bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-Term Follow-Up of Osseointegrated Orbital Prosthetic Reconstruction
Authors: DeSerres Joshua J. , Budden Curtis R. , Wolfaardt Johan F. , Wilkes Gordon H.
Published: September 2017

Background:

Osseointegrated implants have been used for craniofacial prosthetic reconstruction since 1979. The authors sought to review long-term outcomes of osseointegrated orbital reconstruction at the Institute for Reconstructive Sciences in Medicine (iRSM).

Methods:

Twenty-six patients have undergone osseointegrated orbital prosthetic (OOP) reconstruction at iRSM since 1991. A retrospective chart review was performed and patient satisfaction assessed through a questionnaire used in previous osseointegration studies. Multivariate binary logistic regression analysis was performed to assess the relationship between smoking, age, sex, and previous radiation treatment with the occurrence of skin reactions and implant failures. A χ
2 test was used to assess the relationship between implant position within the orbit and development of a skin reaction or implant failure.

Results:

Patients received an average of 5.8 implants during the course of treatment. Follow-up ranged from 6 months to 24 years (mean = 10.6 years). A statistically significant correlation was found between skin reaction and age (P = 0.022), with younger patients more likely to develop a reaction. No variables in our model were significant for predicting implant failure. Overall, there were 39 failures of 155 osseointegrated implants, for a success rate of 74.8%. There was no relationship between skin reaction and implant failure compared to implant position within the orbit. Survey responses were received from 11 of 19 patients (58% response rate). Ninety-one percent of patients were overall satisfied with their prosthesis.

Conclusions:

There are minimal contraindications for consideration of OOP reconstruction. Patients find their prosthesis comfortable, report increased self-confidence, and are happy to have undergone reconstruction.
Use of Pedicled Buccal Fat Pad for Midface Augmentation
Authors: Lee Tae Sung , Park Sanghoon
Published: September 2017

The pedicled buccal fat pad has occasionally been used for the closure of oroantral and oronasal fistulae. However, this versatile and convenient technique has not been used widely in the field of esthetic surgery. The main cosmetic interest in the buccal fat pads was to surgically extract them to reduce cheek prominence. Here, the authors introduce a novel operative technique using the pedicled buccal fat pad for midface augmentation in patients with deficient soft-tissue volume, particularly in the anterior malar or paranasal region. This rather simple surgical method can be performed either individually or concomitantly with reduction malarplasty. The surgical outcomes include a natural appearance with reliable long-term stability.
Predicting the Severity of Acute Pancreatitis With Red Cell Distribution Width at Early Admission Stage
Authors: Zhang Ting , Liu Hua , Wang Dongyan , Zong Pengfei , Guo Changfeng , Wang Feng , Wu Deqing , Tang Maochun , Zhou Jianjun , Zhao Yan
Published: September 2017

Red cell distribution width (RDW) has been proposed as an early prognosis marker with increased mortality in variety of pathophysiological conditions. We hypothesized that elevated RDW could be used in judging the severity of acute pancreatitis (AP). We retrospectively and prospectively studied 545 and 72 AP patients, who were admitted to the Shanghai Tenth People's Hospital of Tongji University, respectively. Compared with mild acute pancreatitis, significantly higher RDW was observed in patients with moderately severe acute pancreatitis and sever acute pancreatitis (14.03 ± 1.74% vs. 13.23 ± 1.23%, P < 0.000). RDW values were also found positively correlated with the patient's blood urea nitrogen (r = 0.120, P = 0.026), creatinine (r = 0.182, P = 0.000), age (r = 0.099, P = 0.028), and bedside index of severity in acute pancreatitis scoring system (r = 0.147, P = 0.001), and were negatively correlated with the serum albumin (r = −0.244, P = 0.000). The area under the receiver-operating characteristics was as follows—RDW: 0.677 (95% confidence interval [CI], 0.619–0.735, P < 0.000); combination of RDW and albumin: 0.693 (95% CI, 0.625–0.761, P < 0.000); and the optimal cutoff value for RDW to predict whether patients with AP should be in intensive care unit (ICU) was 13.55 with a sensitivity of 54.5% and a specificity of 73.6%. In the validation study, AP with RDW ≥ 13.55% had significantly higher ICU admission ratio than those with RDW < 13.55% (44.4% vs. 9.8%, P < 0.000). In conclusion, RDW is positively associated with AP severity, and is likely a useful predictive parameter of AP severity.
Mayer-Rokitansky-Küster-Hauser Syndrome With Bilateral Ovarian Sertoli Cell Tumors: Review of the Literature and Report of a Rare Case
Authors: Juusela Alexander L. , Naghi Ilana , Thani Suresh
Published: September 2017

Background

Patients with Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome are infertile secondary to hypoplasia or complete agenesis of the uterus, yet they remain at risk of primary neoplasms of the ovaries because embryologically the uterus and ovaries develop via separate mechanisms.

