bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a 3-D visible limiter imaging system for the HSX stellarator
Authors: Buelo C. , Stephey L. , Anderson F. S. B. , Eisert D. , Anderson D. T.
Published: December 2017

A visible camera diagnostic has been developed to study the Helically Symmetric eXperiment (HSX) limiter plasma interaction. A straight line view from the camera location to the limiter was not possible due to the complex 3D stellarator geometry of HSX, so it was necessary to insert a mirror/lens system into the plasma edge. A custom support structure for this optical system tailored to the HSX geometry was designed and installed. This system holds the optics tube assembly at the required angle for the desired view to both minimize system stress and facilitate robust and repeatable camera positioning. The camera system has been absolutely calibrated and using Hα and C-III filters can provide hydrogen and carbon photon fluxes, which through an S/XB coefficient can be converted into particle fluxes. The resulting measurements have been used to obtain the characteristic penetration length of hydrogen and C-III species. The hydrogen λiz value shows reasonable agreement with the value predicted by a 1D penetration length calculation.
High-efficiency and wide-bandwidth linear polarization converter based on double U-shaped metasurface
Authors: Mei Zhong Lei , Ma Xue Man , Lu Cui , Zhao Yao Dong
Published: December 2017

In this paper, we propose a high-efficiency and wide-bandwidth linear polarization converter using double U-shaped metasurface. The design is based on the two dimensional artificial electromagnetic materials and micro-antenna array. Theoretical analysis and simulation results show that the proposed polarization converter can realize the orthogonal polarization transformation for the reflected electromagnetic wave, the conversion bandwidth is 6.91-14.31GHz and the polarization conversion ratio is above 90%. Additionally, the measurement results have good agreement with the simulation data. The proposed double U-shaped structure not only has a simple geometry but also can realize the wide bandwidth and high efficiency conversion. Hence it can find wide applications in novel polarization-control devices.
Monoclinic structures of niobium trisulfide
Authors: Bloodgood Matthew A. , Wei Pingrong , Aytan Ece , Bozhilov Krassimir N. , Balandin Alexander A. , Salguero Tina T.
Published: December 2017

Two new polymorphs of niobium trisulfide are established by single crystal x-ray diffraction. NbS3-iv crystallizes in the monoclinic space group P21/c with lattice parameters a = 6.7515(5) Å, b = 4.9736(4) Å, c = 18.1315(13) Å, and β = 90.116(2)°. Its structure is based on chains of [NbS6] trigonal prisms containing Nb–Nb pairs with a bond length of 3.0448(8) Å; this pairing causes the chains to corrugate slightly along their axis, a feature also present in triclinic NbS3-i that leads to semiconductor properties. The stacking arrangement of chains is different in these polymorphs, however, with NbS3-i having an ABCDE repeating sequence of chain bilayers and NbS3-iv having an AB repeating sequence. HRTEM studies show the presence of topotactically-oriented intergrown zones and numerous dislocations, which result in mosaic structuring. A second new polymorph, NbS3-v, crystallizes in the monoclinic space group P21/m with lattice parameters a = 4.950(5) Å, b = 3.358(4) Å, c = 9.079(10) Å, β = 97.35(2)°. In contrast to NbS3-iv, NbS3-v maintains fixed a Nb–Nb bond distance of 3.358(4) Å along the chains, and it has an ABCDE repeating sequence of chain bilayers similar to NbS3-i. High resolution scanning transmission electron microscopy (HR-STEM) imaging of an exfoliated NbS3-v nanoribbon shows the continuous [NbS6] chains oriented along the b-axis. These results provide the first firmly established structural data for monoclinic NbS3. In addition, SEM images show the formation of NbS3 rings and cylinders, and a combination of powder x-ray diffraction and Raman spectroscopy provides a way to distinguish between NbS3 polymorphs.
Skyrmion crystals: Dynamics and phase transition
Authors: Diep H. T. , El Hog Sahbi , Bailly-Reyre Aurélien
Published: December 2017

We study a crystal of skyrmions generated on a square lattice using a ferromagnetic exchange interaction and a Dzyaloshinskii-Moriya interaction between nearest-neighbors under an external magnetic field. The skyrmion crystal has a hexagonal structure which is shown to be stable up to a temperature Tc where a transition to the paramagnetic phase occur. We will show that the dynamics of the skyrmions at T < Tc follows a stretched exponential law.
Towards quantitative magnetic particle imaging: A comparison with magnetic particle spectroscopy
Authors: Paysen Hendrik , Wells James , Kosch Olaf , Steinhoff Uwe , Trahms Lutz , Schaeffter Tobias , Wiekhorst Frank
Published: December 2017

Magnetic Particle Imaging (MPI) is a quantitative imaging modality with promising features for several biomedical applications. Here, we study quantitatively the raw data obtained during MPI measurements. We present a method for the calibration of the MPI scanner output using measurements from a magnetic particle spectrometer (MPS) to yield data in units of magnetic moments. The calibration technique is validated in a simplified MPI mode with a 1D excitation field. Using the calibrated results from MPS and MPI, we determine and compare the detection limits for each system. The detection limits were found to be 5·10-12 Am2 for MPS and 3.6·10-10 Am2 for MPI. Finally, the quantitative information contained in a standard MPI measurement with a 3D excitation is analyzed and compared to the previous results, showing a decrease in signal amplitudes of the odd harmonics related to the case of 1D excitation. We propose physical explanations for all acquired results; and discuss the possible benefits for the improvement of MPI technology.
Chemical synthesis of L1 Fe-Pt-Ni alloy nanoparticles
Authors: Deepchand Vimal , Abel Frank M. , Tzitzios Vasileios , Hadjipanayis George C.
Published: December 2017

