bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinship and familiarity mitigate costs of social conflict between Seychelles warbler neighbors
Authors: Bebbington Kat , Kingma Sjouke A. , Fairfield Eleanor A. , Dugdale Hannah L. , Komdeur Jan , Spurgin Lewis G. , Richardson David S.
Published: October 2017

Significance

In nature, animals must compete with their neighbors for access to limited resources. Since conflict over resources can be extremely costly in terms of time, energy, and reproductive success, investigating how individuals resolve conflict is crucial to understanding the evolution of social behaviors. In the Seychelles warbler, we demonstrate two mechanisms by which individuals minimize costs of conflict and show the benefits individuals gain from doing so. Birds that live near relatives or familiar individuals invest less energy in defending and maintaining territory borders and also show less aging-related signs of physiological damage. Our results suggest that conflict between neighbors can be mitigated by kin-selected benefits of sharing resources with relatives but also through direct mutual benefits of cooperation.
PrimPol is required for replication reinitiation after mtDNA damage
Authors: Torregrosa-Muñumer Rubén , Forslund Josefin M. E. , Goffart Steffi , Pfeiffer Annika , Stojkovič Gorazd , Carvalho Gustavo , Al-Furoukh Natalie , Blanco Luis , Wanrooij Sjoerd , Pohjoismäki Jaakko L. O.
Published: October 2017

Significance

Failure to maintain mtDNA integrity can lead to a wide variety of neuromuscular disorders. Despite its central role in the development of these disorders, many mechanistic details of mtDNA maintenance are still unclear. In the present work, we have studied the role of PrimPol, an unusual primase-polymerase, in mammalian mtDNA maintenance. We report here that PrimPol is specifically required for replication reinitiation after DNA damage. PrimPol synthesizes DNA primers on an ssDNA template, which can be elongated by the mitochondrial replicative polymerase γ, a solution to reprime replication beyond DNA lesions and to facilitate lagging-strand replication. Our findings show that PrimPol has biological relevance for mtDNA maintenance.
Geophysical potential for wind energy over the open oceans
Authors: Possner Anna , Caldeira Ken
Published: October 2017

Significance

Wind speeds over open ocean areas are often higher than those in the windiest areas over land, which has motivated a quest to develop technologies that could harvest wind energy in deep water environments. However, it remains unclear whether these open ocean wind speeds are higher because of lack of surface drag or whether a greater downward transport of kinetic energy may be sustained in open ocean environments. Focusing on the North Atlantic region, we provide evidence that there is potential for greater downward transport of kinetic energy in the overlying atmosphere. As a result, wind power generation over some ocean areas can exceed power generation on land by a factor of three or more.
Maladaptive DNA repair is the ultimate contributor to the death of trimethoprim-treated cells under aerobic and anaerobic conditions
Authors: Giroux Xavier , Su Wei-Lin , Bredeche Marie-Florence , Matic Ivan
Published: October 2017

Significance

Antibiotic resistance leads to substantial mortality and morbidity and significant economic cost because it seriously undermines our ability to treat bacterial infections. Therefore, a better understanding of the effect of antibiotics on bacteria is needed to increase the effectiveness of treatments and slow the emergence of resistance. The bactericidal effects of antibiotics are triggered by target-specific interactions, but there is growing evidence that an important part of their cytotoxicity results from metabolic disturbances induced by treatment. In this article, we report that the perturbation of DNA replication by a wide-spectrum antibiotic, trimethoprim, affects bacterial metabolism, which provokes the production of genotoxic agents and DNA damage, whose processing ultimately contributes to cell death under both aerobic and anaerobic conditions.
Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma
Authors: Ducker Gregory S. , Ghergurovich Jonathan M. , Mainolfi Nello , Suri Vipin , Jeong Stephanie K. , Hsin-Jung Li Sophia , Friedman Adam , Manfredi Mark G. , Gitai Zemer , Kim Hahn , Rabinowitz Joshua D.
Published: October 2017

Significance

Enzymes of the folate cycle are among the most consistently overexpressed proteins in cancer. Whereas multiple clinical agents inhibit thymidylate synthase, no current drugs target the incorporation of one-carbon into folates via serine hydroxymethyltransferase (SHMT). Using genetics, we show that cancer cells require SHMT to generate tumors. We then describe small-molecule SHMT inhibitors, and show that they block the growth of many human cancer cells, with B-cell lymphomas particularly sensitive to SHMT inhibition. We find that this sensitivity arises from the lymphomas’ inability to import the amino acid glycine, which is made as a byproduct of the SHMT reaction. Thus, B-cell lymphomas have an intrinsic defect in amino acid import, which causes a therapeutically targetable metabolic vulnerability.
Visual perception as retrospective Bayesian decoding from high- to low-level features
Authors: Ding Stephanie , Cueva Christopher J. , Tsodyks Misha , Qian Ning
Published: October 2017

