bluuebunny/crossref_metadata_2025 huggingface dataset:
Power‐jitter trade‐off analysis in digital‐to‐time converters
Authors: Santiccioli A. , Samori C. , Lacaita A.L. , Levantino S.
Published: January 2017

Digital‐to‐time converters are one of the main building blocks in time‐domain signal processing. The jitter‐power product is analysed and shown to scale up linearly as the full‐scale delay range in current‐mode logic implementations, and quadratically in CMOS logic. It is also shown that CMOS converters outperforms current‐mode ones only when their output range is lower than about 1.4 times the clock period.
Models for integrating wireless sensor networks into the Internet of Things
Authors: Abidoye Ademola P. , Obagbuwa Ibidun C.
Published: January 2017

Ubiquitous sensing and unique characteristics of wireless sensor networks (WSNs) have led to an increase in application areas such as smart parking, environmental monitoring, automotive industries and sports. In recent years, WSNs have gained more significance as the foundation infrastructure for the Internet of Things (IoT), which has greatly increased the number of connected objects with instantaneous communication and data processing. However, designing energy‐efficient models for integrating WSNs into IoT is a challenging issue due to scalability and interoperability of IoT, and previous approaches designed for WSNs cannot be applied directly. This study proposes two energy‐efficient models for WSNs in the IoT environment: (i) a service‐aware clustering model where individual sensor nodes are assigned roles based on their service delivery; and (ii) an energy‐aware clustering model. Performance evaluation shows better energy efficiency, end‐to‐end delay and network load balance of the proposed models for integrating wireless sensor networks into the IoT protocol compared with low‐energy adaptive clustering hierarchy centralised protocol and fuzzy C‐means clustering protocol.
Specific
characteristics of hemorrhagic Meckel’s diverticulum at double-balloon
endoscopy
Authors: Mizutani Yasuyuki , Nakamura Masanao , Watanabe Osamu , Yamamura Takeshi , Funasaka Kohei , Ohno Eizaburo , Kawashima Hiroki , Miyahara Ryoji , Murino Alberto , Goto Hidemi , Hirooka Yoshiki
Published: January 2017

Background and study aims Diagnosis of Meckel’s diverticulum (MD) before
surgery may be challenging; double-balloon endoscopy (DBE) facilitates
identification of MD in the setting of a gastrointestinal bleeding; however, MD
can be found incidentally without this condition. The purpose of this research
was to determine specific characteristic of hemorrhagic MD and incidental MD at
DBE.

Patients and methods Ectopic gastric mucosa enclosed in the MD and/or
ulceration were defined as “major findings”; ring-like scar surrounding the MD
was defined as “minor finding”. We retrospectively reviewed the medical records
of patients affected by MD and analyzed the findings that significantly affected
the characterization of MD.

Results MD was diagnosed in 33 patients. The axis of the diverticulum was
longer in hemorrhagic MD compared to incidental MD (P = 0.031). The
amount of transfusion was significantly higher (P = 0.018) in the
hemorrhagic MD group. Hemorrhagic MD was significantly more correlated with
major findings (P = 0.01) and minor findings (P < 0.01). The
specificity of major finding was 100 % while the sensitivity of major and/or
minor findings was 96 %.

Conclusions The combination of major and minor findings appears to improve
the diagnostic ability of hemorrhagic MD avoiding unnecessary
diverticulectomy.
Intra-channel stent release technique for fluoroless endoscopic ultrasound-guided lumen-apposing metal stent placement: changing the paradigm
Authors: Anderloni Andrea , Attili Fabia , Carrara Silvia , Galasso Domenico , Di Leo Milena , Costamagna Guido , Repici Alessandro , Kunda Rastislav , Larghi Alberto
Published: January 2017

Background Recently, a novel lumen-apposing fully covered self-expanding metal stent (LA-FCSEMS) mounted on an electrocautery-enhanced delivery system has been developed to perform endoscopic ultrasound (EUS)-guided transluminal drainage. From early experience, however, release of the proximal flange of the stent has mostly been done using endoscopic view guidance to ensure proper positioning.

Aim We describe a new technique that we have named the Intra-Channel Stent Release Technique (ICSRT) to perform stent placement under complete EUS control, without the use of either fluoroscopic or endoscopic views.

Material and methods Data on all consecutive patients who underwent EUS-guided drainage using the new ICSRT between June 2014 and April 2016 were retrospectively retrieved from two institution databases. All EUS procedures were performed by experienced endoscopists with the patient under conscious or deep sedation. The total procedure and stent deployment time, and adverse events related to stent positioning with the ICSRT were evaluated.