This work focuses on the study of the magnetic and structural properties of chemically synthesized FePt1-xNix nanoparticles, with Ni content x in the range 0.2-0.4. We report the effect of Ni substitution on the L10 structure, on both the as-synthesized and annealed nanoparticles. A decrease in nanoparticle size as well as in chemical order is observed with an increase in Ni content, for both the as-made and annealed nanoparticles. The results also show that the post annealing procedure at 700oC significantly enhanced the L10 ordering of the nanoparticles. Substitution of nickel leads to a decrease in coercivity from 14.9 kOe in FePt to 0.8 kOe for FePt0.6Ni0.4 alloy, while the magnetization at 3 T is increased from 48 emu/g to 88 emu/g.
Simplified equation for Young’s modulus of CNT reinforced concrete
Authors: Chandran RameshBabu , Gifty Honeyta A Maria
Published: December 2017

This research investigation focuses on finite element modeling of carbon nanotube (CNT) reinforced concrete matrix for three grades of concrete namely M40, M60 and M120. Representative volume element (RVE) was adopted and one-eighth model depicting the CNT reinforced concrete matrix was simulated using FEA software ANSYS17.2. Adopting random orientation of CNTs, with nine fibre volume fractions from 0.1% to 0.9%, finite element modeling simulations replicated exactly the CNT reinforced concrete matrix. Upon evaluations of the model, the longitudinal and transverse Young’s modulus of elasticity of the CNT reinforced concrete was arrived. The graphical plots between various fibre volume fractions and the concrete grade revealed simplified equation for estimating the young’s modulus. It also exploited the fact that the concrete grade does not have significant impact in CNT reinforced concrete matrix.
Initial mechanisms for the dissociation of carbon from electronically-excited nitrotoluene molecules
Authors: Yuan Bing , Eilers Hergen
Published: December 2017

We calculated the photoinduced decomposition of various nitrotoluene molecules, resulting in the formation of atomic carbon, at the B3LYP/6-311++G(d,p) level of theory using Gaussian 09. In addition, we used TD-DFT (B3LYP/6-311++G(d,p)) to calculate the excitation energies. The results confirm our previously reported experimental results. Specifically, we show that the absorption of 226 nm (5.49 eV) light can lead to the decomposition of nitrotoluene molecules and the formation of atomic carbon. One 226 nm photon is sufficient for the dissociation of carbon from 2-NT and 4-NT molecules. During the dissociation process, the CH3 group provides the dissociated carbon atom and the NO2 group accepts the H atoms from either the CH3 group or the benzene ring before carbon exits the molecular system. For the second and third carbon dissociation of 2-NT, the energy barriers are 6.70 eV and 7.43 eV, respectively, and two 226 nm photons would need to be absorbed by the molecule. If extra NO is present during the first carbon dissociation of 2-NT, it gets involved in the last two decomposition steps and forms a C=NH-N=O structure which stabilizes the decomposition products and lowers the energy barrier from 5.22 eV to 4.70 eV. However, for the second and third carbon dissociation of 2-NT, the NO molecules have no apparent effect. For nitrotoluene molecules with two or three NO2 groups (i.e., 2,4-DNT, 2,6-DNT, 3,4-DNT, and 2,4,6-TNT), the first carbon dissociation energies are between 5.26 eV and 5.57 eV. The carbon dissociation pathways for these molecules are similar to those of 2-NT. In 2,4-DNT, the lowest energy barriers for the second and third carbon dissociation are 6.54 eV and 6.60 eV, respectively, which are about 1 eV higher than the energy barrier for the first carbon dissociation. In case of 2,4-DNT/NO and 2,4,6-TNT/NO, NO acts as a catalyst in the first carbon dissociation processes and forms a C=NH-N=O structure which lowers the energy barriers by 0.48 eV and 0.89 eV, respectively.
Ultraviolet Raman spectroscopy reveals NiO spin-phonon coupling
Authors: Patrick Chris
Published: December 2017

Raman spectroscopy using ultraviolet light reveals spin-phonon coupling properties of NiO for the first time, and the different effects for transverse and longitudinal optical phonons.
STAX Appeal?
Authors: Yehouenou Lauriane , Barnett Barry J , Harri Ardian , Coble Keith H
Published: December 2017

The Stacked Income Protection Plan (STAX) county‐level insurance product is analyzed for cotton producers in Texas. In contrast to studies based on representative farms, this analysis uses actual farm‐level yield data, which allows one to observe the heterogeneity of STAX effectiveness across farms in a county. The findings indicate that, for most farms, STAX is not a very effective alternative to farm‐level crop insurance. However, contrary to observed behavior, the findings suggest that many cotton producers in Texas would benefit from using STAX as a complement to their farm‐level crop insurance.
myTAI: evolutionary transcriptomics with R
Authors: Drost Hajk-Georg , Gabel Alexander , Liu Jialin , Quint Marcel , Grosse Ivo
Published: December 2017

Motivation

Next Generation Sequencing (NGS) technologies generate a large amount of high quality transcriptome datasets enabling the investigation of molecular processes on a genomic and metagenomic scale. These transcriptomics studies aim to quantify and compare the molecular phenotypes of the biological processes at hand. Despite the vast increase of available transcriptome datasets, little is known about the evolutionary conservation of those characterized transcriptomes.