Significance

The nature of perceptual decoding remains an open, fundamental question. Many studies assume that decoding follows the same low- to high-level hierarchy of encoding, yet this assumption was never rigorously tested. We performed such a test, which refutes the assumption to the extent that absolute and relative/ordinal orientations are features of different levels. Additionally, the backward aftereffect we discovered cannot be explained by the efficient-coding theories of adaptation. Finally, we proposed a new theory that explains our data as retrospective Bayesian decoding from high to low levels in working memory. This decoding hierarchy is justified by considering memory stability/distortion of high/low-level features. Thus, our work rejects the currently dominant decoding scheme and offers a framework that integrates perceptual decoding and working memory.
Modulation of apoptotic response by LAR family phosphatases–cIAP1 signaling during urinary tract morphogenesis
Authors: Stewart Katherine , Tang You Chi , Shafer Maxwell E. R. , Graham-Paquin Adda-Lee , Bouchard Maxime
Published: October 2017

Significance

Apoptotic morphogenesis requires strict regulation as both excessive and insufficient cell death is detrimental to tissue function. Here we use the process of ureter maturation, wherein the ureter connects to the bladder by the apoptosis-mediated removal of the intervening common nephric duct (CND), to investigate this paradigm. We find that LAR family phosphatases antagonize cIAP1 activity by decreasing its stability, thereby releasing the brake on CND elimination. In addition, we demonstrate that
Birc2
(cIAP1) mutant embryos exhibit increased CND apoptosis, leading to accelerated ureter maturation and vesicoureteral reflux. Together this highlights the importance of modulating the rate of apoptosis during morphogenesis, which may act as a morphogenetic timer to allow for appropriate tissue rearrangements during embryonic development.
Intragenic DNA methylation and BORIS-mediated cancer-specific splicing contribute to the Warburg effect
Authors: Singh Smriti , Narayanan Sathiya Pandi , Biswas Kajal , Gupta Amit , Ahuja Neha , Yadav Sandhya , Panday Rajendra Kumar , Samaiya Atul , Sharan Shyam K. , Shukla Sanjeev
Published: October 2017

Significance

Recent advances in cancer epigenetics have shown the involvement of epigenetic abnormalities in the initiation and progression of cancer, but their role in cancer-specific aberrant splicing is not clear. The identification of upstream epigenetic regulators of cancer-specific splicing will enable us to therapeutically target aberrant splicing and provide an approach to cancer therapy. Here we have demonstrated a mechanism of intragenic DNA methylation-mediated regulation of alternative splicing by Brother of Regulator of Imprinted Sites (BORIS), which can contribute to breast cancer tumorigenesis by favoring the Warburg effect. The reversal of the Warburg effect was achieved by the inhibition of DNA methylation or down-regulation of BORIS, which may serve as a useful approach to inhibit the growth of breast cancer cells.
β
2
-Adrenoceptor signaling in airway epithelial cells promotes eosinophilic inflammation, mucous metaplasia, and airway contractility
Authors: Nguyen Long P. , Al-Sawalha Nour A. , Parra Sergio , Pokkunuri Indira , Omoluabi Ozozoma , Okulate Adedoyin A. , Windham Li Elizabeth , Hazen Matthew , Gonzalez-Granado Jose M. , Daly Craig J. , McGrath John C. , Tuvim Michael J. , Knoll Brian J. , Dickey Burton F. , Bond Richard A.
Published: October 2017

Significance

Activation of β
2
-adrenoreceptors (β
2
ARs) on airway smooth muscle cells produces airway relaxation, and β
2
AR agonists are the most widely used bronchodilators for treating asthma. Paradoxically, murine models show β
2
AR activation is also required for expression of cardinal features of the asthma phenotype, including airway hyperresponsiveness (AHR), inflammation, and mucous metaplasia. However β
2
ARs are expressed on all the cell types implicated in the pathogenesis and maintenance of asthma, and which cell type(s) control these asthmatic effects is unknown. Here we show activation of β
2
AR signaling solely on airway epithelium is sufficient to restore/promote the cardinal features of asthma, including inflammation, mucous metaplasia, and AHR. These studies support the role of the airway epithelium as a master regulator of key features of asthma.
Molecular photoswitches mediating the strain-driven disassembly of supramolecular tubules
Authors: Fredy Jean W. , Méndez-Ardoy Alejandro , Kwangmettatam Supaporn , Bochicchio Davide , Matt Benjamin , Stuart Marc C. A. , Huskens Jurriaan , Katsonis Nathalie , Pavan Giovanni M. , Kudernac Tibor
Published: October 2017

