bluuebunny/crossref_metadata_2025 huggingface dataset:
Copper-Catalyzed Intermolecular Thioamination of Maleimides with Thiols and Formamides: A One-Step Construction of 3-Amino-4-thiomaleimides Using Formamides as Nitrogen Sources
Authors: Zhao Sheng-Yin , Yang Zhen-Hua , Zhu Jia-Nan , Jin Ze-Hui , Zheng Jian
Published: August 2018

A highly efficient copper-catalyzed intermolecular C(sp2)–H thioamination of maleimides with thiols and formamides in the presence of fluoroboric acid is reported using various readily available formamides as nitrogen sources and solvents. A diverse range of 3-amino-4-thiomaleimides is obtained with good yields under mild conditions, involving C–N and C–S bond formation. This methodology enriches current C–N and C–S bond formation chemistry and features operational simplicity and excellent functional-group tolerance.
Long-Term Results after Diversion Surgery in Extrahepatic Portal Vein Obstruction
Authors: Alvarez Ana , Dore Mariela , Jimenez Gomez Javier , Sánchez Galán Alba , Vilanova-Sánchez Alejandra , Andres Ane , Encinas Jose , Martinez Leopoldo , Hernandez Francisco , Lopez Santamaria Manuel , Triana Junco Paloma
Published: August 2018

Aim Extrahepatic portal vein obstruction (EHPVO) is a frequent cause of noncirrhotic portal hypertension in children. The aim of this study is to analyze long-term results after diversion surgery.

Patients and Methods Retrospective review of EHPVO patients who underwent diversion surgery analyzing number of platelets, leukocytes, prothrombin activity, splenomegaly, and gastrointestinal bleeding 10 years after surgery.

Results Thirty-three patients were evaluated, mostly males (64%) and presenting with gastrointestinal bleeding (46%). Mesoportal shunt (Rex) was performed in 19 patients, mesocaval in 7, distal splenorenal in 7, and proximal splenorenal in 3. While comparing mesoportal shunt to the other portosystemic shunts, an increase in platelets was found with every technique, but it was clearly higher in mesoportal shunt. The highest increase was 6 months after surgery (p = 0.0015) as well as prothrombin activity (p = 0.0003). Leukocytes level also increased without statistical significance. Spleen size (cm) and spleen size Z score (SSAZ) decreased significantly 6 months after mesoportal shunt (p = 0.0168). Before surgery, over 94% patients suffered gastrointestinal bleeding, which reduced significantly afterward with bleeding episodes in only four (12%) of them.

Conclusion Diversion surgery in EHPVO, especially mesoportal shunt of Rex, improves hepatic function (prothrombin activity), reduces hypersplenism (platelets, leukocytes, and spleen size), and decreases gastrointestinal bleeding episodes.
Note: Performance of a novel electrostatic quadrupole doublet for nuclear microprobe application
Authors: Manuel Jack E. , Szilasi Szabolcs Z. , Byers Todd A. , Phillips Dustin Z. , Dymnikov Alexander D. , Reinert Tilo , Rout Bibhudutta , Glass Gary A.
Published: August 2018

The newly designed and constructed electrostatic quadrupole doublet (EQD) at the University of North Texas (UNT) has achieved mass independent focusing of MeV particles to a spot size of 3.3 × 3.5 μm. The EQD is compared to the Louisiana magnetic doublet which is also in use at UNT. Characteristics such as demagnification and sensitivity to aberrations are simulated by the matrix raytracing software, propagation of rays and aberrations by matrices and compared for each focusing system. Particle induced x-ray emission (PIXE) maps of a 2000 mesh Cu grid are compared and show that both doublets produce suitable spot sizes for microprobe analysis. A coarser, 200 mesh grid and incident beams of 2 MeV H+ and O+ show the EQD to be stigmatic given common aperture sizes and lens potentials.
Kupershmidt-(dual-)Nijenhuis structures on a Lie algebra with a representation
Authors: Hu Yuwang , Liu Jiefeng , Sheng Yunhe
Published: August 2018

In this paper, first we study infinitesimal deformations of a Lie algebra with a representation and introduce the notion of a Nijenhuis pair, which gives a trivial deformation of a Lie algebra with a representation. Then we introduce the notion of a Kupershmidt-(dual-)Nijenhuis structure on a Lie algebra with a representation, which is a generalization of the r − n structure (r-matrix-Nijenhuis structure) introduced by Ravanpak, Rezaei-Aghdam, and Haghighatdoost. We show that a Kupershmidt-(dual-)Nijenhuis structure gives rise to a hierarchy of Kupershmidt operators. Finally, we define a Rota-Baxter-Nijenhuis structure to be a Kupershmidt-Nijenhuis structure on a Lie algebra with respect to the adjoint representation and study the relation between Rota-Baxter-Nijenhuis structures and r-matrix-Nijenhuis structures.
X-ray magnetic circular dichroism and near-edge X-ray absorption fine structure of buried interfacial magnetism measured by using a scanning tunneling microscope tip
Authors: Chang H. , Shirato N. , Zhang Y. , Hoffman J. , Rosenmann D. , Freeland J. W. , Bhattacharya A. , Rose V. , Hla S.-W.
Published: August 2018