Results One hundred consecutive patients (51 women; mean age ± SD, 66 ± 15.2 years, range 34 – 95) underwent EUS-guided transluminal drainage with the Hot AXIOS™ device using the new ICSRT. The procedure was technically successful in all but one patient (1 %). The mean total procedural time was 21.9 minutes (range 7 – 50), while the mean time for stent placement was 3.2 minutes (range 1 – 15). No major adverse events occurred.

Discussion The ICSRT has been used to deploy the newly developed lumen-apposing FCSEMS under complete EUS guidance without fluoroscopic and/or endoscopic assistance. The technique appears to be safe and highly effective and should be learned by all interventional endosonographers in order to be able to perform drainage in all clinical scenarios.
Thermodynamics and simulation of hard-sphere fluid and solid: Kinetic Monte Carlo method versus standard Metropolis scheme
Authors: Ustinov E. A.
Published: January 2017

The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure–chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs–Duhem equation as a constraint. A detailed thermodynamic analysis of the hard-sphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems.
Comparative analysis of fourth-harmonic multiplying gyrotron traveling-wave amplifiers operating at different frequency multiplications
Authors: Yeh Y. S. , Kao W. J. , Li L. J. , Guo Y. W.
Published: January 2017

The harmonic multiplying operation in a gyrotron traveling-wave amplifier (gyro-TWA) permits magnetic field reduction and frequency multiplication. This study presents a comparative analysis of fourth-harmonic multiplying gyro-TWAs with three schemes of operation. An improved mode-selective circuit using circular waveguides with various radii provides the rejection points within the range of operating frequencies to suppress the competing modes of gyro-TWAs. The simulated results reveal that gyro-TWAs are the most susceptible to the fundamental-harmonic TE11 competing mode, regardless of the operating scheme, and that the mode-selective circuit can provide an attenuation of more than 20 dB to suppress the competing modes. The amplification of the waves in a gyro-TWA depends on the lengths of the sections, and the simulated results show that the gain increases for all schemes, as the length of the lossy section or the length of the copper section increases. All schemes exhibit nearly the same saturated output powers and bandwidths; however, the saturated gain of the scheme at a high frequency multiplication ratio is less than that of the scheme at a low frequency multiplication ratio. Extensive numerical calculations of power and gain scaling are conducted for all schemes.
Thermoelectric properties of Mg2X (X = Si, Ge) based bulk and quantum well systems
Authors: Yelgel Övgü Ceyda
Published: January 2017

Mg2X (X = Si, Ge) compounds are promising thermoelectric materials for middle temperature applications due to good thermoelectric properties, nontoxicity, and abundantly available constituent elements. So far, these materials used in applications have all been in bulk form. Herein we report a full theory of thermoelectric transport properties of 3D bulk and 2D quantum well systems. The main aim of this present work is to show the effect of quantum confinement on the enhancement of the thermoelectric figure of merit theoretically. Results are given for n-type Mg2Si0.5Ge0.5 solid solutions and n-type Mg2Si/Mg2Ge/Mg2Si quantum well systems where the values of well widths are taken as 10 nm, 15 nm, and 20 nm, respectively. The n-type doping is made by using Sb- and La-elements as dopants. Experimental results for solid solutions are included to provide demonstration of proof of principle for the theoretical model applied for 3D bulk structures. The maximum thermoelectric figure of merits of LaxMg2−xSi0.49Ge0.5Sb0.01 solid solutions are obtained to be 0.64 and 0.56 at 800 K for x = 0 and x = 0.01 sample, respectively. While, at the same temperature, due to the relatively low phonon thermal conductivity the state-of-the-art ZT values of 2.41 and 2.26 have been attained in the Mg2Si/Mg2Ge/Mg2Si quantum well samples with 0.01 wt. % Sb-doped and 0.01 wt. % Sb- and 0.01 wt. % La-doped, respectively.
Communication: Distinguishing between bulk and interface-enhanced crystallization in nanoscale films of amorphous solid water
Authors: Yuan Chunqing , Smith R. Scott , Kay Bruce D.
Published: January 2017

The crystallization of amorphous solid water (ASW) nanoscale films was investigated using reflection absorption infrared spectroscopy. Two ASW film configurations were studied. In one case the ASW film was deposited on top of and capped with a decane layer (“sandwich” configuration). In the other case, the ASW film was deposited on top of a decane layer and not capped (“no cap” configuration). Crystallization of ASW films in the “sandwich” configuration is about eight times slower than in the “no cap.” Selective placement of an isotopic layer (5% D2O in H2O) at various positions in an ASW (H2O) film was used to determine the crystallization mechanism. In the “sandwich” configuration, the crystallization kinetics were independent of the isotopic layer placement whereas in the “no cap” configuration the closer the isotopic layer was to the vacuum interface, the earlier the isotopic layer crystallized. These results are consistent with a mechanism whereby the decane overlayer suppresses surface nucleation and provide evidence that the observed ASW crystallization in “sandwich” films is the result of uniform bulk nucleation.
Application of metabolomics to postharvest science of fresh crops.
Authors: Benkeblia N.
Published: January 2017