Significance

Developing molecular machines has been a leading goal for scientists, but to be practically valuable their mechanically relevant motion must be decoupled from the Brownian storm that dominates in solution. The disassembly of cellular tubules operates by the switching of the shapes of the building blocks, ultimately pulling sets of chromosomes apart. Here, we show that artificial photoswitches can be incorporated within supramolecular microtubules and that individual switching events lead to conversion of light into elastic energy that can be stored, accumulated, and subsequently released to produce a mechanical effect. The work paves the way toward fully artificial supramolecular machines that convert molecular motion into sophisticated operation modes, at length scales that are typically the realm of living matter.
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice
Authors: Mark Welch Jessica L. , Hasegawa Yuko , McNulty Nathan P. , Gordon Jeffrey I. , Borisy Gary G.
Published: October 2017

Significance

Spatial structure is postulated to have a powerful influence on establishing and sustaining the signaling and metabolic exchanges that define relationships among members of the gut microbiota and host. However, information about gut community spatial structure is limited. Simultaneous imaging of components of a 15-member model human gut bacterial community over a range of spatial scales in gnotobiotic mice revealed that the colon is better conceptualized as an incompletely mixed bioreactor, rather than having sharply stratified luminal and mucosal compartments. Identifying host and microbial factors that constrain the ability of community members to establish sizeable single or oligotaxon agglomerations should yield new insights about how “micro”-scale mixing defines community function.
Big data modeling to predict platelet usage and minimize wastage in a tertiary care system
Authors: Guan Leying , Tian Xiaoying , Gombar Saurabh , Zemek Allison J. , Krishnan Gomathi , Scott Robert , Narasimhan Balasubramanian , Tibshirani Robert J. , Pham Tho D.
Published: October 2017

Significance

In modern hospital systems where complicated, severely ill patient populations are the norm, there is currently no reliable way to forecast the use of perishable medical resources to enable a smart and economic way to deliver optimal patient care. We here demonstrate a statistical model using hospital patient data to quantitatively forecast, days in advance, the need for platelet transfusions. This approach can be leveraged to significantly decrease platelet wastage, and, if adopted nationwide, would save approximately 80 million dollars per year. We believe our approach can be generalized to all other aspects of patient care involving timely delivery of perishable medical resources.
Perceiving social interactions in the posterior superior temporal sulcus
Authors: Isik Leyla , Koldewyn Kami , Beeler David , Kanwisher Nancy
Published: October 2017

Significance

Humans spend a large percentage of their time perceiving the appearance, actions, and intentions of others, and extensive previous research has identified multiple brain regions engaged in these functions. However, social life depends on the ability to understand not just individuals, but also groups and their interactions. Here we show that a specific region of the posterior superior temporal sulcus responds strongly and selectively when viewing social interactions between two other agents. This region also contains information about whether the interaction is positive (helping) or negative (hindering), and may underlie our ability to perceive, understand, and navigate within our social world.
Transcription factor ISX mediates the cross talk between diet and immunity
Authors: Widjaja-Adhi Made Airanthi K. , Palczewski Grzegorz , Dale Kali , Knauss Elizabeth A. , Kelly Mary E. , Golczak Marcin , Levine Alan D. , von Lintig Johannes
Published: October 2017

Significance

The intestine is the major entrance site for nutrients, electrolytes, and water while constituting an effective barrier against toxins, antigens, and enteric flora. Hence, the intestinal mucosa harbors one of the largest populations of lymphocytes in the body. Nutrients such as vitamin A have been recognized to influence gut homing and differentiation of these cells. We identified the ISX protein as a critical molecular mediator of this cross talk between diet and immunity. This transcription factor regulates vitamin A production from dietary precursor molecules. Loss of this control in mice disrupts vitamin A homeostasis and impairs immunity. Reported genetic polymorphisms in theIsxgene have been associated with inflammatory disorders in humans, indicating that our findings in mice have clinical implications.
Addressing Substance use Disorder in Primary Care: The Role, Integration, and Impact of Recovery Coaches
Authors: Jack Helen E. , Oller Devin , Kelly John , Magidson Jessica F. , Wakeman Sarah E.
Published: October 2017

Background: Only 10% of people with substance use disorder (SUD) receive treatment, partially due to inadequate access to specialty SUD care and limited management within primary care. “Recovery coaches” (RCs), peers sharing the lived experience of addiction and recovery, are increasingly being integrated into primary care to help reach and treat people experiencing SUD, yet little is known about how their role should be defined or about their clinical integration and impact. Methods: Semistructured interviews with RCs ( n = 5) and their patients ( n = 16) were used to explore patient and RC perspectives on the RC role. Maximum variation sampling was employed to select patients who displayed diversity across gender, RC, housing status, and number of contacts with an RC. Patients were sampled until no new concepts emerged from additional interviews, and a semistructured interview guide was used for data collection. To analyze interview transcripts, the constant comparative method was used to develop and assign inductively developed codes. Two coders separately coded all transcripts and reconciled code assignments. Results: Four core RC activities were identified: system navigation, supporting behavior change, harm reduction, and relationship building. Across these activities, benefits of the RC role emerged, including accessibility, shared experiences, motivation of behavior change, and links to social services. Challenges of the RC model were also evident: patient discomfort with asking for help, lack of clarity in RC role, and tension within the care team. Conclusions: These findings shed light on RCs in primary care. Many patients and coaches perceived that RCs play a valuable role within primary care, providing both tangible system navigation and intangible, social support that promote recovery and might not otherwise be available. Enhanced communication between RCs and health center leadership in defining the RC role may help resolve ambiguity and related tensions between RCs and care team members.
Molecular Cloning, Characterization, and Expression Analysis of Cathepsin A in the Chinese Giant Salamander Andrias davidianus
Authors: Zhang Qihuan , Han Panpan , Huang Bei , Wang Zisheng , Qiao Guo , Wang Puze , Qi Zhitao
Published: October 2017