Results

The myTAI package implements exploratory analysis functions to infer transcriptome conservation patterns in any transcriptome dataset. Comprehensive documentation of myTAI functions and tutorial vignettes provide step-by-step instructions on how to use the package in an exploratory and computationally reproducible manner.

Availability and implementation

The open source myTAI package is available at https://github.com/HajkD/myTAI and https://cran.r-project.org/web/packages/myTAI/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Verbal mood
Authors: Portner Paul
Published: December 2017

Verbal mood is a linguistic category which marks how a clause is used in the computation of subsentential modal meaning. Most prominently exemplified by indicative and subjunctive verb forms, verbal mood has been the subject of much research in linguistics. This chapter outlines the key data showing how verbal mood functions in grammar and presents the most important theories of verbal mood. It evaluates these theories, formalizes and synthesizes their most significant insights, and identifies the most important central issues for future research on this topic.
The Dialectics of Empire, Race, and Diocese
Authors: Cox Jeffrey
Published: December 2017

The history of global Anglicanism is dominated by two master narratives. In the narrative of post-colonial studies, Anglican expansion is one aspect of the expansion of the British Empire. Edward Said’s Orientalism (1978) reconfigured imperialism as cultural domination of the non-Western world, and the imposition of Western styles of religion. The contrasting narrative of mission studies focuses on the victory of the ‘indigenous’ over the ‘foreign’ in the spread of Christianity. Heavily influenced by the works of Lamin Sanneh, this narrative regards missionaries as detonators of indigenous Church growth. This chapter suggests a new narrative of global Anglicanism in which the antagonistic binary struggle between the ‘foreign’ and the ‘indigenous’ is replaced with a dialectical narrative of conflict and collaboration. Western and non-Western Christians cooperate in the ‘contact zone’ of mission and diocese to create a new global Anglicanism, one that is neither fully indigenous nor fully foreign, but new.
Anglicanism in Oceania since 1914
Authors: Gladwin Michael
Published: December 2017

This chapter examines the history of Anglicanism in Oceania. In particular, it demonstrates how Anglo-Catholic, High Church, and monastic expressions of Anglicanism were transposed to Melanesian and Polynesian contexts, producing a unique and evolving set of identities and practices. While a missionary posture of accommodation fostered the inculturation of worship rituals, liturgy, institutional structures, and theologies into indigenous forms, an accompanying paternalistic ethos delayed the creation of an indigenous Church and leadership. The chapter also highlights the crucial role of women and indigenous agency. Finally, the period after 1942 marked a decisive shift from colonial dependency to independent nationhood in places where Anglicanism had taken root. How Anglicans in the region negotiated the tension between tradition and modernity—in Church, society, and state—is a further salient theme of this chapter.
The Vicissitudes of Anglicanism in China, 1912–Present
Authors: Wickeri Philip L.
Published: December 2017

Anglican missionaries went to China in the early nineteenth century, following Western political and commercial expansion to Asia, and all over the world. Somewhat later, missionaries from the United States and the various British societies entered Japan (1859) and Korea (1885). This chapter explores the efforts of British, American, and Canadian missionaries in East Asia, in the context of the broader Christian missionary developments. Anglican and Episcopal work in translation, education, and evangelism laid the foundation for the establishment of the indigenous church in each country, although there were tensions between missionary dominance and local aspirations. The interactions of the early missionaries and their somewhat different approaches in China, Japan, and Korea are significant. The chapter concludes with the efforts that led up to the establishment of the Chung Hua Sheng Kung Hui (Holy Catholic Church of China).
Anglicans in the Horn of Africa
Authors: LeMarquand Grant
Published: December 2017

In the nineteenth and twentieth centuries, Anglican missionaries attempted to bring renewal to the ancient Ethiopian Orthodox Church by teaching the Orthodox clergy and people the content of the Bible. Other Anglican missionaries attempted to reach Ethiopian Jews with the gospel of Christ, and then encouraged Jewish converts to be baptized in the Orthodox Church. In major cities (such as Addis Ababa and Asmara) Anglicans established chaplaincies for British expatriates. Recently, Anglican refugees from South Sudan planted churches in western Ethiopia, especially in the regions of Asosa and Gambella. These churches of Nuer, Anuak, Opo, Mabaan, and Jieng (Dinka) people are found both in refugee camps and in many local villages and towns. This chapter examines these different endeavours as part of one Anglican story.
Anglican Mission amongst Muslims, 1900–1940
Authors: Laing Catriona
Published: December 2017