Magnetism at buried interfaces plays a crucial role in many emerging phenomena, but detection of interfacial magnetism in close proximity to a surface with elemental and chemical sensitivity is a challenging task. Here, we use low temperature synchrotron x-ray scanning tunneling microscopy to investigate x-ray magnetic circular dichroism and the near edge x-ray absorption fine structure of La0.67Sr0.33MnO3-LaNiO3 superlattices. In stark contrast to the weak magnetic signal of Mn when the La0.67Sr0.33MnO3 layers are located on top, a robust x-ray magnetic circular dichroism signal is detected when they are buried underneath the LaNiO3 layers. The near edge x-ray absorption fine structure reveals the valence states of manganese, while the oxygen K-edge x-ray absorption spectra show an increase in hole formation, indicating a cogent charge transfer at the LaNiO3/La0.67Sr0.33MnO3 interface. This work demonstrates that scanning tunneling microscopy can be extended to the synchrotron X-ray study of buried interfaces by controlling the tip-sample separation in the nanometer regime.
Controlling ion kinetic energy distributions in laser produced plasma sources by means of a picosecond pulse pair
Authors: Stodolna Aneta S. , de Faria Pinto Tiago , Ali Faisal , Bayerle Alex , Kurilovich Dmitry , Mathijssen Jan , Hoekstra Ronnie , Versolato Oscar O. , Eikema Kjeld S. E. , Witte Stefan
Published: August 2018

The effect of a pair of picosecond pulses on the ionization and deformation of a liquid tin microdroplet is studied for a range of incident pulse parameters. Faraday cups are used to measure ion kinetic energy distributions, together with high-resolution shadowgraphy to monitor target deformation and expansion. It is found that the introduction of a relatively weak first pulse results in an order-of-magnitude reduction of the number of ions with kinetic energies above 1 keV, and a strong shift of the kinetic energy distribution towards lower energies, while the expansion dynamics of the droplet can be kept similar to the single-pulse case. By controlling the relative intensity and the time delay between pairs of pulses with 52 ps duration, regimes are identified in which spherical final target shapes are combined with a reduced high-energy ion yield. The high-energy part of the observed ion distributions has been fitted with a self-similar expansion model, showing a 30-fold decrease in characteristic ion energy for pulse pairs. This combination of results is of particular importance for plasma sources of EUV radiation for nanolithography applications, in which picosecond-laser-produced target shapes can lead to significant improvements in source conversion efficiency, while a low high-energy ion yield is desirable from a source lifetime perspective.
Correlation anisotropy and stiffness of DNA molecules confined in nanochannels
Authors: Bleha Tomáš , Cifra Peter
Published: August 2018

The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function ⟨C(s)⟩⊥ in the transverse (confined) dimension exhibits a region of negative values in the whole range of channel sizes. Such a clear-cut sign of the opposite orientation of chain segments represents a microscopic validation of the Odijk deflection mechanism in narrow channels. At moderate-to-weak confinement, the negative ⟨C(s)⟩⊥ correlations imply a preference of DNA segments for transverse looping. The inclination for looping can explain a reduction of stiffness as well as the enhanced knotting of confined DNA relative to that detected earlier in bulk at some channel sizes. Furthermore, it is shown that the orientational persistence length Por fails to convey the apparent stiffness of DNA molecules in channels. Instead, correlation lengths P∥ and P⊥ in the axial and transverse directions, respectively, encompass the channel-induced modifications of DNA stiffness.
Advancing the capability of the gated laser-entrance-hole imager on the National Ignition Facility
Authors: Chen Hui , Palmer Nathan , Bell Perry , Bradley David , Dayton Matthew , Kilkenny Joe , Jones Oggie , Patel Pratik , Rever Matthew , Schneider Marilyn , Thibodeau Matthew
Published: August 2018

A new configuration based on the recent off-line calibrations of the gated laser entrance hole diagnostic on the National Ignition Facility provides 4-8 interleaved frames per experiment using the standard two frame sensor settings. Since its implementation, the new design has greatly increased the data return for hundreds of experiments at the National Ignition Facility. The large quantity of images from a variety of physics campaigns has revealed information on plasma evolution in hohlraums.
Contribution assessment of antenna structure and in-gap photocurrent in terahertz radiation of photoconductive antenna
Authors: Zhang Jitao , Tuo Mingguang , Liang Min , Wang Xiong , Xin Hao
Published: August 2018

Photoconductive antenna (PCA) is one of the most widely used terahertz (THz) devices nowadays. Although PCAs have been extensively studied through both theoretical analysis and device design, there still lacks a common agreement upon the mechanism of THz radiation. One of the central questions is how to distinguish and assess the contribution of the antenna structure and in-gap photocurrent to the overall radiation of a PCA. In this work, a three-dimensional full-wave model was first used to quantify the overall far-field radiation of PCAs. The commercial solver (i.e., HFSS) and the Hertzian dipole approximation method were then applied to quantify the far-field radiation solely from the antenna structure and in-gap photocurrent, respectively. The contribution of the antenna structure and in-gap photocurrent can therefore be distinguished by comparing the simulation results among the three methods. The results suggest that, although the THz radiation originates from laser-excited photocurrent within the gap, the overall THz radiation of a PCA is predominated by the antenna structure. As a validation, the cancellation effect was predicated by numerical simulation of coplanar stripline PCA and confirmed with experiment using butterfly shaped stripline PCA. The presented work uncovers the details of the underlying radiation mechanism of the PCA. This could inspire PCA design that aims for engineering the radiation properties of a PCA for specific applications.
First measurements of a scintillator based fast-ion loss detector near the ASDEX Upgrade divertor
Authors: Gonzalez-Martin J. , Ayllon-Guerola J. , Garcia-Munoz M. , Herrmann A. , Leitenstern P. , De Marne P. , Zoletnik S. , Kovacsik A. , Galdon-Quiroga J. , Rivero-Rodriguez J. , Rodriguez-Ramos M. , Sanchis-Sanchez L. , Dominguez J. ,   ASDEX Upgrade Team,   MST1 Team
Published: August 2018