Cathepsin A (CTSA) is serine carboxypeptidase, an important protease in the lysosome. In this study, the full complementary DNA (cDNA) sequence of CTSA in Chinese giant salamanders Andrias davidianus was cloned, and its sequence features were analyzed. Tissue expression patterns of CTSA in healthy and Aeromonas hydrophila-infected salamanders were also investigated. The full cDNA sequence of salamander CTSA was 1,620 base pairs in length, encoding 472 amino acids. Salamander CTSA shared high sequence identities with other vertebrates’ CTSAs, ranging from 62.7% to 68.9%. In healthy salamanders, CTSA was highly expressed in spleen, followed by brain, intestine, and stomach. After A. hydrophila infection, salamander CTSA was significantly upregulated in lung, heart, muscle, and kidney; was downregulated in liver, spleen, and intestine; and exhibited no significant changes in stomach and skin, indicating that salamander CTSA might play defense roles in multiple tissues during bacterial infection. These results provide a solid basis for further study of the immune function of amphibian CTSA.

Received September 18, 2016; accepted June 18, 2017 Published online October 9, 2017
Long‐term effects of acoustic reafference training (ART)
Authors: Pizzera Alexandra , Hohmann Tanja , Streese Lukas , Habbig Anja , Raab Markus
Published: October 2017

In sport visual feedback is often used to enhance performance, mostly neglecting the auditory modality. However, athletes produce natural sounds when they move (acoustic reafferences) which they perceive and use to control their movements. We examined the short‐ and long‐term effects of a training intervention on a complex movement by using acoustic reafferences. Natural step sounds produced during hurdling were recorded and played back to the participants immediately before each trial, with an increase (fast group), decrease (slow group), or no manipulation (control group) in the tempo. All groups increased their hurdling performance regarding overall running time, with the slow group showing the best performance development. After a 10‐week retention, the fast and slow group further increased performance, whereas the control group declined. The repeated experience with acoustic information associated with the rhythmic pattern of hurdling may have helped developing a cognitive representation of that movement, especially regarding long‐term effects.
GABA, A Primary Metabolite Controlled by the Gac/Rsm Regulatory Pathway, Favors a Planktonic Over a Biofilm Lifestyle in Pseudomonas protegens CHA0
Authors: Takeuchi Kasumi
Published: October 2017

In Pseudomonas protegens CHA0 and other fluorescent pseudomonads, the Gac/Rsm signal transduction pathway is crucial for the expression of secondary metabolism and the biological control of fungi, nematodes, and insects. Based on the findings of a previous metabolomic study, the role of intracellular γ-aminobutyrate (GABA) as a potential signal in the Gac/Rsm pathway was investigated herein. The function and regulation of a gabDT (c01870-c01880) gene cluster in strain CHA0 were described. The gabT gene encoded GABA transaminase (GABAT) and enabled the growth of the bacterium on GABA, whereas the upstream gabD gene (annotated as a gene encoding succinic semialdehyde dehydrogenase) had an unknown function. A gacA mutant exhibited low GABAT activity, leading to the markedly greater intracellular accumulation of GABA than in the wild type. In the gacA mutant, the RsmA and RsmE proteins caused translational gabD repression, with concomitant gabT repression. Due to very low GABAT activity, the gabT mutant accumulated GABA to high levels. This trait promoted a planktonic lifestyle, reduced biofilm formation, and favored root colonization without exhibiting the highly pleiotropic gacA phenotypes. These results suggest an important role of GABA in the Gac/Rsm-regulated niche adaptation of strain CHA0 to plant roots.
Advanced Copper Composites Against Copper-TolerantXanthomonas perforansand Tomato Bacterial Spot
Authors: Strayer-Scherer A. , Liao Y. Y. , Young M. , Ritchie L. , Vallad G. E. , Santra S. , Freeman J. H. , Clark D. , Jones J. B. , Paret M. L.
Published: October 2017