With more than 400 000 plant and 1 000 000 estimated metabolites, metabolomics is a promising tool that revealed its efficiency to study the complete set of small naturally present or stresses-elicited metabolites. In its recent progress, metabolomics led to a comprehensive and global analysis of metabolites and metabolic pathways in living tissues. Therefore, this approach is being further used to study the different postharvest stages of fresh crops, and building novel sets of data on the metabolic transition from immature, ripe and senescent fruit, as well as the effects of the different stresses affecting the fresh crop tissues during the handling, minimal processing and storage. Changes in primary and secondary pathways of sugars, organic acids, and, phenolic compounds, ethylene synthesis and fruit texture associated with physiological diseases, disorders and postharvest treatments for preservation and shelf-life extension are helping to track the specific related metabolites. In addition, broader use of metabolomics will speed the discovery of novel gene functions in primary and secondary metabolism and will provide comprehensive data sets necessary to model metabolic networks related to postharvest physiology and biochemistry of fresh crops. The data collected are crucial in setting the appropriate postharvest conditions by diverting the metabolism towards the desired pathways, or slowing down the undesired pathways, leading to efficient and affordable methods to reduce losses and extend the shelf-life of fresh crops. In this review, we aim to give a comprehensive view on the recent advances and applications of metabolomics to postharvest science in order to understand crop deterioration, and therefore, developing or improving existing techniques to extend shelf-life and shelf-life.
Analysis of water sorption isotherms of amorphous food materials by solution thermodynamics with relevance to glass transition: evaluation of plasticizing effect of water by the thermodynamic parameters
Authors: Shimazaki Eriko , Tashiro Akiko , Kumagai Hitomi , Kumagai Hitoshi
Published: January 2017

Relation between the thermodynamic parameters obtained from water sorption isotherms and the degree of reduction in the glass transition temperature (Tg), accompanied by water sorption, was quantitatively studied. Two well-known glassy food materials namely, wheat gluten and maltodextrin were used as samples. The difference between the chemical potential of water in a solution and that of pure water (), the difference between the chemical potential of solid in a solution and that of a pure solid (), and the change in the integral Gibbs free energy () were obtained by analyzing the water sorption isotherms using solution thermodynamics. The parameter correlated well with ΔTg (≡Tg − Tg0; where Tg0 is the glass transition temperature of dry material), which had been taken to be an index of plasticizing effect. This indicates that plasticizing effect of water on foods can be evaluated through the parameter .
A reverse signaling pathway downstream of Sema4A controls cell migration via Scrib
Authors: Sun Tianliang , Yang Lida , Kaur Harmandeep , Pestel Jenny , Looso Mario , Nolte Hendrik , Krasel Cornelius , Heil Daniel , Krishnan Ramesh K. , Santoni Marie-Josée , Borg Jean-Paul , Bünemann Moritz , Offermanns Stefan , Swiercz Jakub M. , Worzfeld Thomas
Published: January 2017

Semaphorins comprise a large family of ligands that regulate key cellular functions through their receptors, plexins. In this study, we show that the transmembrane semaphorin 4A (Sema4A) can also function as a receptor, rather than a ligand, and transduce signals triggered by the binding of Plexin-B1 through reverse signaling. Functionally, reverse Sema4A signaling regulates the migration of various cancer cells as well as dendritic cells. By combining mass spectrometry analysis with small interfering RNA screening, we identify the polarity protein Scrib as a downstream effector of Sema4A. We further show that binding of Plexin-B1 to Sema4A promotes the interaction of Sema4A with Scrib, thereby removing Scrib from its complex with the Rac/Cdc42 exchange factor βPIX and decreasing the activity of the small guanosine triphosphatase Rac1 and Cdc42. Our data unravel a role for Plexin-B1 as a ligand and Sema4A as a receptor and characterize a reverse signaling pathway downstream of Sema4A, which controls cell migration.
Growth differentiation factor 15 is a myomitokine governing systemic energy homeostasis
Authors: Chung Hyo Kyun , Ryu Dongryeol , Kim Koon Soon , Chang Joon Young , Kim Yong Kyung , Yi Hyon-Seung , Kang Seul Gi , Choi Min Jeong , Lee Seong Eun , Jung Saet-Byel , Ryu Min Jeong , Kim Soung Jung , Kweon Gi Ryang , Kim Hail , Hwang Jung Hwan , Lee Chul-Ho , Lee Se-Jin , Wall Christopher E. , Downes Michael , Evans Ronald M. , Auwerx Johan , Shong Minho
Published: January 2017