On paper, Anglican mission to the Middle East in the first half of the twentieth century was a failure. Compared with other missionary efforts, conversion rates in the Muslim world were low. Despite rising hostility towards Western presence in the region, and especially in Egypt, this mission field attracted some of the brightest and most ambitious missionary minds of the early twentieth century. Among then was Constance Padwick, who travelled to Egypt with the Church Missionary Society to develop the evangelistic potential of Christian literature in the Muslim world. Through her work with the printed word and her encounter with the prayers and popular devotion of ‘ordinary’ people, Padwick used the ‘kinships’ she identified between Islam and Christianity to propose a new approach to Christian mission: one that called for prayer, print, and presence among Muslims.
Neural Mobilization Attenuates Mechanical Allodynia and Decreases Proinflammatory Cytokine Concentrations in Rats With Painful Diabetic Neuropathy
Authors: Zhu Guan-Cheng , Tsai Kun-Ling , Chen Yu-Wen , Hung Ching-Hsia
Published: December 2017

Background

Painful diabetic neuropathy (PDN) is a common complication in patients with diabetes. It is related to ischemic nerve damage and the increase in the levels of proinflammatory mediators, such as tumor necrosis factor α (TNF-α) and interleukin 1β (IL-1β). Neural mobilization may have the potential to alleviate PDN, but it has not yet been tested. Also, the physiological mechanism of neural mobilization is unclear.

Objective

The objective of this study was to investigate treatment effect and physiological mechanism of neural mobilization.

Design

This was an experimental study using rats with streptozocin (or streptozotocin)-induced type 1 diabetes.

Methods

Three groups were used in the study, the control group (vehicle), the diabetes group (PDN group), and the neural mobilization treatment group (PDN-NM group) (n = 6). Rats in the vehicle group were healthy rats. Rats in the PDN and PDN-NM groups were rats with diabetes. Rats in the PDN-NM group received treatment in the right sciatic nerve, whereas rats in the PDN group did not. Mechanical pain sensitivity and the levels of IL-1β and TNF-α in the sciatic nerve branches and trunk, the L4 to L6 dorsal horn ganglion, and the spinal cord dorsal horn were measured.

Results

Techanical allodynia was alleviated after treatment, but the effect was limited to the treatment side. The concentrations of proinflammatory cytokines were decreased in the nerves that received treatment compared with those on the other side, indicating that neural mobilization may reduce mechanical sensitivity by decreasing the concentrations of local sensitizing agents.

Limitations

A limitation of this study was that no direct measurement of nerve blood flow was done.

Conclusions

The results of this study showed that neural mobilization effectively alleviated mechanical allodynia in rats with PDN. The side that received treatment had lower concentrations of TNF-α and IL-1β in the sciatic nerve branches and sciatic nerve trunk; this result may have been related to the alleviation of mechanical allodynia.
A Review of a Century of Studies on South American Leaf Blight of the Rubber Tree
Authors: Guyot Jean , Le Guen Vincent
Published: December 2017

In the past, South American leaf blight (SALB) of the rubber tree has been responsible for very severe damage in rubber plantations in South America. It is still the main obstacle holding back the development of rubber cultivation on the American continent and is a major risk for Asia and Africa, which are still exempt from this scourge. However, knowledge about the disease and about rubber tree resistance factors has progressed over the last decade, suggesting some solutions, notably for varietal improvement. This article is an overview of knowledge on this subject, particularly the most recent achievements.
Mindfulness and Chronic Headache/Migraine
Authors: Komandur Biyanka , Martin Paul R. , Bandarian-Balooch Siavash
Published: December 2017

Objectives:

To replicate a study by Schutze and colleagues on a headache sample, rather than a heterogenous chronic pain sample, investigating whether level of mindfulness predicts key components in the Fear-Avoidance Model of chronic pain (pain intensity, negative affect, pain catastrophizing, pain-related fear, pain hypervigilance, and functional disability); to investigate the relationships between level of mindfulness and headache/migraine pain intensity, frequency, and duration.

Materials and Methods:

Participants were 217 individuals who self-reported chronic headache/migraine (51 male, 166 female), aged between 18 and 65 years. Participants completed an online survey measuring demographics, mindfulness, the key components of the Fear-Avoidance Model, and headache pain intensity, duration, and frequency.

Results:

Mindfulness had significant negative correlations (P<0.05) with all variables except headache pain intensity and headache frequency. Mindfulness significantly predicted negative affect, pain catastrophizing, fear of pain, pain hypervigilance, and headache duration (P<0.05). Mindfulness remained a significant predictor of negative affect and pain hypervigilance after controlling for other key components and background characteristics (P<0.05). Mindfulness did not moderate the relationship between pain intensity and pain catastrophizing (P=0.204).

Discussion:

Findings suggest that mindfulness may be integrated into the Fear-Avoidance Model of chronic pain for individuals with chronic headache/migraine. Directions for future research are discussed.
Defining Multiple Chronic Conditions for Quality Measurement
Authors: Drye Elizabeth E. , Altaf Faseeha K. , Lipska Kasia J. , Spatz Erica S. , Montague Julia A. , Bao Haikun , Parzynski Craig S. , Ross Joseph S. , Bernheim Susannah M. , Krumholz Harlan M. , Lin Zhenqiu
Published: December 2017

Background/Objective:

Patients with multiple chronic conditions (MCCs) are a critical but undefined group for quality measurement. We present a generally applicable systematic approach to defining an MCC cohort of Medicare fee-for-service beneficiaries that we developed for a national quality measure, risk-standardized rates of unplanned admissions for Accountable Care Organizations.

Research Design:

To define the MCC cohort we: (1) identified potential chronic conditions; (2) set criteria for cohort conditions based on MCC framework and measure concept; (3) applied the criteria informed by empirical analysis, experts, and the public; (4) described “broader” and “narrower” cohorts; and (5) selected final cohort with stakeholder input.