Case

A 72-year-old nulliparous woman with a history of primary amenorrhea underwent an exploratory laparotomy for a suspected uterine fibroid. In addition to the pelvic mass, the patient was found to have findings consistent with MRKH syndrome. Postoperative pathological examination demonstrated bilateral ovarian Sertoli cell tumors.

Conclusions

The case presented is unique in that 2 rare pathologies, bilateral Sertoli cell tumors of the ovary and MRKH syndrome, developed concomitantly in the same patient.
Do the Surgical Outcomes of Rectovaginal Fistula Repairs Differ for Obstetric and Nonobstetric Fistulas? A Retrospective Cohort Study
Authors: Karp Natalie E. , Kobernik Emily K. , Berger Mitchell B. , Low Chelsea M. , Fenner Dee E.
Published: September 2017

Objectives

Rectovaginal fistulas can occur from both obstetric and nonobstetric (eg, inflammatory bowel disease, iatrogenic, or traumatic) etiologies. Current data on factors contributing to rectovaginal repair success or failure are limited, making adequate patient counseling difficult. Our objective was to compare outcomes of transperineal rectovaginal fistula repair performed in a single referral center on women with obstetric and nonobstetric causes.

Methods

We performed a retrospective cohort study of women who had a transperineal rectovaginal fistula repair performed by a urogynecologist at the University of Michigan from 2005 to 2015. Data were obtained by chart review and included demographics, medical comorbidities, fistula etiology, history of a prior fistula repair, failure of current repair, time to failure, and operative details. Repair failure was defined as fistula symptoms with presence of recurrent fistula on exam or imaging in the postoperative follow-up period. Comparisons between the obstetric and nonobstetric cohorts were performed using χ2, Fisher exact, and Wilcoxon rank sum tests. Relative risks were calculated to identify predictors of failure.

Results

Eighty-eight women were included—53 obstetric and 35 nonobstetric fistulas. The overall fistula repair failure rate was 22.7% (n = 20). Median follow-up was 157.0 days (range, 47.5–402.0). Of all the factors, only nonobstetric etiology was significantly associated with an increased risk of repair failure (relative risk, 3.53 [range, 1.50–8.32]; P = 0.004.

Conclusions

Nonobstetric rectovaginal fistulas have a nearly 4-fold increased risk of repair failure compared with obstetric fistulas. Our results will help surgeons adequately counsel patients on potential outcomes of surgical repair of obstetric versus nonobstetric rectovaginal fistulas.
Palliative care in neuromuscular diseases
Authors: de Visser Marianne , Oliver David J.
Published: September 2017

Purpose of review

Palliative care is an approach that improves the quality of life of patients and their families facing the problem associated with life-threatening illness. Neuromuscular disorders (NMDs) are characterized by progressive muscle weakness, leading to pronounced and incapacitating physical disabilities. Most NMDs are not amenable to curative treatment and would thus qualify for palliative care. Amyotrophic lateral sclerosis is a relentlessly progressive disease, which leads to death about 2 years after onset due to respiratory muscle weakness. Increasingly, neurologists caring for these patients learn to apply the principles of palliative care. However, this does not yet apply to other well known and frequently occurring NMDs.

Recent findings

There is sparse literature on palliative care in NMDs such as Duchenne muscular dystrophy, spinal muscular atrophy, muscular dystrophies, some congenital myopathies, Pompe's disease and myotonic dystrophy type 1. These NMDs are often associated with imminent respiratory insufficiency and/or heart failure leading to a reduced life expectancy. Reasons for underutilization may include misconceptions about palliative care amongst patients, family carers and healthcare professionals or lack of awareness of the usefulness of this approach in these severely affected patients and the possibilities of integration of palliative principles into care for children and adults with NMDs.

There is an urgent need for increased attention to the development of palliative care in chronic progressive neuromuscular diseases associated with increasing functional incapacities and premature death. This will require education and training of the healthcare professionals, involvement of patient associations and funding to perform research.
Metabolic connectivity: methods and applications
Authors: Yakushev Igor , Drzezga Alexander , Habeck Christian
Published: September 2017

Purpose of review

Metabolic connectivity modelling aims to detect functionally interacting brain regions based on PET recordings with the glucose analogue [18F]fluorodeoxyglucose (FDG). Here, we outline the most popular metabolic connectivity methods and summarize recent applications in clinical and basic neuroscience.

Recent findings

Metabolic connectivity is modelled by various methods including a seed correlation, sparse inverse covariance estimation, independent component analysis and graph theory. Given its multivariate nature, metabolic connectivity possess added value relative to conventional univariate analyses of FDG-PET data. As such, metabolic connectivity provides valuable insights into pathophysiology and diagnosis of dementing, movement disorders, and epilepsy. Metabolic connectivity can also identify resting state networks resembling patterns of functional connectivity as derived from functional MRI data.

