{(E)-[(2-methoxyphenyl)azaniumylidene]methyl}phenolato-κO)mercury(II), [HgI2(C28H26N2O4)], 6, were synthesized and characterized by X-ray crystallography and spectroscopic techniques. All six compounds exhibit an infinite one-dimensional ladder in the solid state governed by the formation of hydrogen-bonding and π–π stacking interactions. The crystal structures of these compounds were studied using geometrical and Hirshfeld surface analyses. They have also been studied using M06-2X/def2-TZVP calculations and Bader's theory of `atoms in molecules'. The energies associated with the interactions, including the contribution of the different forces, have been evaluated. In general, the π–π stacking interactions are stronger than those reported for conventional π–π complexes, which is attributed to the influence of the metal coordination, which is stronger for Zn than either Cd or Hg. The results reported herein might be useful for understanding the solid-state architecture of metal-containing materials that contain M
II
X
2 subunits and aromatic organic ligands.
Crystal structure and Hirshfeld surface analysis of a bromochalcone: (E)-1-(3-bromophenyl)-3-(2,6-dichlorophenyl)prop-2-en-1-one
Authors: Bindya S. , Chidan Kumar C. S. , Naveen S. , Siddaraju B. P. , Quah Ching Kheng , Raihan Md. Abu
Published: January 2019

In the title chalcone derivative, C15H9BrCl2O, the aryl rings are inclined to each by 14.49 (17)°, and the configuration about the C=C bond is E. There is a short intramolecular C—H...Cl contact present resulting in the formation of an S(6) ring motif. In the crystal, the shortest intermolecular contacts are Cl...O contacts [3.173 (3) Å] that link the molecules to form a 21 helix propagating along the b-axis direction. The helices stack up the short crystallographic a axis, and are linked by offset π–π interactions [intercentroid distance = 3.983 (1) Å], forming layers lying parallel to the ab plane. A quantification of the intermolecular contacts in the crystal were estimated using Hirshfeld surface analysis and two-dimensional fingerprint plots.
Crystal structures of Ca4+x
Y3–x
Si7O15+x
N5–x
(0 ≤ x ≤ 1) comprising of an isolated [Si7(O,N)19] unit
Authors: Kobayashi Makoto , Yasunaga Takuya , Kato Hideki , Fujii Kotaro , Yashima Masatomo , Kakihana Masato
Published: January 2019

Single crystals of the solid solution series Ca4+x
Y3–x
Si7O15+x
N5–x
were obtained by a solid-state reaction method using a flux for x = 0, 0.5 and 1, resulting in Ca4Y3Si7O15N5 (tetracalcium triyttrium heptasilicon oxynitride), Ca4.5Y2.5Si7O15.5N4.5 and Ca5Y2Si7O16N4 (pentacalcium diyttrium heptasilicon oxynitride). Single-crystal X-ray analysis revealed that the three compounds are isotypic and belong to space-group type P63/m. Ca2+ and Y3+ cations are distributed over two crystallographic sites (site symmetry \overline{3}.. and 1) in a disordered manner. The corresponding (Ca,Y)-centred polyhedra are connected by edge-sharing, resulting in the formation of a layer structure extending parallel to (001). Three [Si(O,N)]4 tetrahedra (two with point group symmetry m.., one with 3.. and half-occupancy) are condensed into an isolated [Si7(O,N)19] unit, in which an [Si(O,N)]4 tetrahedron is located at the center of a 12-membered oxynitride ring with composition [Si6O15N3]. The present compounds are the first to have such an [Si7(O,N)19] unit in their structures.
Organizational readiness for change: an inherent concern for Indian small and medium enterprises (SMEs)
Authors: Budhiraja Sunil
Published: January 2019

Purpose

This paper aims to discuss various determinants of organizational readiness to change for India small and medium enterprises (SMEs) and proposes a framework to strengthen the employees’ readiness to change which is integral to organizational readiness for change (ORC).