Reduced mitochondrial electron transport chain activity promotes longevity and improves energy homeostasis via cell-autonomous and –non-autonomous factors in multiple model systems. This mitohormetic effect is thought to involve the mitochondrial unfolded protein response (UPRmt), an adaptive stress-response pathway activated by mitochondrial proteotoxic stress. Using mice with skeletal muscle–specific deficiency of Crif1 (muscle-specific knockout [MKO]), an integral protein of the large mitoribosomal subunit (39S), we identified growth differentiation factor 15 (GDF15) as a UPRmt-associated cell–non-autonomous myomitokine that regulates systemic energy homeostasis. MKO mice were protected against obesity and sensitized to insulin, an effect associated with elevated GDF15 secretion after UPRmt activation. In ob/ob mice, administration of recombinant GDF15 decreased body weight and improved insulin sensitivity, which was attributed to elevated oxidative metabolism and lipid mobilization in the liver, muscle, and adipose tissue. Thus, GDF15 is a potent mitohormetic signal that safeguards against the onset of obesity and insulin resistance.
Watching cellular machinery in action, one molecule at a time
Authors: Monachino Enrico , Spenkelink Lisanne M. , van Oijen Antoine M.
Published: January 2017

Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.
ARF1 at the crossroads of podosome construction and function
Authors: Genot Elisabeth
Published: January 2017

Podosomes are actin-based proteolytic microdomains of the plasma membrane found in cells that travel across tissues. In this issue, Rafiq et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201605104) reveal that the small guanosine triphosphatase ARF1, a well-known orchestrator of membrane traffic at the Golgi, regulates podosome formation, maintenance, and function.
UNC-84: “LINC-ing” chromosome movement and double strand break repair
Authors: Silva Nicola , Jantsch Verena
Published: January 2017

Assaults to our DNA take place at a high frequency and are incompatible with life. In this issue, Lawrence et al. (2016. J. Cell Biol. https://doi.org/10.1083/jcb.201604112) demonstrate that a novel complex links the nucleus with cytoplasmic microtubules for the promotion of DNA repair by homologous recombination.
Why proteomics is not the new genomics and the future of mass spectrometry in cell biology
Authors: Sidoli Simone , Kulej Katarzyna , Garcia Benjamin A.
Published: January 2017

Mass spectrometry (MS) is an essential part of the cell biologist’s proteomics toolkit, allowing analyses at molecular and system-wide scales. However, proteomics still lag behind genomics in popularity and ease of use. We discuss key differences between MS-based -omics and other booming -omics technologies and highlight what we view as the future of MS and its role in our increasingly deep understanding of cell biology.
Cell cycle progression dictates the requirement for BCL2 in natural killer cell survival
Authors: Viant Charlotte , Guia Sophie , Hennessy Robert J. , Rautela Jai , Pham Kim , Bernat Claire , Goh Wilford , Jiao Yuhao , Delconte Rebecca , Roger Michael , Simon Vanina , Souza-Fonseca-Guimaraes Fernando , Grabow Stephanie , Belz Gabrielle T. , Kile Benjamin T. , Strasser Andreas , Gray Daniel , Hodgkin Phillip D. , Beutler Bruce , Vivier Eric , Ugolini Sophie , Huntington Nicholas D.
Published: January 2017

Natural killer (NK) cells are innate lymphoid cells with antitumor functions. Using an N-ethyl-N-nitrosourea (ENU)–induced mutagenesis screen in mice, we identified a strain with an NK cell deficiency caused by a hypomorphic mutation in the Bcl2 (B cell lymphoma 2) gene. Analysis of these mice and the conditional deletion of Bcl2 in NK cells revealed a nonredundant intrinsic requirement for BCL2 in NK cell survival. In these mice, NK cells in cycle were protected against apoptosis, and NK cell counts were restored in inflammatory conditions, suggesting a redundant role for BCL2 in proliferating NK cells. Consistent with this, cycling NK cells expressed higher MCL1 (myeloid cell leukemia 1) levels in both control and BCL2-null mice. Finally, we showed that deletion of BIM restored survival in BCL2-deficient but not MCL1-deficient NK cells. Overall, these data demonstrate an essential role for the binding of BCL2 to BIM in the survival of noncycling NK cells. They also favor a model in which MCL1 is the dominant survival protein in proliferating NK cells.
Human immunity against EBV—lessons from the clinic
Authors: Tangye Stuart G. , Palendira Umaimainthan , Edwards Emily S.J.
Published: January 2017