Metabolic connectivity is a valuable concept in the fast-developing field of brain connectivity, at least as reasonable as functional connectivity of functional MRI. So far, the value of metabolic connectivity is best established in neurodegenerative disorders, but studies in other brain diseases as well as in the healthy state are emerging. Growing evidence indicates that metabolic connectivity may serve a marker of normal and pathological cognitive function. A relationship of metabolic connectivity with structural and functional connectivity is yet to be established.
Pregabalin Toxicity Manifesting as Reversible Encephalopathy With Continuous Triphasic Waves in Electroencephalogram
Authors: Parekh Mihir , Dash Gopal Krishna , Ahamed Isthiaque
Published: September 2017

A 74-year-old man with peripheral neuropathy due to diabetes presented with deliberate ingestion of 450 mg of pregabalin (PBG) over a period of 8 hours followed by altered mental status. A bedside electroencephalogram was performed to rule out nonconvulsive status epilepticus, which showed continuous triphasic waves (TWs) with slow background activity. He recovered after 48 hours of stopping PBG, and his repeat electroencephalogram after 72 hours did not show any TWs. We present a rare case of PBG-induced TWs thereby highlighting the extent of the etiologic spectrum of TWs and discussing the literature related to this association.
Benign Neonatal Sleep Myoclonus Evokes Somatosensory Responses
Authors: Losito Emma , Eisermann Monika , Vignolo Patricia , Hovhannisyan Shushanik , Magny Jean François , Kaminska Anna
Published: September 2017

Purpose:

Benign neonatal sleep myoclonus is a common nonepileptic condition occurring in neurologically normal full-term newborns. During jerks, EEG has always been described as normal. The aim of this study was to describe EEG changes associated with the myoclonic jerks.

Methods:

Polygraphic video-EEG recordings of four full-term neonates presenting benign neonatal sleep myoclonus were studied. Myoclonic jerks were analyzed regarding their topography, frequency, propagation pattern, and reflex component. EEG averaging time-locked to myoclonic jerks and to somatosensory stimuli (realized by tapping on palms and feet) was performed to study eventual EEG correlates of myoclonus and to asses somatosensory evoked responses—for the latter, two control newborns were added.

Results:

Visual analysis of the EEG disclosed theta band slow waves on central and vertex electrodes concomitant to myoclonic jerks and jerk-locked back-averaging disclosed a sequence of deflections, not preceding, but following the myoclonus. This response predominated on the vertex electrode (CZ) and consisted of five components (N1, P1, N2, P2, and N3), with only the three later components being constantly present (at 110, 200, and 350–500 ms, respectively). Back-averaging locked to the tactile stimuli in four subjects and two control newborns showed similar components and were comparable to those described in the literature as late somatosensory evoked responses in full-term newborns.

Conclusions:

Myoclonic jerks in benign neonatal sleep myoclonus can evoke visually identifiable EEG potentials on vertex electrodes corresponding to somatosensory responses. This EEG aspect may be misleading and could give rise to an anti-seizure treatment that mostly worsens the condition.
Integrated analysis of patterns of DNA breaks reveals break formation mechanisms and their population distribution during replication stress
Authors: Zhu Yingjie , Biernacka Anna , Pardo Benjamin , Forey Romain , Dojer Norbert , Yousefi Raziyeh , Nde Jules , Fongang Bernard , Mitra Abhishek , Li Ji , Skrzypczak Magdalena , Kudlicki Andrzej , Pasero Philippe , Ginalski Krzysztof , Rowicka Maga
Published: September 2017

DNA double-strand breaks (DSBs) can be detected by label-based sequencing or pulsed-field gel electrophoresis (PFGE). Sequencing yields population-average DSB frequencies genome-wide, while PFGE reveals percentages of broken chromosomes. We constructed a mathematical framework to combine advantages of both: high-resolution DSB locations and their population distribution. We also use sequencing read patterns to identify replication-induced DSBs and active replication origins. We describe changes in spatiotemporal replication program upon hydroxyurea-induced replication stress. We found that one-ended DSBs, resulting from collapsed replication forks, are population-representative, while majority of two-ended DSBs (79-100%) are not. To study replication fork collapse, we used strains lacking the checkpoint protein Mec1 and the endonuclease Mus81 and quantified that 19% and 13% of hydroxyurea-induced one-ended DSBs are Mec1-and Mus81-dependent, respectively. We also clarified that Mus81-induced one-ended DSBs are Mec1-dependent.
accuMUlate: A mutation caller designed for mutation accumulation experiments
Authors: Winter David J. , Wu Steven H. , Howell Abigail A. , Azevedo Ricardo B. R. , Zufall Rebecca A. , Cartwright Reed A.
Published: September 2017

Motivation

Mutation accumulation (MA) is the most widely used method for directly studying the effects of mutation. Modern sequencing technologies have led to an increased interest in MA experiments. By sequencing whole genomes from MA lines, researchers can directly study the rate and molecular spectra of spontaneous mutations and use these results to understand how mutation contributes to biological processes. At present there is no software designed specifically for identifying mutations from MA lines. Studies that combine MA with whole genome sequencing use custom bioinformatic pipelines that implement heuristic rules to identify putative mutations.