Design/methodology/approach

This paper is based upon the subjective viewpoint of the author.

Findings

The paper brings forward the opportunities and challenges of Indian SMEs with a suggestive framework on employee readiness for change (ERC).

Practical implications

The paper will help SMEs consider a framework to assess ERC before implementing a change.

Originality/value

The exists no framework for Indian SMEs to look-up as a benchmark to assess their ORC and ERC. Hence the paper will contribute to the literature and will be a handy reference for SMEs.
How can universities align bricks with modern learning?
Authors: van Sprang Hester , Driessen Jasper , Groen Brenda
Published: January 2019

Purpose

This study aims to explore modern learning (ML) scenarios in Dutch higher education towards 2030 and corresponding consequences for facility management (FM) and corporate real estate strategies (CRES) of universities of applied sciences (UAS).

Design/methodology/approach

The designing an accommodation strategy model is used to retrieve the match between demand and supply in real estate of Dutch UAS for both present and future. Application of this model resulted in a scenario-planning session with six education experts to determine future demand in education towards 2030. Subsequently, corporate real estate (CRE) managers of nine Dutch UAS were interviewed concerning this subject (one per UAS).

Findings

The results show that CRES of Dutch UAS is only partly aligned to consequences of ML scenarios towards 2030. Most UAS have real estate portfolios that are only partially flexible, so changes in qualitative and quantitative demand due to ML scenarios are not easy to adapt to. The consequences for FM and real estate of the ML scenarios “institute learning” and “mass customization” seem manageable for Dutch UAS, whereas the other ML scenarios, namely, “navigator” and “natural learning”, would create major portfolio problems.

Originality/value

There is an ongoing interest in developments in higher education combined with FM and CRES and its alignment with the corporate vision. Previous studies into modern ways of learning mainly focused on the past and present. However, this study is explorative and explores possible future ML scenarios. These scenarios can contribute to awareness amongst UAS in The Netherlands and abroad regarding their long-term vision. Moreover, these scenarios will help Dutch UAS facility and CRE managers to develop a more future-proof strategic real estate strategy aligned with the corporate vision.
Structural damage localization through multi-channel empirical mode decomposition
Authors: Salehi Mehdi , Azami Mansour
Published: January 2019

Purpose

The purpose of this paper is to develop a new structural damage detection technique based on multi-channel empirical mode decomposition (MEMD) of vibrational response data.

Design/methodology/approach

Empirical mode decomposition (EMD) is an empirical data-based signal decomposition method which has been applied in many engineering problems. Utilizing classical EMD to reveal the damage-indicating features of structural vibration response encounters some difficulties due to the inconsistency of modes obtained from different data channels. To overcome this problem, MEMD has been employed. To this end, MEMD algorithm has been adopted to impulse response vector of measured DOFs. The proposed method has been carried out concerning both numerical and experimental beam models. Damage has been modeled by reducing the flexural rigidity in some predefined beam sections. The effects of various factors such as measurement grid density, damage severity and damage position are investigated.

Findings

The results of both numerical and experimental case studies have been promising. The method could determine the damage location in all cases. The efficiency of method gets better when damage is located far from inflation points of the corresponding mode. In such cases, utilizing higher modes can make up the efficiency.

Research limitations/implications

Since the present research is the first investigation of MEMD in damage localization, just one-dimensional structures have been studied. Extending the method to more complicated geometries needs further attempt.

Originality/value

Although a number of relevant studies have been carried out based on EMD, up to the author’s best knowledge, this is the first attempt to structural damage localization using MEMD.
Examining predictive factors and effects of in-class multitasking with mobile phones
Authors: Deng Liping , Ku Kelly Yee Lai , Kong Qiuyi
Published: January 2019

Purpose

The study aims to give a descriptive account of university students’ engagement with non-learning-related activities during class time and explore the relationship between off-task multitasking and learning. The predictive factors for off-task multitasking from individual, social and class-related dimensions are also examined.