The mammalian immune system has evolved over many millennia to be best equipped to protect the host from pathogen infection. In many cases, host and pathogen have coevolved, each acquiring sophisticated ways of inducing or protecting from disease. Epstein-Barr virus (EBV) is a human herpes virus that infects >90% of individuals. Despite its ubiquity, infection by EBV is often subclinical; this invariably reflects the necessity of the virus to preserve its host, balanced with sophisticated host immune mechanisms that maintain viral latency. However, EBV infection can result in various, and often fatal, clinical sequelae, including fulminant infectious mononucleosis, hemophagocytic lymphohistiocytosis, lymphoproliferative disease, organomegaly, and/or malignancy. Such clinical outcomes are typically observed in immunosuppressed individuals, with the most extreme cases being Mendelian primary immunodeficiencies (PIDs). Although these conditions are rare, they have provided critical insight into the cellular, biochemical, and molecular requirements for robust and long-lasting immunity against EBV infection. Here, we review the virology of EBV, mechanisms underlying disease pathogenesis in PIDs, and developments in immune cell–mediated therapy to treat disorders associated with or induced by EBV infection.
Extraoral bitter taste receptors in health and disease
Authors: Lu Ping , Zhang Cheng-Hai , Lifshitz Lawrence M. , ZhuGe Ronghua
Published: January 2017

Bitter taste receptors (TAS2Rs or T2Rs) belong to the superfamily of seven-transmembrane G protein–coupled receptors, which are the targets of >50% of drugs currently on the market. Canonically, T2Rs are located in taste buds of the tongue, where they initiate bitter taste perception. However, accumulating evidence indicates that T2Rs are widely expressed throughout the body and mediate diverse nontasting roles through various specialized mechanisms. It has also become apparent that T2Rs and their polymorphisms are associated with human disorders. In this review, we summarize the physiological and pathophysiological roles that extraoral T2Rs play in processes as diverse as innate immunity and reproduction, and the major challenges in this emerging field.
Final report on the key comparison, CCM.M.P-K15.1 in the pressure range from 1.0 × 10-4 Pa to 1.0 Pa
Authors: Wuethrich Christian , Hongyan Yu
Published: January 2017

At the CCM WG-LP meeting in Berlin in April 2011 the National Institute of Metrology of the people's republic of China asked for an opportunity to be linked to the CCM.M.P-K15 comparison which just ended. METAS, which had been active as pilot for the CCM.M.P-K15, agreed to make a link with NIM. The NIM introduced a new static expansion system in his laboratory.

Two spinning rotor gauges and a control electronic are used as transfer standard. The circulation of the transfer standard was made in spring 2012. The drift of the accommodation coefficient of the two SRG was measured by the pilot before and after the comparison. The stability of the transfer standards was excellent and the equivalence between METAS and NIM has been demonstrated.

A link to the CCM.M.P­K15 has been established using the results from METAS. It has been possible to achieve a link with a small uncertainty due to the strong correlation of the measurements of METAS in the two comparisons.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
MAPPI-DAT: data management and analysis for protein–protein interaction data from the high-throughput MAPPIT cell microarray platform
Authors: Gupta Surya , De Puysseleyr Veronic , Van der Heyden José , Maddelein Davy , Lemmens Irma , Lievens Sam , Degroeve Sven , Tavernier Jan , Martens Lennart
Published: January 2017

Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments.

Availability and Implementation

MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT.

Supplementary information

Supplementary data are available at Bioinformatics online.
Hop Stunt Viroid: Effects on Vegetative Growth and Yield of Hop Cultivars, and Its Distribution in Central Washington State
Authors: Kappagantu Madhu , Nelson Mark E. , Bullock Jeff M. , Kenny Stephen T. , Eastwell Kenneth C.
Published: January 2017

Hop stunt viroid (HSVd) is an economically important pathogen that reduces growth and yield of hops. Visual symptoms of infected hop are highly dependent on cultivar. A study was conducted using six cultivars of hop to determine the impact on yield. Average dry cone yields of infected ‘Glacier’, ‘Cascade’, and ‘Willamette’ were reduced by 62, 14, and 34%, respectively, relative to noninoculated healthy plants. No significant yield reduction was observed for ‘Nugget’, ‘Columbus’, and ‘Galena’. The α-acid and β-acid contents showed a parallel pattern. Horticultural parameters of Willamette and Nugget were measured in the final year of the study. Internode length, shoot length, and side-arm length were reduced by 29, 26, and 73%, respectively, for infected Willamette bines relative to noninfected bines; no effects were observed resulting from infection of Nugget. To understand the current potential impact of HSVd, a survey was conducted to determine its distribution in central Washington. The survey revealed that 17% of hop plants tested are infected. Hop yield and hop plant longevity will be significantly affected by this level of infection.

[Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Treatment Outcome Comparison Between Telepsychiatry and Face-to-face Buprenorphine Medication-assisted Treatment for Opioid Use Disorder: A 2-Year Retrospective Data Analysis
Authors: Zheng Wanhong , Nickasch Michael , Lander Laura , Wen Sijin , Xiao Minchan , Marshalek Patrick , Dix Ebony , Sullivan Carl
Published: January 2017

Objectives:

To retrospectively review clinic records to assess the difference between face-to-face and telepsychiatry buprenorphine medication-assisted treatment (MAT) programs for the treatment of opioid use disorder on 3 outcomes: additional substance use, average time to achieve 30 and 90 consecutive days of abstinence, and treatment retention rates at 90 and 365 days.

Methods:

Medical records of patients (N = 100) who were participating in telepsychiatry and in face-to-face group-based outpatient buprenorphine MAT programs were reviewed and assessed using descriptive statistical analysis.

Results:

In comparison with the telepsychiatry MAT group, the face-to-face MAT group showed no significant difference in terms of additional substance use, time to 30 days (P = 0.09) and 90 days of abstinence (P = 0.22), or retention rates at 90 and 365 days (P = 0.99).

Conclusions:

We did not find any significant statistical difference between telepsychiatry buprenorphine MAT intervention through videoconference and face-to-face MAT treatment in our Comprehensive Opioid Addiction Treatment model for individuals diagnosed with opioid use disorder in terms of additional substance use, average time to 30 and 90 days of abstinence, and treatment retention rates.
A Perioperative Systems Design to Improve Intraoperative Glucose Monitoring Is Associated with a Reduction in Surgical Site Infections in a Diabetic Patient Population
Authors: Ehrenfeld Jesse M. , Wanderer Jonathan P. , Terekhov Maxim , Rothman Brian S. , Sandberg Warren S.
Published: January 2017

Background

Diabetic patients receiving insulin should have periodic intraoperative glucose measurement. The authors conducted a care redesign effort to improve intraoperative glucose monitoring.

Methods

With approval from Vanderbilt University Human Research Protection Program (Nashville, Tennessee), the authors created an automatic system to identify diabetic patients, detect insulin administration, check for recent glucose measurement, and remind clinicians to check intraoperative glucose. Interrupted time series and propensity score matching were used to quantify pre- and postintervention impact on outcomes. Chi-square/likelihood ratio tests were used to compare surgical site infections at patient follow-up.

Results

The authors analyzed 15,895 cases (3,994 preintervention and 11,901 postintervention; similar patient characteristics between groups). Intraoperative glucose monitoring rose from 61.6 to 87.3% in cases after intervention (P = 0.0001). Recovery room entry hyperglycemia (fraction of initial postoperative glucose readings greater than 250) fell from 11.0 to 7.2% after intervention (P = 0.0019), while hypoglycemia (fraction of initial postoperative glucose readings less than 75) was unchanged (0.6 vs. 0.9%; P = 0.2155). Eighty-seven percent of patients had follow-up care. After intervention the unadjusted surgical site infection rate fell from 1.5 to 1.0% (P = 0.0061), a 55.4% relative risk reduction. Interrupted time series analysis confirmed a statistically significant surgical site infection rate reduction (P = 0.01). Propensity score matching to adjust for confounders generated a cohort of 7,604 well-matched patients and confirmed a statistically significant surgical site infection rate reduction (P = 0.02).

Conclusions

Anesthesiologists add healthcare value by improving perioperative systems. The authors leveraged the one-time cost of programming to improve reliability of intraoperative glucose management and observed improved glucose monitoring, increased insulin administration, reduced recovery room hyperglycemia, and fewer surgical site infections. Their analysis is limited by its applied quasiexperimental design.
Dynamic Mechanical Interactions Between Neighboring Airspaces Determine Cyclic Opening and Closure in Injured Lung
Authors: Broche Ludovic , Perchiazzi Gaetano , Porra Liisa , Tannoia Angela , Pellegrini Mariangela , Derosa Savino , Sindaco Alessandra , Batista Borges João , Degrugilliers Loïc , Larsson Anders , Hedenstierna Göran , Wexler Anthony S. , Bravin Alberto , Verbanck Sylvia , Smith Bradford J. , Bates Jason H. T. , Bayat Sam
Published: January 2017

Objectives:

Positive pressure ventilation exposes the lung to mechanical stresses that can exacerbate injury. The exact mechanism of this pathologic process remains elusive. The goal of this study was to describe recruitment/derecruitment at acinar length scales over short-time frames and test the hypothesis that mechanical interdependence between neighboring lung units determines the spatial and temporal distributions of recruitment/derecruitment, using a computational model.

Design:

Experimental animal study.

Setting:

International synchrotron radiation laboratory.

Subjects:

Four anesthetized rabbits, ventilated in pressure controlled mode.