Bacterial spot, caused by Xanthomonas spp., is a widespread and damaging bacterial disease of tomato (Solanum lycopersicum). For disease management, growers rely on copper bactericides, which are often ineffective due to the presence of copper-tolerant Xanthomonas strains. This study evaluated the antibacterial activity of the new copper composites core-shell copper (CS-Cu), multivalent copper (MV-Cu), and fixed quaternary ammonium copper (FQ-Cu) as potential alternatives to commercially available micron-sized copper bactericides for controlling copper-tolerant Xanthomonas perforans. In vitro, metallic copper from CS-Cu and FQ-Cu at 100 μg/ml killed the copper-tolerant X. perforans strain within 1 h of exposure. In contrast, none of the micron-sized copper rates (100 to 1,000 μg/ml) from Kocide 3000 significantly reduced copper-tolerant X. perforans populations after 48 h of exposure compared with the water control (P < 0.05). All copper-based treatments killed the copper-sensitive X. perforans strain within 1 h. Greenhouse studies demonstrated that all copper composites significantly reduced bacterial spot disease severity when compared with copper-mancozeb and water controls (P < 0.05). Although there was no significant impact on yield, copper composites significantly reduced disease severity when compared with water controls, using 80% less metallic copper in comparison with copper-mancozeb in field studies (P < 0.05). This study highlights the discovery that copper composites have the potential to manage copper-tolerant X. perforans and tomato bacterial spot.
Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers
Authors: Hüebschmann Daniel , Kurzawa Nils , Steinhauser Sebastian , Rentzsch Philipp , Krämer Stephen , Andresen Carolin , Park Jeongbin , Eils Roland , Schlesner Matthias , Herrmann Carl
Published: October 2017

Metazoans are crucially dependent on multiple layers of gene regulatory mechanisms which allow them to control gene expression across developmental stages, tissues and cell types. Multiple recent research consortia have aimed to generate comprehensive datasets to profile the activity of these cell type- and condition-specific regulatory landscapes across many different cell lines and primary cells. However, extraction of genes or regulatory elements specific to certain entities from these datasets remains challenging. We here propose a novel method based on non-negative matrix factorization for disentangling and associating huge multi-assay datasets including chromatin accessibility and gene expression data. Taking advantage of implementations of NMF algorithms in the GPU CUDA environment full datasets composed of tens of thousands of genes as well as hundreds of samples can be processed without the need for prior feature selection to reduce the input size. Applying this framework to multiple layers of genomic data derived from human blood cells we unravel mechanisms of regulation of cell type-specific expression in T-cells and monocytes.
Many rare genetic variants have unrecognized large-effect disruptions to exon recognition
Authors: Cheung Rocky , Insigne Kimberly D. , Yao David , Burghard Christina P. , Jones Eric M. , Goodman Daniel B. , Kosuri Sriram
Published: October 2017

Any individual’s genome contains ∼4-5 million genetic variants that differ from reference, and understanding how these variants give rise to trait diversity and disease susceptibility is a central goal of human genetics1. A vast majority (96-99%) of an individual’s variants are common, though at a population level the overwhelming majority of variants are rare2–5. Because of their scarcity in an individual’s genome, rare variants that play important roles in complex traits are likely to have large functional effects6,7. Mutations that cause an exon to be skipped can have severe functional consequences on gene function, and many known disease-causing mutations reduce or eliminate exon recognition8. Here we explore the extent to which rare genetic variation in humans results in near complete loss of exon recognition. We developed a Multiplexed Functional Assay of Splicing using Sort-seq (MFASS) that allows us to measure exon inclusion in thousands of human exons and surrounding intronic sequence simultaneously. We assayed 27,733 extant variants in the Exome Aggregation Consortium (ExAC)9within or adjacent to 2,339 human exons, and found that 3.8% (1,050) of the variants, almost all of which were extremely rare, led to large-effect defects in exon recognition. Importantly, we find that 83% of these splice-disrupting variants (SDVs) are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predicta priori. Our results indicate that loss of exon recognition is an important and underappreciated means by which rare variants exert large functional effects, and that MFASS enables their empirical assessment for splicing defects at scale.
Dynamical localization of a thylakoid membrane binding protein is required for acquisition of photosynthetic competency
Authors: Gutu Andrian , Chang Frederick , O‘Shea Erin K.
Published: October 2017

Vipp1 is highly conserved and essential for photosynthesis, but its function is unclear as it does not participate directly in light-dependent reactions. We analyzed Vipp1 localization in live cyanobacterial cells and show that Vipp1 is highly dynamic, continuously exchanging between a diffuse fraction that is uniformly distributed throughout the cell and a punctate fraction that is concentrated at high curvature regions of the thylakoid located at the cell periphery. Experimentally perturbing the spatial distribution of Vipp1 by relocalizing it to the nucleoid causes a severe growth defect during the transition from non-photosynthetic (dark) to photosynthetic (light) growth. However, the same perturbation of Vipp1 in dark alone or light alone growth conditions causes no growth or thylakoid morphology defects. We propose that the punctuated dynamics of Vipp1 at the cell periphery in regions of high thylakoid curvature enable acquisition of photosynthetic competency, perhaps by facilitating biogenesis of photosynthetic complexes involved in light-dependent reactions of photosynthesis.
Delta integrates 3D physical structure with topology and genomic data of chromosomes
Authors: Tang Bixia , Li Feifei , Li Jing , Zhao Wenming , Zhang Zhihua
Published: October 2017

Motivation

The regulation of gene transcription and DNA replication are tightly associated with the 3D chromosomal structures and genomic features, e.g. epigenetic marks, transcription factor bindings and non-coding RNAs. The interaction between the features and the chromosomal structures forming a multilayer 3D regulatory network. Therefore, it is necessary to integrate the physical 3D architecture of genome and features to comprehensive depict their connection to gene regulation.