Results

Here we describeaccuMUlate, a program that is designed to detect mutations from MA experiments.accuMUlateimplements a probabilistic model that reflects the design of a typical MA experiments while being flexible enough to accommodate properties unique to any particular experiment. For each putative mutation identified from this modelaccuMUlatecalculates a set of summary statistics that can be used to filter sites that may be false positives. A companion tool,denominate, can be used to apply filtering rules based on these statistics to simulated mutations and thus identify the number of callable sites per sample.

Availability

Source code and releases available fromhttps://github.com/dwinter/accuMUlate.
Measuring the reproducibility and quality of Hi-C data
Authors: Yardımcı Galip Gürkan , Ozadam Hakan , Sauria Michael E.G. , Ursu Oana , Yan Koon-Kiu , Yang Tao , Chakraborty Abhijit , Kaul Arya , Lajoie Bryan R. , Song Fan , Zhang Ye , Ay Ferhat , Gerstein Mark , Kundaje Anshul , Li Qunhua , Taylor James , Yue Feng , Dekker Job , Noble William S.
Published: September 2017

Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study. Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established (e.g., ratio of intra to interchromosomal interactions) and novel (e.g., QuASAR-QC) measures to identify low quality experiments. In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available athttp://github.com/kundajelab/3DChromatin_ReplicateQCto facilitate adoption in the community.
Single synapses control mossy cell firing
Authors: Drakew Alexander , Maier Urban , Tippmann Anja , Frotscher Michael
Published: September 2017

The function of mossy cells (MCs) in the dentate gyrus has remained elusive. Here we determined the functional impact of single mossy fibre (MF) synapses on MC firing in mouse entorhino-hippocampal slice cultures. We stimulated single MF boutons and recorded Ca2+transients in the postsynaptic spine and unitary excitatory postsynaptic potentials (EPSPs) at the MC soma. Synaptic responses to single presynaptic stimuli varied strongly between different MF synapses, even if they were located on the same MC dendrite. Synaptic strengths ranged from subthreshold EPSPs to direct postsynaptic action potential (AP) generation. Induction of synaptic plasticity at these individual MF synapses resulted in potentiation or depression depending on the initially encountered synaptic state, indicating that synaptic transmission at MF synapses on MCs is determined by their previous functional history. With these unique functional properties MF-MC synapses control MC firing individually thereby enabling modulation of the dentate network by single granule cells.
Generation and validation of homozygous fluorescent knock-in cells using CRISPR/Cas9 genome editing
Authors: Koch Birgit , Nijmeijer Bianca , Kueblbeck Moritz , Cai Yin , Walther Nike , Ellenberg Jan
Published: September 2017

Gene tagging with fluorescent proteins is essential to investigate the dynamic properties of cellular proteins. CRISPR/Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and permits functionality and physiological expression of the fusion protein. It is essential to evaluate such genome-edited cell lines carefully in order to preclude off-target effects caused by either (i) incorrect insertion of the fluorescent protein, (ii) perturbation of the fusion protein by the fluorescent proteins or (iii) non-specific genomic DNA damage by CRISPR/Cas9. In this protocol1, we provide a step-by-step description of our systematic pipeline to generate and validate homozygous fluorescent knock-in cell lines.

We have used the paired Cas9D10A nickase approach to efficiently insert tags into specific genomic lociviahomology-directed repair with minimal off-target effects. It is time- and cost-consuming to perform whole genome sequencing of each cell clone. Therefore, we have developed an efficient validation pipeline of the generated cell lines consisting of junction PCR, Southern Blot analysis, Sanger sequencing, microscopy, Western blot analysis and live cell imaging for cell cycle dynamics. This protocol takes between 6-9 weeks. Using this protocol, up to 70% of the targeted genes can be tagged homozygously with fluorescent proteins and result in physiological levels and phenotypically functional expression of the fusion proteins.