A new reciprocating scintillator based fast-ion loss detector has been installed a few centimeters above the outer divertor of the ASDEX Upgrade tokamak and between two of its lower Edge Localized Modes (ELM) mitigation coils. The detector head containing the scintillator screen, Faraday cup, calibration lamp, and collimator systems are installed on a motorized reciprocating system that can adjust its position via remote control in between plasma discharges. Orbit simulations are used to optimize the detector geometry and velocity-space coverage. The scintillator image is transferred to the light acquisition systems outside of the vacuum via a lens relay (embedded in a 3D-printed titanium holder) and an in-vacuum image guide. A charge coupled device camera, for high velocity-space resolution, and an 8 × 8 channel avalanche photo diode camera, for high temporal resolution (up to 2 MHz), are used as light acquisition systems. Initial results showing velocity-space of neutral beam injection prompt losses and fast-ion losses induced by a (2, 1) neoclassical tearing mode are presented.
A rotation sensor based on alkali-metal vapor cell
Authors: Zhang Ke , Yang Hong-Ying , Li Ai-Xian , Wang Yan-Hua , Zhao Nan
Published: August 2018

Accurate rotation sensors are highly demanded in both industrial applications and academic research. We experimentally demonstrate an angle measurement method based on an alkali-metal vapor cell. In our experiment, the rotation signal is converted to the polarization of the laser beam passing through a quarter-wave plate coaxially mounted on a detected object. The polarization is then measured by monitoring the transmission of the laser beam through the vapor cell. Using this method, we demonstrate an angle measurement sensitivity of 2×10−5°/Hz without a magnetic shield. The results shown in this paper provide a prototype of the angle measurement with high accuracy, compactness, and low cost.
Interface electrical properties between MCNO thin film and organic compounds
Authors: Zhang Fei , Huang ZhiMing
Published: August 2018

The Mn-Co-Ni-O (MCNO) thin film deposited on indium tin oxide (ITO) glass has a bandgap of 1.52 eV and can replace WO3, MoO3, or V2O5 films as the electron transport layer (ETL). The PN junctions can be formed for MCNO/(4,4′-Bis(9H-carbazol-9-yl) biphenyl) and MCNO/(4,4′,4′′-Tri(9-carbazoyl) triphenylamine) multi-layers, which can improve the electrical properties under both positive and negative voltages. There is a transition point for the curves of (Rv+-Rv−)/Rv+ ratio versus voltage. It is reasonable to exploit the range below this point, which is the high-efficiency working scope for the MCNO thin film as the ETL layer, and its property of electron extraction can be enhanced by the PN junction. (6,6)-Phenyl-C61-butyric Acid Methyl Ester (PCBM) is an n-type semiconductor, and the ITO/MCNO/PCBM multi-layers suffer no effect of the built-in electric field.
Meta-facet fiber for twisting ultra-broadband light with high phase purity
Authors: Zhao Yifan , Zhang Jinrun , Du Jing , Wang Jian
Published: August 2018

From metamaterial to metasurface and metadevice, the artificial structure with sub-wavelength scale on diverse platforms offers the ability to shape light in a custom way. The optical fiber is a robust and flexible media that has seen wide applications in optical communications, optical sensing, microscopy, and endoscope imaging. Here, we consider metasurface on a large-core fiber platform for twisting light. Using the designed and fabricated meta-facet fiber, we demonstrate (i) the excitation of both linearly polarized and circularly polarized twisted light (OAM+1, OAM−1) from either meta-facet side or planar-facet side, (ii) phase-front reconstruction of twisted light simply from a tilt interferogram using the Fourier-transform method, and (iii) ultra-broadband response from 1480 to 1640 nm with high phase purity above 93% for twisting light. The demonstrations on meta-facet fiber for twisting ultra-broadband light with high phase purity may open up perspectives to more emerging applications in information, biology, and medical science.
Wet-chemical bromination of Ge (100): A facile surface passivation tool
Authors: Abrenica Graniel Harne A. , Lebedev Mikhail V. , Okorn Gilbert , van Dorp Dennis H. , Fingerle Mathias
Published: August 2018

We demonstrate that wet-chemical surface bromination is an effective and a simple etching method for Ge surface oxide removal, providing excellent reoxidation resistance. Oxide removal and halide passivation for n-type Ge (100) were investigated using time-resolved photoluminescence and X-ray photoemission spectroscopy (XPS). In contrast to HCl, HBr treated Ge surfaces show a strong decrease in minority carrier lifetime, pointing to a surface state spectrum modification. The results from XPS using in situ sample preparation confirm that HBr effectively removes GeO2 and suboxides, providing an air stable surface. Isopropyl alcohol rinsing after Br passivation maintains the chemical surface composition and the electronic structure. In contrast, during H2O treatment in an Ar atmosphere, the brominated Ge surface is unstable, evidenced by emerging Ge-OH groups. The distinct observed upward shift of the surface Fermi level indicates an e- donating behavior of H2O.
First-principles calculations of elastic and piezoelectric constants and spontaneous polarization in Cd-IV-N2 compounds
Authors: Lyu Sai , Lambrecht Walter R. L.
Published: August 2018