Results

Here, we present an integrative visualization and analysis platform,Delta, to facilitate visually annotating and exploring the 3D physical architecture of genomes.Deltatakes Hi-C or ChIA-PET contact matrix as input and predicts the topology associated domains and chromatin loops in the genome, and generates a physical 3D model which represents the plausible consensus 3D structure of the genome.Deltafeatures a highly interactive visualization tool, which enhanced the integration of genome topology/physical structure and extensive genome annotation, by juxtaposition of the 3D model with diverse genomic assay outputs. Finally, we showcased thatDeltacould be helpful to reveal potentially interesting findings by a case study on the β-globin gene region.

Availability and implementation

http://delta.big.ac.cn/.

Contact

tangbx@big.ac.cn.

Supplementary information

Supplementary data are available at Bioinformatics online.
Codon-Dependent Translational Accuracy Controls Protein Quality inEscherichia colibut not inSaccharomyces cerevisiae
Authors: Jossé Lyne , Sampson Connor D. D. , Tuite Mick F. , Howland Kevin , von der Haar Tobias
Published: October 2017

In order to generate a functional proteome, gene expression pathways must assemble proteins accurately according to the rules of the genetic code. General gene expression accuracy is known to be high, but errors nevertheless occur with measurable frequencies. Here we develop a mass-spectrometry (MS) based assay for the detection of a particular type of gene expression error, amino acid misincorporation. This assay allows assessing a much broader range of misincorporation events compared to current, very sensitive but also very specific enzyme reporter assays. Our assay uncovers a remarkably rich pool of error products for a model protein expressed inE. coli, which depend quantitatively on codon usage in the expression construct. This codon usage dependence can be explained in part as a function of the composition of the tRNA pool in this organism. We further show that codon-dependent differences in error levels correlate with measurable changes in specific protein activity. In contrast toE. coli, error levels are lower, and appear not to be codon usage dependent, when the same model protein is expressed inS. cerevisiae.
A spontaneously blinking fluorescent protein for simple single laser super-resolution live cell imaging
Authors: Arai Yoshiyuki , Takauchi Hiroki , Ogami Yuhei , Fujiwara Satsuki , Nakano Masahiro , Nagai Takeharu
Published: October 2017

Super-resolution imaging techniques based on single molecule localization microscopy (SMLM) broke the diffraction limit of optical microscopy in living samples with the aid of photoswitchable fluorescent probes and intricate microscopy systems. Here, we developed a fluorescent protein, SPOON, which can be switched-off by excitation light illumination and switched-on by thermally-induced dehydration resulting in an apparent spontaneous blinking behavior. This unique property of SPOON provides a simple SMLM-based super-resolution imaging platform which requires only a single 488 nm laser.
Mix-and-diffuse serial synchrotron crystallography
Authors: Beyerlein Kenneth R. , Dierksmeyer Dennis , Mariani Valerio , Kuhn Manuela , Sarrou Iosifina , Ottaviano Angelica , Awel Salah , Knoska Juraj , Fuglerud Silje , Jönsson Olof , Stern Stephan , Wiedorn Max O. , Yefanov Oleksandr , Adriano Luigi , Bean Richard , Burkhardt Anja , Fischer Pontus , Heymann Michael , Horke Daniel A. , Jungnickel Katharina E. J. , Kovaleva Elena , Lorbeer Olga , Metz Markus , Meyer Jan , Morgan Andrew , Pande Kanupriya , Panneerselvam Saravanan , Seuring Carolin , Tolstikova Aleksandra , Lieske Julia , Aplin Steve , Roessle Manfred , White Thomas A. , Chapman Henry N. , Meents Alke , Oberthuer Dominik
Published: October 2017

Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.
Assurance of learning: moving from a compliance to an improvement culture
Authors: Bennett Misty M. , Smart Karl L. , Kumar Anil
Published: October 2017

Purpose

The purpose of this paper is to describe an organizational change effort that the College of Business Administration at a Midwestern university undertook to transform assurance of learning (AoL) from an inefficient process focused on responding to accreditors to the one that embraced continuous improvement focused on student learning.