Editorial Summary

This protocol provides a detailed workflow describing how to insert fluorescent markers into all alleles of a gene of interest using CRISPR/Cas 9 technology and how to generate and validate homozygous fluorescent knock-in cell lines.
Cortical Connectivity In A Macaque Model Of Congenital Blindness
Authors: Magrou Loïc , Barone Pascal , Markov Nikola T. , Killackey Herbert , Giroud Pascale , Berland Michel , Knoblauch Kenneth , Dehay Colette , Kennedy Henry
Published: September 2017

Brain-mapping of the congenitally blind human reveals extensive plasticity(1). The visual cortex of the blind has been observed to support higher cognitive functions including language and numerical processing(2, 3). This functional shift is hypothesized to reflect a metamodal cortical function, where computations are defined by the local network. In the case of developmental deafferentation, local circuits are considered to implement higher cognitive functions by accommodating diverse long-distance inputs(4–7). However, the extent to which visual deprivation triggers a reorganization of the large-scale network in the cortex is still controversial(8). Here we show that early prenatal ablation of the retina, an experimental model of anophthalmia in macaque, leads to a major reduction of area V1 and the creation of a default extrastriate cortex (DEC)(9, 10). Anophthalmic and normal macaques received retrograde tracer injections in DEC, as well as areas V2 and V4 post-natally. This revealed a six-fold expansion of the spatial extent of local connectivity in the DEC and a surprisingly high location of the DEC derived from a computational model of the cortical hierarchy(11). In the anophthalmic the set of areas projecting to the DEC, area V2 and V4 does not differ from that of normal adult controls, but there is a highly significant increase in the relative cumulative weight of the ventral stream areas input to the early visual areas. These findings show that although occupying the territory that would have become primary visual cortex the DEC exhibits features of a higher order area, thus reflecting a combination of intrinsic and extrinsic factors on cortical specification. Understanding the interaction of these contributing factors will shed light on cortical plasticity during primate development and the neurobiology of blindness.
A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals
Authors: Ros-Freixedes Roger , Gonen Serap , Gorjanc Gregor , Hickey John M
Published: September 2017

Background

This paper describes a heuristic method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals. Low-coverage sequencing assembles high-coverage sequence information for every individual by accumulating data from the genome segments that they share with many other individuals into consensus haplotypes. Deriving the consensus haplotypes accurately is critical for achieving a high phasing and imputation accuracy. In order to enable accurate phasing and imputation of sequence information for the whole population we allocate the available sequencing resources among individuals with existing phased genomic data by targeting the sequencing coverage of their haplotypes.

Results

Our method, called AlphaSeqOpt, prioritizes haplotypes using a score function that is based on the frequency of the haplotypes in the sequencing set relative to the target coverage. AlphaSeqOpt has two steps: (1) selection of an initial set of individuals by iteratively choosing the individuals that have the maximum score conditional to the current set, and (2) refinement of the set through several rounds of exchanges of individuals. AlphaSeqOpt is very effective for distributing a fixed amount of sequencing resources evenly across haplotypes, which results in a reduction of the proportion of haplotypes that are sequenced below the target coverage. AlphaSeqOpt can provide a greater proportion of haplotypes sequenced at the target coverage by sequencing less individuals, as compared with other methods that use a score function based on the haplotypes population frequency. A refinement of the initially selected set can provide a larger more diverse set with more unique individuals, which is beneficial in the context of low-coverage sequencing. We extend the method with an approach to filter rare haplotypes based on their flanking haplotypes, so that only those that are likely to derive from a recombination event are targeted.

Conclusions

We present a method for allocating sequencing resources so that a greater proportion of haplotypes are sequenced at a coverage that is sufficiently high for population-based imputation with low-coverage sequencing. The haplotype score function, the refinement step, and the new approach of filtering rare haplotypes make AlphaSeqOpt more effective for that purpose than methods reported previously for reducing sequencing redundancy.
Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage
Authors: Carella Philip , Gogleva Anna , Tomaselli Marta , Alfs Carolin , Schornack Sebastian
Published: September 2017

The expansion of plants onto land was a formative event that brought forth profound changes to the Earth’s geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogenPhytophthora palmivoracolonizes liverworts, the earliest divergent land plant lineage. We show thatP. palmivoraestablishes a complex tissue-specific interaction withMarchantia polymorpha, where it completes a full infection cycle within air chambers of the dorsal photosynthetic layer. Remarkably,P. palmivorainvaginatesM. polymorphacells with haustoria-like structures that accumulate host cellular trafficking machinery and the membrane-syntaxin MpSYP13B but not the related MpSYP13A. Our results indicate that the intracellular accommodation of filamentous microbes is an ancient plant trait that is successfully exploited by pathogens likeP. palmivora.
Formation of functional, non-amyloidogenic fibres by recombinantBacillus subtilisTasA
Authors: Erskine Elliot , Morris Ryan J , Schor Marieke , Earl Chris , Gillespie Rachel M. C. , Bromley Keith , Sukhodub Tetyana , Clark Lauren , Fyfe Paul K. , Serpell Louise C. , Stanley-Wall Nicola R. , MacPhee Cait E.
Published: September 2017