Interventions:

The lung was consecutively imaged at ~ 1.5-minute intervals using phase-contrast synchrotron imaging, at positive end-expiratory pressures of 12, 9, 6, 3, and 0 cm H2O before and after lavage and mechanical ventilation induced injury. The extent and spatial distribution of recruitment/derecruitment was analyzed by subtracting subsequent images. In a realistic lung structure, we implemented a mechanistic model in which each unit has individual pressures and speeds of opening and closing. Derecruited and recruited lung fractions (F
derecruited, F
recruited) were computed based on the comparison of the aerated volumes at successive time points.

Measurements and Main Results:

Alternative recruitment/derecruitment occurred in neighboring alveoli over short-time scales in all tested positive end-expiratory pressure levels and despite stable pressure controlled mode. The computational model reproduced this behavior only when parenchymal interdependence between neighboring acini was accounted for. Simulations closely mimicked the experimental magnitude of F
derecruited and F
recruited when mechanical interdependence was included, while its exclusion gave F
recruited values of zero at positive end-expiratory pressure greater than or equal to 3 cm H2O.

Conclusions:

These findings give further insight into the microscopic behavior of the injured lung and provide a means of testing protective-ventilation strategies to prevent recruitment/derecruitment and subsequent lung damage.
DNA methylation differences at regulatory elements are associated with the cancer risk factor age in normal breast tissue
Authors: Johnson Kevin C. , Houseman E. Andres , King Jessica E. , Christensen Brock C.
Published: January 2017

Background

The underlying biological mechanisms through which epidemiologically defined breast cancer risk factors contribute to disease risk remain poorly understood. Identification of the molecular changes associated with cancer risk factors in normal tissues may aid in determining the earliest events of carcinogenesis and informing cancer prevention strategies.

Results

Here we investigated the impact cancer risk factors have on the normal breast epigenome by analyzing DNA methylation genome-wide (Infinium 450K array) in cancer-free women from the Susan G. Komen Tissue Bank (n = 100). We tested the relation of established breast cancer risk factors: age, body mass index, parity, and family history of disease with DNA methylation adjusting for potential variation in cell-type proportions. We identified 787 CpG sites that demonstrated significant associations (Q-value < 0.01) with subject age. Notably, DNA methylation was not strongly associated with the other evaluated breast cancer risk factors. Age-related DNA methylation changes are primarily increases in methylation enriched at breast epithelial cell enhancer regions (P = 7.1E-20), and binding sites of chromatin remodelers (MYC and CTCF). We validated the age-related associations in two independent populations of normal breast tissue (n = 18) and normal-adjacent to tumor tissue (n = 97). The genomic regions classified as age-related were more likely to be regions altered in cancer in both pre-invasive (n = 40, P=3.0E-03) and invasive breast tumors (n = 731, P=1.1E-13).

Conclusions

DNA methylation changes with age occur at regulatory regions, and are further exacerbated in cancer suggesting that age influences breast cancer risk in part through its contribution to epigenetic dysregulation in normal breast tissue.
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies
Authors: Teschendorff Andrew E , Breeze Charles E , Zheng Shijie C , Beck Stephan
Published: January 2017

Background

Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While a number of reference-based deconvolution algorithms have emerged, their potential remains underexplored and a comparative evaluation of these algorithms beyond tissues such as blood is still lacking.

Results

Here we present a novel framework for reference-based inference, which leverages cell-type specific DNAse Hypersensitive Site (DHS) information from the NIH Epigenomics Roadmap to construct an improved reference DNA methylation database. We show that this leads to a marginal but statistically significant improvement of cell-count estimates in whole blood as well as in mixtures involving epithelial cell-types. Using this framework we compare a widely used state-of-the-art reference-based algorithm (called constrained projection) to two non-constrained approaches including CIBERSORT and a method based on robust partial correlations. We conclude that the widely-used constrained projection technique may not always be optimal. Instead, we find that the method based on robust partial correlations is generally more robust across a range of different tissue types and for realistic noise levels. We call the combined algorithm which uses DHS data and robust partial correlations for inference, EpiDISH (Epigenetic Dissection of Intra-Sample Heterogeneity). Finally, we demonstrate the added value of EpiDISH in an EWAS of smoking.