Design/methodology/approach

A case study approach was employed along with the analysis of historical documents, interviews with stakeholders in the college, and a review from an external expert to reveal root problematic causes behind the current state of AoL in the college. Lewin’s model of planned change was applied at the beginning of the process to identify the ways to unfreeze the current state of assessment, implement changes, and refreeze by identifying rewards and incentives for faculty to institutionalize the new assessment culture of student learning.

Findings

Four root problematic areas were revealed behind the current state of AoL in the college: faculty resistance and lack of engagement, structural and communication challenges, inconsistency across degree programs, and misalignment of the college vision and mission with program learning goals. Improved communication and coordination between assessment groups and increasing faculty ownership were identified as the key factors for a successful AoL process.

Practical implications

Colleges looking to improve coordination of AoL activities and increase faculty engagement in the AoL process can implement many of the initiatives described in this study.

Originality/value

This case study takes into account new trends in the area of assessment and AoL and addresses common problems that colleges face regarding accreditation in an area where empirical studies do not exist.
The nature of qualitative construction partnering research: literature review
Authors: Venselaar Marieke , Wamelink Hans
Published: October 2017

Purpose

The purpose of this paper is to investigate the nature of qualitative construction partnering research.

Design/methodology/approach

In total, 20 qualitative peer-reviewed papers about construction partnering research are reviewed.

Findings

The results show four methodological gaps. All identified gaps have in common that specific time and place dependent details that may have influenced understanding of studied individuals are underexposed.

Research limitations/implications

The main limitation of this study is that empirical-based papers are divided into either qualitative or quantitative research, but the boundary between those categories is not as black and white as it may look like in first instance.

Practical implications

The identified gaps are translated to recommendations for further study. This will help the reader to become more aware of the difficulties and decisions encountered by the researcher, and in that way the reader is more aware and gains more understanding of the context-related character of the study. Applying the recommendations will lead to different conclusions and recommendations to improve construction partnering in working practice.

Social implications

More focus on local time- and place-dependent factors of the studied individuals as well as the process of studying it, inevitably leads to encountering (and becoming more aware of) personal, subjective and unexplainable decisions and behavior. Describing and analyzing these personal, subjective and unexplainable points in the research process will improve the quality of the research.

Originality/value

This study contributes to the further development of academic research on this topic and increase effectiveness of partnering in the construction sector.
Proposed models to measure the quality of highway projects
Authors: El-Hamrawy Saad Abdel-Karim , Abu El-Maaty Ahmed Ebrahim , Akal Ahmed Yousry
Published: October 2017

Purpose

Quality measurement is the trigger for quality improvement. Indeed, what gets measured gets done. The real scope of quality improvement in construction projects is the difficulty and-maybe-lack of quality measurement methods. The purpose of this paper is to identify the factors influencing the quality performance of highway projects in Egypt. Furthermore, this paper also contributes to develop models to measure the quality level of these projects.

Design/methodology/approach

A literature review is conducted to compile a list of factors influencing the quality of highway projects. The resulting list of factors is subjected to a questionnaire survey which was sent to owners, consultants and contractors of highway projects in Egypt. Furthermore, linear regression analysis and statistical fuzzy approaches are adopted for modeling process.

Findings

The survey results show that availability of experienced staff in the owner’s and contractor’s teams during the project execution, asphalt quality and type used in the construction process, pavement is not designed according to the regional conditions, and contractor’s labors and equipment capability are among the most important factors influencing quality performance.

Originality/value

The main contribution of this study is to develop models to measure the quality of highway projects in Egypt. The first model is based on the linear regression analysis, while the second one is based on a statistical fuzzy approach which is a hybrid approach from the fuzzy logic and regression analysis. Validation of the models reveals that the linear regression and the statistical fuzzy models can accurately assess expected quality of any future highway projects at confidence levels 68.97 and 87.44 percent, respectively.
Risk analysis of schedule delays in international highway projects in Vietnam using a structural equation model
Authors: Vu Hong Anh , Cu Viet Hung , Min Lian Xing , Wang Jian Qiong
Published: October 2017

Purpose

As in other developing countries, increased highway development in Vietnam provides enormous opportunities for international construction companies (ICCs). However, a prolonged schedule delay (SD) can have an extremely detrimental impact on a project’s efficiency, cost and investment reputation. The purpose of this paper is to identify potential SD risk factors in international highway projects (IHPs) in Vietnam, and to explore the effects of and influences on such factors. A specific risk management framework is proposed as a useful tool for ICCs.

Design/methodology/approach

A system of SD risk indicators is presented for IHPs in Vietnam through a questionnaire survey. The system comprises 50 indicators that are grouped into 12 main factors. A structural equation model (SEM) is then used to assess the influences and mechanisms of these factors. Based on the obtained results, corresponding suggestions for preventing SD risks are presented and discussed.

Findings

First, among the 12 aforementioned major factors, the authors identify eight facors that have significant effects on IHP SDs. Second, the SEM analysis reveals that policy flaws and the fiscal ability of the owner play the most important roles, on account of their direct and indirect influences on SDs.