Bacterial biofilms are communities of microbial cells encased within a self-produced polymeric matrix. In theBacillus subtilisbiofilm matrix the extracellular fibres of TasA are essential. Here a recombinant expression system allows interrogation of TasA, revealing that monomeric and fibre forms of TasA have identical secondary structure, suggesting that fibrous TasA is a linear assembly of globular units. Recombinant TasA fibres form spontaneously, and share the biological activity of TasA fibres extracted fromB. subtilis, whereas a TasA variant restricted to a monomeric form is inactive and subjected to extracellular proteolysis. The biophysical properties of both native and recombinant TasA fibres indicate that they are not functional amyloid-like fibres. A gel formed by TasA fibres can recover after physical shear force, suggesting that the biofilm matrix is not static and that these properties may enableB. subtilisto remodel its local environment in response to external cues. Using recombinant fibres formed by TasA orthologues we uncover species variability in the ability of heterologous fibres to cross-complement theB. subtilis tasAdeletion. These findings are indicative of specificity in the biophysical requirements of the TasA fibres across different species and/or reflect the precise molecular interactions needed for biofilm matrix assembly.

Contributions

Conceived and designed the experiments: CE, EE, RG, CEM, RJM, MS, NSW; Performed the experiments: KB, LC, CE, EE, PKF, RG, CEM, RJM, MS, TS; Contributed new analytical tools: CE, EE, RG, TS; Analysed the data: CE, EE, CEM, RJM, MS, LCS, NSW; Wrote the paper: EE, RJM, CEM, MS, NSW.
Assessing robustness against potential publication bias in coordinate based fMRI meta-analyses using the Fail-Safe N
Authors: Acar Freya , Seurinck Ruth , Eickhoff Simon B. , Moerkerke Beatrijs
Published: September 2017

The importance of integrating research findings is incontrovertible and coordinate based meta-analyses have become a popular approach to combine results of fMRI studies when only peaks of activation are reported. Similar to classical meta-analyses, coordinate based meta-analyses may be subject to different forms of publication bias which impacts results and possibly invalidates findings. We develop a tool that assesses the robustness to potential publication bias on cluster level. We investigate the possible influence of the file-drawer effect, where studies that do not report certain results fail to get published, by determining the number of noise studies that can be added to an existing fMRI meta-analysis before the results are no longer statistically significant. In this paper we illustrate this tool through an example and test the effect of several parameters through extensive simulations. We provide an algorithm for which code is freely available to generate noise studies and enables users to determine the robustness of meta-analytical results.
Conservation of preparatory neural events regardless of how movement is initiated
Authors: Lara Antonio H. , Elsayed Gamaleldin F. , Cunningham John P. , Churchland Mark M.
Published: September 2017

Voluntary movement is believed to be preceded by a preparatory stage. Evidence arises from experiments where a delay separates instruction and execution cues. While this sequence emulates some real-world situations (e.g., swatting a fly upon landing) movements are commonly made at a moment of one’s choosing (reaching for a coffee cup) or are made reactively (intercepting a falling cup). To ascertain whether neural events are conserved across such contexts, we examined motor cortex population-level responses in monkeys when reaches were initiated either after an imposed delay, at a self-chosen time, or reactively with very low latency. We found that the same preparatory and movement-related events were conserved. However, preparation was temporally flexible and could be remarkably brief. Our findings support the existing hypothesis that preparation is an obligatory stage that achieves a consistent state prior to movement. Yet our results reveal that preparation can unfold more rapidly than previously supposed.
Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity
Authors: Mao Peng , Brown Alexander J. , Malc Ewa P. , Mieczkowski Piotr A. , Smerdon Michael J. , Roberts Steven A. , Wyrick John J.
Published: September 2017

DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome-depleted regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad axis and is regulated by histone modifications. Our data also indicate that MMS-induced mutations at adenine nucleotides are significantly enriched on the nontranscribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers.
Bis[N-2-hydroxyethyl,N-methyldithiocarbamato-κ2S,S)'-4-{[(pyridin-4-ylmethylidene)hydrazinylidene}methyl]pyridine-κN1)zinc(II): crystal structure and Hirshfeld surface analysis
Authors: Broker Grant A. , Jotani Mukesh M. , Tiekink Edward R. T.
Published: September 2017

In the title compound, [Zn(C4H8NOS2)2(C12H10N4)], the ZnIIatom exists within a NS4donor set defined by two chelating dithiocarbamate ligands and a pyridyl-Natom derived from a terminally bound 4-pyridinealdazine ligand. The distorted coordination geometry tends towards square-pyramidal with the pyridyl-N atom occupying the apical position. In the crystal, hydroxyl-O—H...O(hydroxyl) and hydroxyl-O—H...N(pyridyl) hydrogen-bonding give rise to a supramolecular double-chain along [1-10]; methyl-C—H...π(chelate ring) interactions help to consolidate the chain. The chains are connected into a three-dimensional architectureviapyridyl-C—H...O(hydroxyl) interactions. In addition to the contacts mentioned above, the Hirshfeld surface analysis points to the significance of relatively weak π–π interactions between pyridyl rings [inter-centroid distance = 3.901 (3) Å].
Adaptive finite element method for eigensolutions of regular second and fourth order Sturm-Liouville problems via the element energy projection technique
Authors: Yuan Si , Ye Kangsheng , Wang Yongliang , Kennedy David , Williams Frederic W.
Published: September 2017

Purpose

The purpose of this paper is to present a numerically adaptive finite element (FE) method for accurate, efficient and reliable eigensolutions of regular second- and fourth-order Sturm–Liouville (SL) problems with variable coefficients.