Conclusions

Estimating cell-type fractions and subsequent inference in EWAS may benefit from the use of non-constrained reference-based cell-type deconvolution methods.
Modern-Day SIV Viral Diversity Generated by Extensive Recombination and Cross-Species Transmission
Authors: Bell Sidney M. , Bedford Trevor
Published: January 2017

Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST. We modeled host species as a discrete character trait on the viral phylogeny and inferred historical host switches and the pairwise transmission rates between each pair of 24 primate hosts. We identify 14 novel, well-supported, ancient cross-species transmission events. We also find that lentiviral lineages vary widely in their ability to infect new host species: SIVcol(from colobus monkeys) is evolutionarily isolated, while SIVagms (from African green monkeys) frequently move between host subspecies. We also examine the origins of SIVcpz(the predecessor of HIV-1) in greater detail than previous studies, and find that there are still large portions of the genome with unknown origins. Observed patterns of CST are likely driven by a combination of ecological circumstance and innate immune factors.
Novel insights into the molecular heterogeneity of hepatocellular carcinoma
Authors: Jovel Juan , Lin Zhen , O’keefe Sandra , Willows Steven , Wang Weiwei , Zhang Guangzhi , Patterson Jordan , Kelvin David J. , Wong Gane Ka-Shu , Mason Andrew L.
Published: January 2017

Hepatocellular carcinoma (HCC) is influenced by numerous factors, which results in diverse genetic, epigenetic and transcriptional scenarios, thus posing obvious challenges for disease management. We scrutinized the molecular heterogeneity of HCC with a multi-omics approach in two small cohorts of resected and explanted livers. Whole-genome transcriptomics was conducted, including polyadenylated transcripts and micro (mi)-RNAs. Copy number variants (CNV) were inferred from whole genome low-pass sequencing data. Fifty-six cancer-related genes were screened using an oncology panel assay. HCC was associated with a dramatic transcriptional deregulation of hundreds of protein-coding genes suggesting downregulation of drugs catabolism, induction of inflammatory responses, and increased cell proliferation in resected livers. Moreover, several long non-coding RNAs and miRNAs not reported previously in the context of HCC were found deregulated. In explanted livers, downregulation of genes involved in energy-producing processes and upregulation of genes aiding in glycolysis were detected. Numerous CNV events were observed, with conspicuous hotspots on chromosomes 1 and 17. Amplifications were more common than deletions, and spanned regions containing genes potentially involved in tumorigenesis. CSF1R, FGFR3, FLT3, NPM1, PDGFRA, PTEN, SMO and TP53 were mutated in all tumors, while other 26 cancer-related genes were mutated with variable penetrance. Our results highlight a remarkable molecular heterogeneity between HCC tumors and reinforce the notion that precision medicine approaches are urgently needed for cancer treatment. We expect that our results will serve as a valuable dataset that will generate hypotheses for us or other researchers to evaluate to ultimately improve our understanding of HCC biology.
HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
Authors: Fan Xian , Chaisson Mark , Nakhleh Luay , Chen Ken
Published: January 2017

Achieving complete, accurate, and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a Hybrid Structural variant Assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variants (SVs) in human genomes. By identifying homologous SV-containing reads from different technologies through a bipartite-graph-based clustering algorithm, our approach turns a whole genome assembly problem into a set of independent SV assembly problems, each of which can be effectively solved to enhance the assembly of structurally altered regions in human genomes. We used data generated from a haploid hydatidiform mole genome (CHM1) and a diploid human genome (NA12878) to test our approach. The result showed that, compared with existing methods, our approach had a low false discovery rate and substantially improved the detection of many types of SVs, particularly novel large insertions, small indels (10–50 bp), and short tandem repeat expansions and contractions. Our work highlights the strengths and limitations of current approaches and provides an effective solution for extending the power of existing sequencing technologies for SV discovery.
Between hope and fear: developing social media guidelines
Authors: Opgenhaffen Michaël , Claeys An-Sofie
Published: January 2017

Purpose

The purpose of this paper is to examine employers’ policy with regard to employees’ social media use. Specifically, the authors examine the extent to which employers allow the use of social media in the workplace, what opportunities can be related to employees’ social media use and how social media guidelines are implemented within organizations.

Design/methodology/approach

In-depth interviews were conducted with HR and communication managers of 16 European companies from different sectors and of varying size.

Findings

Some organizations believe that social media should be accessible to employees while others ban them from the workplace. Most respondents believe that organizations can benefit from employees sharing work-related content with their own network. However, they encourage the sharing and retweeting of official corporate messages rather than employees developing their own messages. This fear regarding employees’ messages on social media is reflected in the broad adoption of social media guidelines.

Research limitations/implications

Future research should chart the nature of existing social media guidelines (restrictive vs incentive). Accordingly, the perceived sense and nonsense of social media guidelines in companies should be investigated, not only among the managers but also among employees.

Practical implications

Organizations should remain in dialogue with employees with regard to social media. Managers seem overly concerned with potential risks and forget the opportunities that can arise when employees operate as ambassadors.

Originality/value

The use of in-depth interviews allowed the authors to assess the rationale behind social media guidelines within organizations in depth and formulate suggestions to organizations and communication managers.