Density functional perturbation theory calculations are carried out for the elastic and piezoelectric constants of Cd-IV-N2 compounds, which are derived from the III-N compounds by an ordered substitution of group III elements by Cd and group-IV. The spontaneous polarizations are determined as well. Properties directly derived from the elastic constants, such as the sound velocities, Debye temperature, and polycrystalline averages, are presented. The results are compared with those of Zn-IV-N2 and group-III nitrides. Generally, the elastic constants are found to be somewhat smaller than those in corresponding Zn-IV-N2 by about 15%–25%. Clear trends with the atomic number are obtained within the series with elastic constants decreasing with the atomic number and spontaneous polarization and piezoelectric coefficients increasing with the atomic number.
Mode penetration induced by transient magnetic perturbations
Authors: Beidler M. T. , Callen J. D. , Hegna C. C. , Sovinec C. R.
Published: August 2018

Three dimensional magnetic fields in tokamaks can induce forced magnetic reconnection (FMR) and produce magnetic islands on resonant surfaces. Conventional analytic solutions to FMR focus on describing the time asymptotic state given a steady-state field error. The focus of this work is to understand the nonlinear dynamics of mode penetration, an evolution from a high-slip, flow-screened metastable equilibrium into a low-slip, field-penetrated metastable equilibrium. In this work, we extend previous work by incorporating a temporally varying external magnetic field as a simple model for a magnetohydrodynamic (MHD) event that produces resonant magnetic perturbations. Proof-of-principle, extended-MHD, NIMROD computations vary parameterizations of the transient external perturbation to probe the threshold for mode penetration. We test these computational results against analytical theory that captures the temporal evolution properties of the electromagnetic and viscous forces during and after a transient. We find qualitative agreement between computational and analytical results. However, computational tools are necessary to accurately capture the threshold conditions for mode penetration induced by an MHD transient.
Synchronization of infra-slow oscillations of brain potentials with respiration
Authors: Karavaev A. S. , Kiselev A. R. , Runnova A. E. , Zhuravlev M. O. , Borovkova E. I. , Prokhorov M. D. , Ponomarenko V. I. , Pchelintseva S. V. , Efremova T. Yu. , Koronovskii A. A. , Hramov A. E.
Published: August 2018

We study the synchronization of infra-slow oscillations in human scalp electroencephalogram signal with the respiratory signal. For the cases of paced respiration with a fixed frequency and linearly increasing frequency, we reveal the phase and frequency locking of infra-slow oscillations of brain potentials by respiration. It is shown that for different brain areas, the infra-slow oscillations and respiration can exhibit synchronous regimes of different orders.
Hydrocarbon- and metal-polluted soil bioremediation: progress and challenges
Authors: Kuyukina Maria , Krivoruchko Anastasiya , Ivshina Irina
Published: August 2018

The problem of soil contamination with petroleum hydrocarbons and heavy metals is becoming particularly acute for large oil-producing countries, like the Russian Federation. Both hydrocarbon and metal contaminants impact negatively the soil biota and human health, thus requiring efficient methods for their detoxification and elimination. Bioremediation of soil co-contaminated with hydrocarbon and metal pollutants is complicated by the fact that, although the two components must be treated differently, they mutually affect the overall removal efficiency. Heavy metals are reported to inhibit biodegradation of hydrocarbons by interfering with microbial enzymes directly involved in biodegradation or through the interaction with enzymes involved in general metabolism. Here we discuss recent progress and challenges in bioremediation of soils co-contaminated with hydrocarbons and heavy metals, focusing on selecting metal-resistant biodegrading strains and biosurfactant amendments.
Thiocyanate biodegradation: harnessing microbial metabolism for mine remediation
Authors: Watts Mathew P , Moreau John W
Published: August 2018

Thiocyanate (SCN–) forms in the reaction between cyanide (CN–) and reduced sulfur species, e.g. in gold ore processing and coal-coking wastewater streams, where it is present at millimolar (mM) concentrations1. Thiocyanate is also present naturally at nM to µM concentrations in uncontaminated aquatic environments2. Although less toxic than its precursor CN–, SCN– can harm plants and animals at higher concentrations3, and thus needs to be removed from wastewater streams prior to disposal or reuse. Fortunately, SCN– can be biodegraded by microorganisms as a supply of reduced sulfur and nitrogen for energy sources, in addition to nutrients for growth4. Research into how we can best harness the ability of microbes to degrade SCN– may offer newer, more cost-effective and environmentally sustainable treatment solutions5. By studying biodegradation pathways of SCN– in laboratory and field treatment bioreactor systems, we can also gain fundamental insights into connections across the natural biogeochemical cycles of carbon, sulfur and nitrogen6.
DUSP6 mediates T cell receptor-engaged glycolysis and restrains T
FH
cell differentiation
Authors: Hsu Wei-Chan , Chen Ming-Yu , Hsu Shu-Ching , Huang Li-Rung , Kao Cheng-Yuan , Cheng Wen-Hui , Pan Chien-Hsiung , Wu Ming-Sian , Yu Guann-Yi , Hung Ming-Shiu , Leu Chuen-Miin , Tan Tse-Hua , Su Yu-Wen
Published: August 2018