Originality/value

Considering stakeholders and external environmental effects, a system of indicators is introduced to explore SD risks to IHPs. In particular, an SEM is used to assess the effects of potential SD factors and characterize their interacting influences. This study could help ICCs to avoid or mitigate project delays and cost overruns in Vietnam, and also provide valuable lessons for other developing countries.
Assessing collaborative performance on construction projects through knowledge exchange
Authors: Staykova Gergana , Underwood Jason
Published: October 2017

Purpose

How knowledge exchange (KE) can be used for the continuous assessment and improvement of collaborative performance of project-based organisations in construction is explored. Collaboration on construction projects must be facilitated by people alongside practice of continuous performance assessment and improvement. Currently available assessment tools fail to explicitly define appropriate behaviours and actions due to a poor understanding of what it means for people to collaborate. In contrast, it is established that KE is the focus of collaborative efforts on construction projects; therefore, as most knowledge resides with people, it represents their role in collaboration. The paper aims to discuss these issues.

Design/methodology/approach

Through a phenomenological/interpretivist and qualitative methodology, how KE can be used for the continuous assessment and improvement of collaborative performance in project-based organisations in construction is explored. A single case study of a UK rail strategic alliance was adopted and six semi-structured interviews were conducted and analysed through a thematic analysis.

Findings

An assessment tool is proposed based on a set of 20 characteristics of KE, divided into seven categories and linked to indicators of collaboration. The tool can be applied to highly collaborative projects where BIM and Lean are implemented, and project participants are collocated. By measuring their performance against the set criteria, project teams can assess which of their behaviours and actions are inappropriate, and focus their efforts on correcting them.

Originality/value

Defining the abstract indicators traditionally used to assess collaboration in terms of characteristics pertinent to day-to-day communication amongst participants on collaborative projects to facilitate the continuous assessment and improvement of collaborative performance.
Impact of the built environment and care services within rural nursing homes in China on quality of life for elderly residents
Authors: Yu Jingyu , Ma Guixia , Jiang Xiaoyan
Published: October 2017

Purpose

The ageing of rural Chinese populations is challenging health and social policy, driving growth in rural nursing homes. Living environment plays a role in enhancing elderly quality of life (QoL), however, the impact of the built environment and care services are under-studied. The purpose of this paper is to investigate the influence of the built environment and care services on the QoL of elderly people within rural nursing homes in China.

Design/methodology/approach

A total of 242 residents of nursing home were surveyed, of which 76 percent were male and 24 percent were female. In total, 25.6 percent were aged between 60 and 69, 40.1 percent between 70 and 79, 31 percent between 80 and 89, and 3.3 percent were 90 or above. Quantitative data were analyzed through factor analysis, reliability test and multiple regression modeling.

Findings

The authors identified six built environment factors (room distance, space, barrier-free design, indoor environment, fire safety, and support facilities) and three services factors (i.e. daily care services, cleaning services, and healthcare services). QoL was measured over four dimensions: QoL, physical health, psychological health, and social relationships. Elderly QoL could be accurately predicted from room distance, space, barrier-free design, indoor environment, daily care services, and cleaning services.

Practical implications

Interventions in design of the built environment and the provision of care services are proposed, including dimensions of living space, heating, and provisions for qualified care providers.

Originality/value

This paper provides a clear picture about elderly special requirements on their built environment and healthcare services, helping architects, engineers and facilities managers understand elderly needs and improve built environment during design and operation stages.
Cross-sectional comparison of public-private partnerships in transport infrastructure development in Nigeria
Authors: Babatunde Solomon Olusola , Perera Srinath
Published: October 2017

Purpose

Although scientific research community has shown considerable interest in identifying critical success factors (CSFs) for public-private partnership (PPP) projects, yet effort at assessing and compare CSFs within similar PPP infrastructure projects received scant attention. The purpose of this paper is to identify, assess, and compare the CSFs in PPP transport infrastructure projects.

Design/methodology/approach

The study adopted literature review and three PPP case studies including structured interviews and review of documentary reports in each case study. The outcome of literature review provided a total list of 26 identified success factors, which was used to design a case study protocol using failure mode and effect analysis (FMEA) technique. FMEA was conducted on each 26 identified success factor to assess their criticality in the three PPP case studies.

Findings

The results of FMEA revealed a total of ten CSFs in the concession of the road; four CSFs in the concession of the airport; and eight CSFs in the concession of the seaport. Also, the cross-case analysis showed the three prevalent CSFs, this includes government involvement by providing guarantees, political support, and project economic viability.

Practical implications

The study findings including lessons learnt in each case study would positively influence policy development towards PPP transport infrastructure projects and the manner in which partners (i.e. public and private sector) go about the development of PPP transport projects.

Originality/value

This research would help PPP stakeholders to focus their attention and priorities in managing the identified CSFs in achieving long-term success in PPP transport infrastructure projects implementation.