Design/methodology/approach

After the conventional FE solution for an eigenpair (i.e. eigenvalue and eigenfunction) of a particular order has been obtained on a given mesh, a novel strategy is introduced, in which the FE solution of the eigenproblem is equivalently viewed as the FE solution of an associated linear problem. This strategy allows the element energy projection (EEP) technique for linear problems to calculate the super-convergent FE solutions for eigenfunctions anywhere on any element. These EEP super-convergent solutions are used to estimate the FE solution errors and to guide mesh refinements, until the accuracy matches user-preset error tolerance on both eigenvalues and eigenfunctions.

Findings

Numerical results for a number of representative and challenging SL problems are presented to demonstrate the effectiveness, efficiency, accuracy and reliability of the proposed method.

Research limitations/implications

The method is limited to regular SL problems, but it can also solve some singular SL problems in an indirect way.

Originality/value

Comprehensive utilization of the EEP technique yields a simple, efficient and reliable adaptive FE procedure that finds sufficiently fine meshes for preset error tolerances on eigenvalues and eigenfunctions to be achieved, even on problems which proved troublesome to competing methods. The method can readily be extended to vector SL problems.
The relationship between innovation and total quality management and the innovation effects on organizational performance
Authors: Antunes Marina Godinho , Quirós Joaquín Texeira , Justino Maria do Rosário Fernandes
Published: September 2017

Purpose

The purpose of this paper is to analyze the relationship between innovation and total quality management (TQM), and also to identify the effects of innovation on organizational performance. This research proposes a conceptual model that intends to study several research hypotheses.

Design/methodology/approach

The data were obtained through an online questionnaire, sent to small- and medium-sized Portuguese companies, having being conducted the study based on responses received from 287 valid questionnaires, and using a multivariate statistical analysis for statistical development.

Findings

The findings indicate that companies that adopt strategies of process innovation get improvements in their performance, both operationally and financially, while product innovation only provides improvements in the financial performance of organizations. It was also found that TQM practices encourage the definition of innovation strategies of products and processes. On the other hand, it was found that only companies that adopt innovation strategies of their processes promote the adoption of TQM practices, and there is a statistically significant relationship between product innovation and the implementation of TQM practices.

Originality/value

This research analyzed the dimensions studied in different aspects. It considered product innovation and process innovation, and with respect to performance, this dimension was analyzed through two different perspectives, namely, financial performance and operational performance. This research also provides a particular contribution to the literature with the analysis of the interdependencies between innovation and TQM in small- and medium-sized Portuguese companies.
Lean Six Sigma for public sector organizations: is it a myth or reality?
Authors: Antony Jiju , Rodgers Bryan , Cudney Elizabeth A.
Published: September 2017

Purpose

Lean Six Sigma (LSS) as a process excellence has been widely adopted in both manufacturing and service organizations; however, its application in the public sector has not been widely explored. Is LSS still a myth or reality in our public sector organizations? The purpose of this paper is to make an attempt to debate about the use of LSS and its potential applications in the public sector context.

Design/methodology/approach

The initial approach is to critically evaluate the role of LSS in various public sector contexts, followed by showcasing four case studies from four different public sector settings: higher education, police service, public hospital and local government.

Findings

LSS methodology can be embraced by all public sector organizations to create efficient and effective processes to provide enhanced customer experience and value at reduced operational costs.

Research limitations/implications

This paper seeks to contribute to and broaden the limited body of evidence of the applicability of LSS to public sector organizations and identifies areas for further research and review.

Practical implications

LSS will continue to grow across many public sector organizations in Europe and other parts of the world over the forthcoming years. However, what will eventually determine if LSS is viewed by public sector organizations as just a passing management fad or not largely depends on the leadership and success of its execution. If LSS is deployed in its true sense across the public sector organizations at a global level, the hard cash savings generated can reach several billions.

Originality/value

The paper yields an immense value to both research scholars and practitioners who are engaged in the introduction of LSS as a business process improvement strategy to achieve and sustain competitive advantage. Moreover, this paper makes an attempt to dispel the myth of LSS which have been quite prevalent in many public sector organizations around us today.
Can sector-specific REIT strategies outperform a diversified benchmark?
Authors: Moss Alex , Clare Andrew , Thomas Stephen , Seaton James
Published: September 2017

Purpose

The authors in this paper aim to investigate the performance of different portfolios of REITs which specialise by property type compared to the performance of a diversified free-float market capitalisation-weighted benchmark index to determine whether superior risk-adjusted returns can be achieved.