Significance

Naive T cells at quiescent state utilize mitochondrial respiration to generate ATP. In response to antigen, activated T cells through T cell receptor (TCR) and CD28 differentiate to T
H
1, T
H
2, or T
H
17 effector cells with an induction of aerobic glycolysis. Here, we demonstrate a role for DUSP6 in the glycolysis commitment during T cell activation. DUSP6 deficiency prompts activated T cells to rely on glucose-independent fuels. We show that DUSP6 fine-tunes TCR-MAPK signaling, which determines follicular helper T (T
FH
) effector-cell differentiation regardless of a glycolytic defect. Our findings imply that glycolysis is required for survival of activated T cells but optional for IL-21 production in T
FH
cell differentiation.
Extracellular matrix protein 1 promotes follicular helper T cell differentiation and antibody production
Authors: He Lan , Gu Wangpeng , Wang Meng , Chang Xiaoyan , Sun Xiaoyu , Zhang Yuan , Lin Xuan , Yan Chenghua , Fan Weiguo , Su Pan , Wang Yanming , Yi Chunyan , Lin Guomei , Li Li , Jiang Yu , Lu Junxia , Dong Chen , Wang Haikun , Sun Bing
Published: August 2018

Significance

T
FH
cell differentiation and antigen-specific antibody production is critical for humoral responses. In this work, we show that extracellular matrix protein 1 (ECM1) is a critical positive regulator in T-follicular helper (T
FH
) differentiation by repressing IL-2–STAT5–Bcl6 signaling pathway. Importantly, ECM1 effectively enhanced T
FH
differentiation, germinal center responses, and neutralizing antibody production both in antigen-immunized conditions and influenza infection, which indicate ECM1 may serve as a positive regulator for humoral responses in vivo.
Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds
Authors: Litvinov Rustem I. , Kononova Olga , Zhmurov Artem , Marx Kenneth A. , Barsegov Valeri , Thirumalai D. , Weisel John W.
Published: August 2018

Significance

The fibrin network is the scaffold of blood clots that prevent bleeding. Fibrin formation is driven by noncovalent “knob-hole” bonds that determine the mechanical properties of clots. Counterintuitively, the strength of knob-hole bonds first increased (catch bond) and then decreased (slip bond) with tensile force, thereby displaying a rare dual catch–slip behavior. We resolved the structural mechanism of tension-activated strengthening of the knob-hole bond. Our theory quantitatively accounts for the biphasic catch–slip force response, which comprises an important aspect of fibrin structural bionanomechanics. The shear-enhanced strengthening of noncovalent knob-hole bonds might favor fibrin polymerization under blood flow and might prevent breakup of nascent blood clots in the circulation.
Phospholipid retention in the absence of asymmetry strengthens the outer membrane permeability barrier to last-resort antibiotics
Authors: Powers Matthew J. , Trent M. Stephen
Published: August 2018

Significance

The outer membrane of Gram-negative bacteria prevents the entry of many antibiotics and limits treatment options for Gram-negative infections. This unique membrane is effective due to its asymmetric lipid composition, with the glycolipid lipid A [LPS or lipooligosaccharide (LOS)] in the outer leaflet at the cell surface and glycerophospholipids in the inner leaflet. Furthering our understanding of how outer membrane asymmetry is maintained is critical for the development of novel therapeutics to target multidrug-resistant bacteria. Here, we used a Gram-negative bacterium without LOS to probe for factors that impact cell-envelope maintenance in the absence of LOS. Our approach enabled us to explore fundamental mechanisms of cell-envelope biology and expand our holistic view of the asymmetrical, Gram-negative outer membrane.
MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP
Authors: Husić Edin , Li Xinyue , Hujdurović Ademir , Mehine Miika , Rizzi Romeo , Mäkinen Veli , Milanič Martin , Tomescu Alexandru I
Published: August 2018

Motivation

Discovering the evolution of a tumor may help identify driver mutations and provide a more comprehensive view on the history of the tumor. Recent studies have tackled this problem using multiple samples sequenced from a tumor, and due to clinical implications, this has attracted great interest. However, such samples usually mix several distinct tumor subclones, which confounds the discovery of the tumor phylogeny.

Results

We study a natural problem formulation requiring to decompose the tumor samples into several subclones with the objective of forming a minimum perfect phylogeny. We propose an Integer Linear Programming formulation for it, and implement it into a method called MIPUP. We tested the ability of MIPUP and of four popular tools LICHeE, AncesTree, CITUP, Treeomics to reconstruct the tumor phylogeny. On simulated data, MIPUP shows up to a 34% improvement under the ancestor-descendant relations metric. On four real datasets, MIPUP’s reconstructions proved to be generally more faithful than those of LICHeE.

Availability and implementation

MIPUP is available at https://github.com/zhero9/MIPUP as open source.

Supplementary information

Supplementary data are available at Bioinformatics online.
Robotic-Assisted Spine Surgery Using the Mazor XTM System: 2-Dimensional Operative Video
Authors: Tan Lee A , Lehman Ronald A
Published: August 2018

We demonstrate the setup and workflow of performing robotic spine surgery using the Mazor XTM system (MAZOR Robotics Inc, Orlando, Florida) in this video. An illustrative case was presented, including detailed steps for S2AI screw and lumbar pedicle screw placement using robotic assistance. A step-by-step narration is provided along with discussion of surgical nuances. Robotic spine surgery can be a safe and efficient method for screw placement, which can potentially reduce the risk of screw malposition. Spine surgeons should be familiar with this technology and keep this technique in their armamentarium.

There is no identifying information in this video. A patient consent was obtained for publishing of the material included in the video.
Relationship Between Opioid Analgesic Prescription and Unemployment in Patients Seeking Acupuncture for Chronic Pain in Urban Primary Care
Authors: Chuang Elizabeth , Gil Eric N , Gao Qi , Kligler Benjamin , McKee M Diane
Published: August 2018

Objective

The widespread use of opioid analgesics to treat chronic nonmalignant pain has contributed to the ongoing epidemic of opioid-related morbidity and mortality. Previous studies have also demonstrated a relationship between opioid analgesic use and unemployment due to disability. These studies have been limited to mainly white European and North American populations. The objective of this study is to explore the relationship between opioid analgesic use for chronic nonmalignant pain in an urban, mainly black and Hispanic, low-income population.