Subjects:

Subjects were patients with chronic conditions. Participants included 21.8 million Medicare fee-for-service beneficiaries in 2012 aged 65 years and above with ≥1 of 27 Medicare Chronic Condition Warehouse condition(s).

Results:

In total, 10 chronic conditions were identified based on our criteria; 8 of these 10 were associated with notably increased admission risk when co-occurring. A broader cohort (2+ of the 8 conditions) included 4.9 million beneficiaries (23% of total cohort) with an admission rate of 70 per 100 person-years. It captured 53% of total admissions. The narrower cohort (3+ conditions) had 2.2 million beneficiaries (10%) with 100 admissions per 100 person-years and captured 32% of admissions. Most stakeholders viewed the broader cohort as best aligned with the measure concept.

Conclusions:

By systematically narrowing chronic conditions to those most relevant to the outcome and incorporating stakeholder input, we defined an MCC admission measure cohort supported by stakeholders. This approach can be used as a model for other MCC outcome measures.
Resistance in chronic myeloid leukemia: definitions and novel therapeutic agents
Authors: Talati Chetasi , Pinilla-Ibarz Javier
Published: December 2017

Purpose of review

Chronic myeloid leukemia (CML) is hallmarked by the presence of fusion protein kinase derived from a reciprocal translocation between chromosome 9 and 22, breakpoint cluster region (BCR)–Abelson leukemia virus (ABL) 1, causing aberrant regulation of the downstream pathways leading to unchecked CML leukemia stem cells (LSCs) proliferation. Since the discovery of tyrosine kinase inhibitors (TKI), CML, once a fatal disease, has become a chronic illness if managed appropriately. Changing treatment landscape has unsurfaced the challenge of TKI resistance that is clinically difficult to overcome.

Recent findings

In this review, we discuss the concept of TKI resistance and pathways leading to the resistance which allows for a survival advantage to CML LSCs. Aside from BCR–ABL-dependent mechanisms of resistance which involves aberrant expression in the regulatory pumps involving efflux and influx of the TKI affecting drug bioavailability, activation of alternate survival pathways may be accountable for primary or secondary resistance. Activation of these pathways, intrinsically and extrinsically to LSCs, may be mediated through various upstream and downstream signaling as well as conditions affecting the microenvironment. Several therapeutic approaches that combine TKI with an additional agent that inhibits the activation of an alternate pathway have been studied as part of clinical trials which we will discuss here.

We categorize the resistance into BCR–ABL-dependent and BCR–ABL-independent subgroups to further describe the complex molecular pathways which can potentially serve as a therapeutic target. We further discuss novel combination strategies currently in early or advanced phase clinical trials aimed to overcome the TKI resistance. We further highlight the need for further research despite the tremendous strides already made in the management of CML.
Implementation of a Workflow Initiative for Integrating Transitional Care Management Codes in a Geriatric Primary Care Practice
Authors: Steckbeck Julia , McBain Christi , Terrien Kerry L. , Isom David , Stadler Daniel , Stahl James E. , Batsis John A.
Published: December 2017

We implemented a transitional care management service led by a nurse care manager. An interdisciplinary team developed a workflow using a Plan-Do-Study-Act cycle for contacting patients. Of the 146 (97.9%) eligible patients, 143 (97.9%) had a phone call within 48 hours. There were 84 of 120 (70.0%) and 117 of 120 (97.5%) attendance rates of those attending visits within 7 and 14 days. A care manager–led workflow was successfully and easily implemented within a primary care practice.
Evoked Death-Related Thoughts in the Aftermath of Terror Attack
Authors: Ring Lia , Lavenda Osnat , Hamama-Raz Yaira , Ben-Ezra Menachem , Pitcho-Prelorentzos Shani , David Udi Y. , Zaken Adi , Mahat-Shamir Michal
Published: December 2017

ICD-11 has provided a revised definition for adjustment disorder (AjD). The current study examined whether mortality salience effect, a possible consequence of a terror attack, may serve as a significant predictor associated with each of the AjD subscales. Using an online survey, 379 adult participants were recruited and filled out self-reported questionnaires dealing with adjustment disorder symptoms as well as mortality salience effect. Findings revealed that mortality salience effect was a significant predictor of all AjD subscales. The importance of mortality salience effect for AjD is discussed in light of terror management theory.
Validation of a new American Association for the Surgery of Trauma (AAST) anatomic severity grading system for acute cholecystitis
Authors: Vera Kenneth , Pei Kevin Y. , Schuster Kevin M. , Davis Kimberly A.
Published: December 2017

BACKGROUND

The American Association for the Surgery of Trauma (AAST) established anatomic grading to facilitate risk stratification and risk-adjusted outcomes in emergency general surgery. Cholecystitis severity was graded based on clinical, imaging, operative, and pathologic criteria. We aimed to validate the AAST anatomic grading system for acute cholecystitis.

METHODS

This is a retrospective cohort study including consecutive patients admitted with acute cholecystitis at an urban, tertiary medical center between 2013 and 2016. Grade 1 is acute cholecystitis, Grade 2 is gangrenous or emphysematous cholecystitis, Grade 3 is localized perforation, and Grades 4 and 5 have regional and systemic peritonitis, respectively. Concordance between the AAST grade and outcome including mortality, length of stay (LOS), ICU use, readmission, and complications were assessed using logistic regression.