Design/methodology/approach

First, the authors examine the performance of portfolios constructed using the criteria of equal weight, minimum variance, maximum Sharpe and risk parity rather than free-float market capitalisation. Second, the authors apply an automated trading strategy of trend following to see if this filter will improve risk-adjusted returns.

Findings

The two-step process of forming combinations of REIT sectors with the subsequent addition of a trend following overlay can offer clear benefits relative to a passive benchmark investment.

Research limitations/implications

Although three of the four strategies were shown to outperform the benchmark index on a risk-adjusted basis, one issue was that the efficient portfolios tended to have large weightings to relatively few sectors. The authors also found that maximum drawdowns (losses) of the strategies tended to be rather high, as was the benchmark.

Practical implications

The methods outlined in this paper can be applied to construct superior risk-adjusted REIT portfolios globally.

Originality/value

Although studies have been undertaken separately on REIT specialisation and trend following in equity and commodity markets, this paper is the first to combine the two topics, and therefore has particular value for real estate fund managers globally.
Corporate real estate, capital structure and value creation
Authors: Bosch-Badia Maria-Teresa , Montllor-Serrats Joan , Panosa-Gubau Anna-Maria , Tarrazon-Rodon Maria-Antonia
Published: September 2017

Purpose

This paper aims to analyse the corporate rent-vs-buy decision on real estate through the trade-off theory and default option in the framework of a corporation that aims to optimise its capital structure.

Design/methodology/approach

The methodological core of this paper comprises the trade-off theory that approaches the optimal capital structure by counterbalancing debt tax savings with bankruptcy costs. Impacts on the default option and the default barrier are made explicit. The paper also explores the practical applicability of the renting scenarios in the European context by examining the regimes of real estate investment trusts in different countries from the demand-side of commercial renting.

Findings

Analytical relationships with tax savings, bankruptcy costs, default option and default barrier are identified for the renting-vs-buying real estate decisions.

Research limitations/implications

The theoretical model assumes simplifications, such as constant debt, to make it operational. The paper centres exclusively on the trade-off capital structure theory.

Practical implications

This paper is an analysis of corporate real estate decisions together with capital structure. Applications are not only quantitative but also conceptual and strategic.

Originality/value

Identifying the main variables that govern the impact of corporate real estate decisions on capital structure and interweaving different approaches generates a conceptual framework that enlightens strategic thinking in this field.
Modeling of thickness effect on the creep properties of Ni-based superalloys
Authors: Wang Xinmei , Wang Yao , Wang Xinzhong
Published: September 2017

Purpose

Specimen thickness has great influences on the creep behavior of single crystal Ni-based superalloys when it is less than 3.0 mm, which is known as thickness debit effect. Experiments have detected that oxidation can influence the microstructure of the Ni-based superalloys. Here, a model is proposed to bring in both the oxidation effect and void caused damage to account for the thickness debit effect. The paper aims to discuss these issues.

Design/methodology/approach

The model uses the simple Norton type creep relation to describe the creep rate evolution. The damage evolution caused by void is taken to be stress controlled. The load baring area changes are calculated with the consideration of oxidation and void evolutions.

Findings

Simulations on specimens with different thickness from 3.0 to 0.3 mm are carried out. The results show that the present model can reproduce the decrease of the creep strength with the decreases of the specimen thickness. The damage plays a major role in the creep behavior of the thick specimen. Both the damage and the oxidation are important for the thin specimen which should be paid attention to during the calculation of the creep response of the thin-wall turbine blade.

Originality/value

A model is proposed to account for the thickness debit effect on the creep behavior of Ni-based superalloys. Both oxidation influence and void caused damage are introduced. The simulation results show the capability of the model to reproduce the thickness debit effect.
Go online or get sidelined
Authors: Richardson Jayson W. , Heintzelman Sara
Published: September 2017

Synopsis

Young professors Baxter, Jim, and Robert are eager to start a new graduate certificate in educational leadership with a focus on technology. The department supports their initiative. The department is even supportive of offering this certificate fully online. Support waned when, in an effort to boost student enrollment, it is suggested that additional graduate courses and programs within the department also move fully online. In department meetings, faculty members argue about the rigor of online courses and if it is possible to convert existing courses and programs to an online delivery format. Tammy and Larry are veteran faculty members who do not want to teach online and have made it clear to the rest of the faculty they are not eager to change. When there are not enough students to offer their programs in the traditional format, all faculty members are forced to begin teach online.

Research methodology

This is a disguised field-researched case.

Relevant courses and levels

This case may be used in a variety of graduate business or education courses, such as introduction to business, business ethics, educational leadership, technology leadership, or higher education.

Theoretical bases

Students should have some understanding of systems change, ethical decision making, and human resources development.