Design

This is a cross-sectional observational study.

Setting

Subjects were recruited from six urban primary care health centers.

Subjects

Adults with chronic neck, back, or osteoarthritis pain participating in an acupuncture trial were included.

Methods

Survey data were collected as a part of the Acupuncture Approaches to Decrease Disparities in Pain Treatment two-arm (AADDOPT-2) comparative effectiveness trial. Participants completed a baseline survey including employment status, opioid analgesic use, the Brief Pain Inventory, the global Patient Reported Outcomes Measurement Information Systems quality of life measure, the Patient Health Questionnaire-9 (PHQ-9), and demographic information. A multivariable logistic regression model was built to examine the association between opioid analgesic use and unemployment.

Results

Opioid analgesic use was associated with three times the odds of unemployment due to disability while controlling for potential confounders, including depression, pain severity, pain interference, global physical and mental functioning, and demographic characteristics.

Conclusions

This study adds to the growing body of evidence that opioid analgesics should be used with caution in chronic nonmalignant pain.
rClone Red facilitates bacterial gene expression research by undergraduates in the teaching laboratory
Authors: Campbell A Malcolm , Eckdahl Todd T
Published: August 2018

rClone Red is a low-cost and student-friendly research tool that has been used successfully in undergraduate teaching laboratories. It enables students to perform original research within the financial and time constraints of a typical undergraduate environment. Students can strengthen their understanding of the initiation of bacterial translation by cloning ribosomal binding sites of their own design and using a red fluorescent protein reporter to measure translation efficiency. Online microbial genome sequences and the mFold website enable students to explore homologous rRNA gene sequences and RNA folding, respectively. In this report, we described how students in a genetics course who were given the opportunity to use rClone Red demonstrated significant learning gains on 16 of 20 concepts, and made original discoveries about the function of ribosome binding sites. By combining the highly successful cloning method of golden gate assembly with the dual reporter proteins of green fluorescent protein and red fluorescent protein, rClone Red enables novice undergraduates to make new discoveries about the mechanisms of translational initiation, while learning the core concepts of genetic information flow in bacteria.
An Integrative Review of Clinical Reasoning Teaching Strategies and Outcome Evaluation in Nursing Education
Authors: Brown Tyo Mirinda , McCurry Mary K.
Published: August 2018

BACKGROUND

This study explored teaching strategies used to promote clinical reasoning in nursing education and identify outcomes used to evaluate effectiveness.

METHOD

The integrative review framework by Whittemore and Knafl (2005) was used in this study.

RESULTS

Strategies included simulation (n = 10); active learning strategies such as case studies, reflection, journaling, and collaborative learning (n = 13); teaching strategies such as think aloud or case studies with simulation (n = 12); and experiential or clinical experiences (n = 2). Although most studies used exams, worksheets (n = 19), or observations by clinical instructors (n = 2) to measure effectiveness, some studies (n = 8) also used surveys to measure student satisfaction, engagement, or perception; three studies measured the student’s ability to use the instrument.

CONCLUSION

Improving clinical thinking requires development of innovative, effective teaching strategies. Instruments that can accurately evaluate teaching and learning strategies are needed to advance this educational initiative and improve quality of care.
Individualized Compared With Standard Postdischarge Oxycodone Prescribing After Cesarean Birth
Authors: Osmundson Sarah S. , Raymond Britany L. , Kook Bradley T. , Lam LeAnn , Thompson Elizabeth B. , Schornack Leslie A. , Voorhees Catherine E. , Richardson Michael G.
Published: August 2018

OBJECTIVE:

To evaluate whether individualized postdischarge oxycodone prescribing guided by inpatient opioid use reduces the number of unused opioid tablets after cesarean birth.

METHODS:

We conducted a randomized, controlled trial of women aged 18 years or older undergoing cesarean birth. Participants were randomized at discharge in a 1:1 ratio to a standard (30 tablets of 5 mg oxycodone) or an individualized oxycodone prescription (predicted based on each patient's inpatient opioid use). All women were contacted starting 14 days after cesarean birth to assess number of oxycodone tablets used and adequacy of pain control. The Tennessee Controlled Substance Monitoring Database was accessed to confirm dispensed opioids. The primary outcome was number of unused oxycodone tablets prescribed for pain control after cesarean birth. A total sample size of 160 women was necessary to detect a 30% difference in leftover tablets between groups with 80% power and α of 0.05.

RESULTS:

Between June 14, 2017, and August 26, 2017, we screened 323 women and randomized 172. Baseline characteristics and inpatient opioid use were similar between groups. Women in the individualized group were prescribed fewer tablets (14 [interquartile range 12–16] vs 30 [interquartile range 30–30], P<.001) and had 50% fewer unused tablets than women in the standard group (5 [interquartile range 1–8] vs 10 [interquartile range 0–22], P<.001). Overall, 13% (23/172) used no opioids after discharge and 26% (44/172) used all prescribed opioids. There were no differences between the standard and individualized groups in the proportion of women who used no opioids or all opioids and no difference in the proportion of dispensed opioids used (60% [interquartile range 23–100] vs 61% [29–89], P=.93). Women in the individualized group used only half the number of prescribed opioids as women in the standard group (8 [interquartile range 4–14] vs 15 [interquartile range 6–30], P<.001). Patient-reported pain outcomes did not differ significantly by group.