RESULTS

A total of 315 patients were included. There was very good inter-rater (two independent raters) reliability for anatomic grading, κ = 1.00, p < 0.005. The majority of patients were Grade 1 or Grade 2 (94%). Incidence of complications, LOS, ICU use, and any adverse event increased with increasing anatomic grade. When compared to Grade 1 disease, patients with Grade 2 were more likely to undergo cholecystectomy (OR 4.07 [1.93–8.56]). Grade 3 patients were at higher risk of adverse events (OR 3.83 [1.34–10.94]), longer LOS (OR 1.73 [1.03–2.92]), and ICU use (OR 8.07 [2.43–26.80]).

CONCLUSIONS

AAST severity scores were independently associated with clinical outcomes in patients with acute cholecystitis. Despite low-grade disease, complications were common, and therefore a refinement of the scoring system may be necessary for more granular prediction.

LEVEL OF EVIDENCE

Epidemiologic/prognostic, level III
Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference
Authors: Young Alexandra L , Marinescu Razvan V , Oxtoby Neil P , Bocchetta Martina , Yong Keir , Firth Nicholas , Cash David M , Thomas David L , Dick Katrina M , Cardoso Jorge , Swieten John van , Borroni Barbara , Galimberti Daniela , Masellis Mario , Tartaglia Maria Carmela , Rowe James B , Graff Caroline , Tagliavini Fabrizio , Frisoni Giovanni , Laforce Robert , Finger Elizabeth , Mendonça Alexandre , Sorbi Sandro , Warren Jason D , Crutch Sebastian , Fox Nick C , Ourselin Sebastien , Schott Jonathan M , Rohrer Jonathan D , Alexander Daniel C
Published: December 2017

The heterogeneity of neurodegenerative diseases is a key confound to disease understanding and treatment development, as study cohorts typically include multiple phenotypes on distinct disease trajectories. Here we present a new machine learning technique – Subtype and Stage Inference (SuStaIn) – able to uncover data-driven disease phenotypes with distinct temporal progression patterns, from widely available crosssectional patient studies. Results from imaging studies in two neurodegenerative diseases reveal new subgroups and their distinct trajectories of regional neurodegeneration. In genetic frontotemporal dementia, SuStaIn identifies genotypes from imaging alone, validating its ability to identify subtypes, and characterises within-group heterogeneity for the first time. In Alzheimer’s disease, SuStaIn uncovers three subtypes, uniquely revealing their temporal complexity. SuStaIn provides fine-grained patient stratification, which substantially enhances the ability to predict conversion between diagnostic categories over standard models that ignore subtype (p=7.18×10--4) or temporal stage (p=3.96×10−5). SuStaIn thus offers new promise for enabling disease subtype discovery and precision medicine.
Analysis of EEG networks and their correlation with cognitive impairment in preschool children with epilepsy
Authors: Kinney-Lang Eli , Yoong Michael , Hunter Matthew , Tallur Krishnaraya Kamath , Shetty Jay , McLellan Ailsa , Chin Richard FM , Escudero Javier
Published: December 2017

Objective: Cognitive impairment (CI) is common in children with epilepsy and can have devastating effects on their quality of life and that of their family. Early identification of CI is a priority to improve outcomes, but the current gold standard of detection with psychometric assessment is resource intensive and not always available. This paper proposes a novel technique of network analysis using routine clinical electroencephalography (EEG) to help identify CI in children with early-onset epilepsy (CWEOE) (0-5 y.o.).

Methods: We analyzed functional networks from routinely acquired EEGs of 51 newly diagnosed CWEOE from a prospective population-based study. Combinations of connectivity metrics (e.g. phase-slope index (PSI)) with sub-network analysis (e.g. cluster-span threshold (CST)) identified significant correlations between network properties and cognition scores via rank correlation analysis with Kendall’s τ. Predictive properties were investigated using a 5-fold cross-validated K-Nearest Neighbor classification model with normal cognition, mild/moderate CI and severe CI classes.

Results: Phase-dependent connectivity metrics had higher sensitivity to cognition scores, with sub-networks identifying significant functional network changes over a broad range of spectral frequencies. Approximately 70.5% of all children were appropriately classified as normal cognition, mild/moderate CI or severe CI using CST network features. CST classification predicted CI classes 55% better than chance, and reduced misclassification penalties by half.

Conclusions: CI in CWEOE can be detected with sensitivity at 85% (with respect to identifying either mild/moderate or severe CI) and specificity of 84%, by EEG network analysis.

Significance: This study outlines a data-driven methodology for identifying candidate biomarkers of CI in CWEOE from network features. Following additional replication, the proposed method and its use of routinely acquired EEG forms an attractive proposition for supporting clinical assessment of CI.
Comprehensive analysis ofVerticillium nonalfalfae in silicosecretome uncovers putative effector proteins expressed during hop invasion
Authors: Marton Kristina , Flajšman Marko , Radišek Sebastjan , Košmelj Katarina , Jakše Jernej , Javornik Branka , Berne Sabina
Published: December 2017

Background

The vascular plant pathogenVerticillium nonalfalfaecauses Verticillium wilt in several important crops. VnaSSP4.2 was recently discovered as aV. nonalfalfaevirulence effector protein in the xylem sap of infected hop. Here, we expanded our search for candidate secreted effector proteins (CSEPs) in theV. nonalfalfaepredicted secretome using a bioinformatic pipeline built onV. nonalfalfaegenome data, RNA-Seq and proteomic studies of the interaction with hop.