Design/methodology/approach

Contextualized in a comprehensive university in Hong Kong, the study adopts a survey design and involves 79 samples.

Findings

The data show that Hong Kong university students are avid users of mobile phones and heavily engage with digital devices. Off-task multitasking with mobile phones is a common phenomenon, yet not related to learning performance. Among the various media and apps on mobile phones, instant messenger stands out as the most frequently used app on a daily basis and inside the classroom. The individual device-use habit and classroom engagement are significant predictors for off-task multitasking during class time.

Practical implications

This paper will allow teachers and students to be more aware of the causes and effects of off-task multitasking behaviors during class time and derive practical guidance and strategies to pay heed to and resist the disruptive influence of technologies on learning.

Originality/value

The existing scholarly work show a mixed and incomplete picture regarding the effects and determining factors of students’ multitasking. This study includes three variables from individual, social and teaching/learning dimensions and seeks to evaluate their predictive strengths. The results of the study will deepen our understanding of the patterns of off-task multitasking.
Assessing the level of knowledge and practice of breastfeeding among factory working mothers in Kathmandu, Nepal
Authors: Sharma Ira , Khadka Arati
Published: January 2019

Purpose

The purpose of this paper is to assess the level of knowledge and practice of breastfeeding among factory working mothers in Kathmandu who had a minimum of one child of less than two years of age.

Design/methodology/approach

A cross-sectional survey, with the help of a semi-structured questionnaire, was completed. χ2 or Fisher exact tests were applied for analysis using the SPSS program.

Findings

In total, 36.0 percent of the mothers had adequate knowledge, and 40.0 percent had an appropriate practice of breastfeeding (BF). Also, 30 percent of them were supplementing their BF with additional milk and 54.0 percent began to give additional food at less than six months of age, mainly due to insufficient breast milk. However, 40.0 percent of mothers practiced exclusive BF; 34.0 percent of mothers continued BF until their child reached two years of age. BF was initiated within an hour by 64.0 percent of mothers. Regarding knowledge, the majority of them (82 percent) knew about initiation time of the feed, 64.0 percent of mothers knew that breast milk had positive effects on a child’s health while 48.0 percent knew that it also had good effects on the mothers’ health. There was a positive association between available facilities and BF knowledge levels (p-value<0.00, χ2=4.25, df=1). The associations of knowledge levels against the education status of mothers (p-value=0.11, χ2=2.59, df=1) and practice level of initiation of breast milk (p-value=0.96, χ2=0.02, df=1) were not significant.

Originality/value

The knowledge and practices of BF among factory working mothers are not satisfactory. Hence, an effective way to encourage BF is to increase the availability of facilities for the practice of BF at a mother’s workplace.
Strategic choices of exploration and exploitation alliances under market uncertainty
Authors: Li Wan , Wang Liang
Published: January 2019

Purpose

The purpose of this paper is to provide a better understanding of what drives firms’ choice between exploration alliances and exploitation alliances by examining the role of organizational slack and its interaction with market uncertainty.

Design/methodology/approach

An empirical study is conducted based on 1,614 alliances formed by 581 US biotechnology firms, and the hypotheses are tested using a zero-inflated multilevel Poisson model.

Findings

The results indicate that firms’ strategic choice to pursue exploration or exploitation alliances is a reflection of organizational intention and adaptation to environmental turbulence. More specifically, firms with more financial slack tend to form more exploration alliances and fewer exploitation alliances. However, under high market uncertainty, firms with financial slack tend to establish more exploitative partnerships and avoid exploration collaborations.

Originality/value

This paper contributes to the literature on exploration–exploitation alliances, which tends to fall short of providing an understanding of why organizations pursue such alliances. By identifying the impact of organizational slack and its interaction with market uncertainty, this study shows that organizations are able to respond to environmental change, and those with capabilities are likely to craft their strategic choice configurations based on their own characteristics.