CONCLUSION:

Individualized opioid prescribing based on inpatient use reduces the number of unused oxycodone tablets compared with standard prescribing.

CLINICAL TRIALS REGISTRATION:

ClinicalTrials.gov, NCT03168425.
Rattlesnake Envenomation in the Third Trimester of Pregnancy
Authors: Ghosh Niloy , Henderson Jonathan A. , Kim Hyunyoung G. , Ancar Farren M.
Published: August 2018

BACKGROUND:

Snakebites in pregnancy can be life-threatening to both the mother and fetus as a result of inflammatory and toxic properties of the venom. Prompt medical treatment is critical to prevent adverse consequences.

CASE:

A 26-year-old woman at 37 6/7 weeks of gestation was bitten by a rattlesnake on the right middle finger, resulting in severe pain radiating up to the upper arm and swelling involving the entire hand. A total of 18 vials of crotalidae polyvalent immune fab was administered over 11 hours. Three days after the incident, the patient delivered a healthy neonate vaginally and without complications. Both mother and newborn were well at 1-month follow-up.

CONCLUSION:

Our case supports managing snakebites in pregnancy similar to managing cases in nonpregnant individuals, including using crotalidae polyvalent immune fab antivenom.
The Adverse Outcome Index
Authors: Atallah Fouad , Bernstein Peter S. , Diaz Danilo Acosta , Minkoff Howard
Published: August 2018

The Adverse Outcome Index, originally designed to provide an objective inventory of adverse outcomes, is often promoted as a tool for assessing the quality of inpatient obstetric care. Although the Adverse Outcome Index is well described, and its outcomes are easy to collect, it has notable drawbacks such as “paradoxical measures” (eg, blood transfusions are counted as adverse measures even when they are used appropriately) and the dominance of certain measures within the Adverse Outcome Index that can drive scores (eg, neonatal intensive care unit admissions). In this article, we argue that in addition to the limitations noted, the Adverse Outcome Index, although providing a reasonable measure of inpatient obstetric acuity, fails to be a reliable measure of quality. This is particularly important because many organizations are seeking quality measures and the Adverse Outcome Index may become a candidate tool. We believe that introducing an adjudication process to the Adverse Outcome Index would greatly enhance its role as a quality indicator. Until newly proposed quality measures are perfected and adopted, a quality-adjusted Adverse Outcome Index will allow this widely used measure to provide a more reliable determination of those adverse events potentially amenable to performance improvement.
Balloon Uterine Tamponade Device After Peripartum Hysterectomy for Morbidly Adherent Placenta
Authors: Waks Ashten , Tabsh Kareem , Tabsh Khalil , Afshar Yalda
Published: August 2018

BACKGROUND:

Perioperative hemorrhage is a common complication of peripartum hysterectomy for morbidly adherent placenta. We present an application of a balloon uterine tamponade device in the setting of a cesarean delivery and subsequent supracervical hysterectomy for abnormal placentation.

CASE:

A 33-year-old gravid woman, 6 para 3022, at 33 2/7 weeks of gestation was admitted in preterm labor, with placenta previa and suspected morbidly adherent placenta, for a planned cesarean delivery and hysterectomy. After supracervical hysterectomy, colloid resuscitation and packing failed to provide hemostasis. A transcervical balloon uterine tamponade device subsequently was placed intraperitoneally and left on tension owing to the need for further tamponade.

CONCLUSION:

Use of a balloon uterine tamponade device intraperitoneally posthysterectomy was associated with hemorrhage control. This application may facilitate timely management and streamlining of obstetric resources for postpartum hemorrhage.
Adjuvant Use of Rifampin for Refractory Intrahepatic Cholestasis of Pregnancy
Authors: Liu James , Murray Amanda M. , Mankus Erin B. , Ireland Kayla E. , Acosta Ometeotl M. , Ramsey Patrick S.
Published: August 2018

BACKGROUND:

Intrahepatic cholestasis of pregnancy is an incompletely understood disease that poses significant fetal risks, including stillbirth. Treatment of intrahepatic cholestasis of pregnancy is aimed at relieving maternal symptoms and improving fetal outcomes.

CASE:

A 21-year-old gravid woman, 3 para 0111, presented at 27 2/7 weeks of gestation with severe intrahepatic cholestasis of pregnancy. Her clinical course was refractory to first-line therapy with ursodiol, and she was started on rifampin with rapid improvement of symptoms and transaminitis. Despite maternal improvement, she was delivered at 31 weeks of gestation for persistent nonreassuring fetal status.

CONCLUSION:

Rifampin may be an effective adjunctive therapy for intrahepatic cholestasis of pregnancy refractory to ursodiol alone. Additional research is needed to assess short-term and long-term maternal and newborn outcomes, because fetal deterioration still occurred in spite of maternal improvement.
The First National Summit on Women's Health
Authors: Brown Haywood L. , Carson Sandra A. , Lawrence Hal C.
Published: August 2018

OBJECTIVE:

To identify the current challenges in obstetrics and gynecology residency education and propose solutions to overcome these obstacles.

METHODS:

The American College of Obstetricians and Gynecologists (ACOG) hosted the first National Summit on Women's Health on May 31 and June 1, 2017, with a follow-up meeting December 20–21, 2017, at ACOG headquarters in Washington, DC. Invitees from 20 related societies briefly presented their organizations' perspectives and discussed focused questions about specific challenges, proposed solutions, and anticipated obstacles. Finally, participants summarized their top two recommendations to improve current residency training.