Results

The secretome, rich in carbohydrate active enzymes, proteases, redox proteins and proteins involved in secondary metabolism, cellular processing and signaling, includes 263 CSEPs. Several homologs of known fungal effectors (LysM, NLPs, Hce2, Cerato-platanins, Cyanovirin-N lectins, hydrophobins and CFEM domain containing proteins) and avirulence determinants in the PHI database (Avr-Pita1 and MgSM1) were found. The majority of CSEPs were non-annotated and were narrowed down to 44 top priority candidates based on their likelihood of being effectors. These were examined by spatio-temporal gene expression profiling of infected hop. Among the highestin plantaexpressed CSEPs, five deletion mutants were tested in pathogenicity assays. A deletion mutant ofVnaUn.279, a lethal pathotype specific gene with sequence similarity to SAM-dependent methyltransferase (LaeA), had lower infectivity and showed highly reduced virulence, but no changes in morphology, fungal growth or conidiation were observed.

Conclusions

Several putative secreted effector proteins that probably contribute toV. nonalfalfaecolonization of hop were identified in this study. Among them,LaeAgene homolog was found to act as a potential novel virulence effector ofV. nonalfalfae. The combined results will serve for future characterization ofV. nonalfalfaeeffectors, which will advance our understanding of Verticillium wilt disease.
Modeling acute myeloid leukemia in a continuum of differentiation states
Authors: Cho H. , Ayers K. , DePills L. , Kuo Y-H. , Park J. , Radunskaya A. , Rockne R.
Published: December 2017

Here we present a mathematical model of movement in an abstract space representing states of cellular differentiation. We motivate this work with recent examples that demonstrate a continuum of cellular differentiation using single cell RNA sequencing data to characterize cellular states in a high-dimensional space, which is then mapped into ℝ2or ℝ3with dimension reduction techniques. We represent trajectories in the differentiation space as a graph, and model directed and random movement on the graph with partial differential equations. We hypothesize that flow in this space can be used to model normal differentiation processes as well as predict the evolution of abnormal differentiation processes such as those observed during pathogenesis of acute myeloid leukemia (AML).
Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato
Authors: Tashkandi Manal , Ali Zahir , Aljedaani Fatimah , Shami Ashwag , Mahfouz Magdy M.
Published: December 2017

CRISPR/Cas systems confer molecular immunity against phages and conjugative plasmids in prokaryotes. Recently, CRISPR/Cas9 systems have been used to confer interference against eukaryotic viruses. Here, we engineered Nicotiana benthamiana and tomato (Solanum lycopersicum) plants with the CRISPR/Cas9 system to confer immunity against the Tomato yellow leaf curl virus (TYLCV). Targeting the TYLCV genome with Cas9-single guide RNA at the sequences encoding the coat protein (CP) or replicase (Rep) resulted in efficient virus interference, as evidenced by low accumulation of the TYLCV DNA genome in the transgenic plants. The CRISPR/Cas9-based immunity remained active across multiple generations in the N. benthamiana and tomato plants. Together, our results confirmed the efficiency of the CRISPR/Cas9 system for stable engineering of TYLCV resistance in N. benthamiana and tomato, and opens the possibilities of engineering virus resistance against single and multiple infectious viruses in other crops.
The co-regulatory interaction of transpiration and water potential, and implications for stomatal conductance models
Authors: Beyer Robert , Pretzsch Hans , Cournède Paul-Henry
Published: December 2017

Leaf water potential decreases with increasing transpiration rate according to an analogue of Ohm’s law, while transpiration rate decreases with decreasing leaf water potential in the framework of stomatal control. This interaction is not accommodated in present-day models of stomatal conductance. We formally derive the equilibrium between these two counteracting processes for steady-state water conditions. We show that the mechanism considered causes an attenuation of the immediate effect of atmospheric variables on transpiration, which can improve existing models of stomatal conductance that presume noninterdependent variables. Parameters from European beech (Fagus sylvaticaL.) are used to illustrate the results.
Decomposing the Apoptosis Pathway Into Biologically Interpretable Principal Components
Authors: Wang Min , Kornblau Steven M. , Coombes Kevin R.
Published: December 2017

Principal component analysis (PCA) is one of the most common techniques in the analysis of biological data sets, but applying PCA raises two challenges. First, one must determine the number of significant principal components (PCs). Second, because each PC is a linear combination of genes, it rarely has a biological interpretation. Existing methods to determine the number of PCs are either subjective or computationally extensive. We review several methods and describe a new R package, PCDimension, that implements additional methods, the most important being an algorithm that extends and automates a graphical Bayesian method. Using simulations, we compared the methods. Our newly automated procedure performs best when considering both accuracy and speed. We applied the method to a proteomics data set from acute myeloid leukemia patients. Proteins in the apoptosis pathway could be explained using six PCs. By clustering the proteins in PC space, we were able to replace the PCs by six “biological components”, three of which could be immediately interpreted from the current literature. We expect this approach combining PCA with clustering to be widely applicable.
Somatic Mutations Predict Acute Myeloid Leukemia Years Before Diagnosis
Authors: Desai Pinkal , Mencia-Trinchant Nuria , Savenkov Oleksandr , Simon Michael S. , Cheang Gloria , Lee Sangmin , Samuels Michael , Ritchie Ellen K , Guzman Monica L. , Ballman Karla V , Roboz Gail J. , Hassane Duane C.
Published: December 2017

Background

Somatic mutations observed in clonal hematopoiesis are associated with increased age and risk of hematological malignancies. However, the limited number of acute myeloid leukemia (AML) patients in studies of clonal hematopoiesis thus far has precluded determination of the spectrum of mutations leading to AML and their impact on risk and time to diagnosis.