RESULTS:

Summit participants identified four primary areas of focus: 1) align curriculum with relevant topics to practice, 2) ensure faculty have the necessary resources and time to teach effectively, 3) consider using the final months of medical school to get a jump start on residency fund of knowledge and skills, and 4) use better assessments during the course of residency.

CONCLUSION:

Representatives of the Council on Resident Education in Obstetrics and Gynecology, the American Board of Obstetrics and Gynecology, and the Accreditation Council for Graduate Medical Education must work together to address these priorities and reach consensus on the curricular content of core training in obstetrics and gynecology.
Cervical Pessary After Arrested Preterm Labor
Authors: Hermans Frederik J. R. , Schuit Ewoud , Bekker Mireille N. , Woiski Mallory , de Boer Marjon A. , Sueters Marieke , Scheepers Hubertina C. J. , Franssen Maureen T. M. , Pajkrt Eva , Mol Ben Willem J. , Kok Marjolein
Published: August 2018

OBJECTIVE:

To assess the effectiveness of cervical pessary in reducing the rate of preterm birth in women at high risk for preterm birth who did not deliver after an episode of threatened preterm labor.

METHODS:

In a multicenter open-label randomized controlled trial, a cervical pessary was compared with no intervention (control group) (one-to-one ratio). Women between 24 and 34 weeks of gestation at high risk for preterm birth based on a short cervical length (less than 15 mm) or an intermediate cervical length (between 15 and 30 mm) with a positive fetal fibronectin test who did not deliver after an episode of threatened preterm labor were eligible. The primary outcome was birth before 37 weeks of gestation. Secondary outcomes were a composite adverse neonatal outcome, preterm birth before 34 and 32 weeks of gestation, and side effects. A total sample size of 200 women carrying singletons was planned so as to have adequate statistical power to detect a reduction in the rate of preterm birth from 40% to 20%. Women with twin gestations were also enrolled but were considered only in secondary analyses. After a planned interim analysis, the trial was stopped for futility.

RESULTS:

From November 2013 through September 2016, 130 women with a singleton pregnancy (65 pessary, 65 no treatment) were recruited. The groups had comparable baseline characteristics. In the cervical pessary group, 31 (48%) women delivered before 37 weeks of gestation compared with 25 (39%) in the no-treatment group (relative risk 1.2, 95% CI 0.83–1.8). Nine (15%) children in the cervical pessary group had the composite adverse perinatal outcome compared with eight (13%) in the control group (relative risk 1.2, 95% CI 0.49–2.9).

CONCLUSION:

In women at high risk for preterm birth who did not deliver after an episode of threatened preterm labor, treatment with a cervical pessary is not effective.

CLINICAL TRIAL REGISTRATION:

Netherlands Trial Register, NTR4210.
What Is New in Opioids?
Authors: Schorge John O.
Published: August 2018

This month we focus on current research in opioids. Dr. Schorge discusses five recent publications, which are concluded with a “bottom-line” that is the take-home message. A complete reference for each can be found on Box 1 on this page along with direct links to abstracts.
Treatment of adolescent idiopathic scoliosis and evaluation of the adolescent patient
Authors: Kelly John J. , Shah Neil V. , Freetly Taylor J. , Dekis Joanne C. , Hariri Omar K. , Walker Sarah E. , Borrelli Jenna , Post Nicholas H. , Diebo Bassel G. , Urban William P. , Paulino Carl B.
Published: August 2018

Adolescent idiopathic scoliosis (AIS) is a three-dimensional, multi-faceted deformity of the vertebral column. Although screening is mandated by several states, debate exists surrounding the efficacy or utility of in-school scoliosis screenings. Detailed history and physical examination are crucial to this diagnosis of exclusion. Assessment of curves has long been limited to static radiography; however, use of MRI may permit detection of associated spinal anomalies, while three-dimensional gait analysis may permit improved understanding of functional improvement in AIS patients before and after treatment. Nonoperative management includes bracing, which is a complex, yet important, component to treatment of AIS. The Bracing in Adolescents with Idiopathic Scoliosis Trial (BrAIST) and other studies have revealed the potential for halting curve progression and a positive dose-response relationship of bracing. Surgical management has focused on the mainstay of posterior spinal fusion with pedicle screw fixation and rod instrumentation, with new techniques under development that modify fusion and fixation or focus on different approaches altogether (i.e. vertebral body tethering). This article details evaluation and treatment of AIS, supplemented by a review of the historical progression of management, to equip readers with an appreciation for the complex nature of this pathology and its treatment.
Effect of Deformity and Malunion of the Anterior Pelvic Ring
Authors: Archdeacon Michael T. , Collinge Cory A. , Schumaier Adam P. , Glogovac Georgina
Published: August 2018

Pelvic fractures are common after high-energy trauma and are often associated with ligamentous injury. Treatment is guided by assessing stability of the pelvic ring, and unstable injuries frequently require surgery to achieve a desirable outcome. Assessment of pelvic ring stability is often possible with physical examination and standard imaging studies (plain radiographs and computed tomography); however, these “static” imaging modalities may not adequately identify dynamically unstable pelvic injuries that require surgery. Cadaveric and clinical data suggest that the injured pelvis may recoil significantly from the point of maximal displacement, and some unstable injuries may not be recognized until patients present with clinical symptoms. This article presents the case of a patient who sustained a minimally displaced pelvic ring injury that was stable on bedside examination and static imaging, but ultimately was unstable. She developed a substantial pelvic malunion with significant pain and activity limitations. The patient subsequently underwent successful pelvic ring reconstruction, and she remains asymptomatic at 2 years.