Methods

The relationship between baseline mutations and subsequent AML was determined in a case-control study design. 212 women eventually diagnosed with AML (median time: 9.8 years) were identified from the Women’s Health Initiative cohort alongside 212 matched AML-free controls. Deep sequencing of 67 genes was performed on DNA isolated from peripheral blood to detect subclonal mutations.

Results

The presence of any mutation was associated with increased odds of eventual AML (odds ratio [OR] 4.0; 95% confidence interval [CI], 2.5-6.3). These odds were further elevated with mutations in IDH1/2 (OR 8.4; 95% CI, 1.4-51.9), TP53 (OR 54.2; 95% CI, 2.9-1017.7), or spliceosome genes (OR 5.6; 95% CI, 1.5-20.6). Eventual AML diagnosis occurred in all or most participants with mutations in TP53 (N=23/23) or IDH1/2 (N=15/16). Mutations indicated sooner AML diagnosis (median 8.0 vs. 11.9 years; P < 0.001) with TP53 mutations demonstrating increased odds of AML within 5 years (OR 3.6; 95% CI, 1.4-9.1).

Conclusions

Mutations are present in peripheral blood of AML patients a decade prior to AML diagnosis with mutations in TP53 producing especially rapid presentation. Strategies for monitoring of high-risk populations are needed and clinical trials of potential early interventions can be considered.
Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals
Authors: Casadei Cecilia M. , Tsai Ching-Ju , Barty Anton , Hunter Mark S. , Zatsepin Nadia A. , Padeste Celestino , Capitani Guido , Benner W. Henry , Boutet Sébastien , Hau-Riege Stefan P. , Kupitz Christopher , Messerschmidt Marc , Ogren John I. , Pardini Tom , Rothschild Kenneth J. , Sala Leonardo , Segelke Brent , Williams Garth J. , Evans James E. , Li Xiao-Dan , Coleman Matthew , Pedrini Bill , Frank Matthias
Published: December 2017

Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.
Structural characterization of a novel monotreme-specific protein with antimicrobial activity from the milk of the platypus
Authors: Newman Janet , Sharp Julie A. , Enjapoori Ashwantha Kumar , Bentley John , Nicholas Kevin R. , Adams Timothy E. , Peat Thomas S.
Published: December 2017

Monotreme lactation protein (MLP) is a recently identified protein with antimicrobial activity. It is present in the milk of monotremes and is unique to this lineage. To characterize MLP and to gain insight into the potential role of this protein in the evolution of lactation, the crystal structure of duck-billed platypus (Ornithorhynchus anatinus) MLP was determined at 1.82 Å resolution. This is the first structure to be reported for this novel, mammalian antibacterial protein. MLP was expressed as a FLAG epitope-tagged protein in mammalian cells and crystallized readily, with at least three space groups being observed (P1,C2 andP21). A 1.82 Å resolution native data set was collected from a crystal in space groupP1, with unit-cell parametersa= 51.2,b= 59.7,c= 63.1 Å, α = 80.15, β = 82.98, γ = 89.27°. The structure was solved by SAD phasing using a protein crystal derivatized with mercury in space groupC2, with unit-cell parametersa= 92.7,b = 73.2,c= 56.5 Å, β = 90.28°. MLP comprises a monomer of 12 helices and two short β-strands, with much of the N-terminus composed of loop regions. The crystal structure of MLP reveals no three-dimensional similarity to any known structures and reveals a heretofore unseen fold, supporting the idea that monotremes may be a rich source for the identification of novel proteins. It is hypothesized that MLP in monotreme milk has evolved to specifically support the unusual lactation strategy of this lineage and may have played a central role in the evolution of these mammals.
Acetonyltriphenylphosphonium 2,3,5-triphenyltetrazolium tetrachloridocuprate(II)
Authors: Diop Mouhamadou Birame , Diop Libasse , Oliver Allen G.
Published: December 2017

The title compound, (C21H20OP)(C19H15N4)[CuCl4], was obtained by reacting CuCl2·2H2O with a mixture of one equivalent of acetonyltriphenylphosphonium chloride and one equivalent of 2,3,5-triphenyltetrazolium chloride in acetonitrile. In the structure, the Cu centre in the dianion is bonded to four chloride ligands and adopts a distorted tetrahedral geometry. The phosphonium cation likewise adopts the expected tetrahedral geometry. The tetrazolium ring forms dihedral angles of 77.68 (10), 26.85 (11) and 66.48 (10)° with the planes of the benzene rings of the substituent groups. In the crystal, weak C—H...Cl hydrogen-bonding interactions involving both cations and the anion give rise to a three-dimensional supramolecular structure.