bluuebunny/crossref_metadata_2025 huggingface dataset:
Objectively estimating the temporal evolution of accuracy and skill in a global ocean reanalysis
Authors: Storto Andrea , Masina Simona
Published: January 2017

ABSTRACT

The accuracy of ocean reanalyses is acknowledged to have increased dramatically during the last few decades, as a consequence of the evolution of the oceanic and atmospheric observing networks. Because of evolution of the atmospheric observing system, a similar accuracy increase also occurs in assimilation‐free global ocean simulations. However, the temporal evolution of traditional accuracy metrics based on comparing reanalyses with observations is affected by the change in the number and spatial sampling of the verifying observations themselves. To disentangle the accuracy evolution and the changes in the verifying dataset, procedures insensitive to the latter are recommended. A simple and easy‐to‐implement methodology inspired by bootstrapping is proposed, specifically conceived for objectively estimating the accuracy and skill evolution of reanalyses over long (e.g. inter‐decadal) periods. This allows the artificial impact of the observational network evolution on the verification metrics, which generally led to under‐estimated accuracy at the beginning of the reanalysis period and much too sharp an increase later, to be overcome. Applied to the assessment of ocean temperature accuracy and skill in a state‐of‐the‐art eddy‐permitting global ocean reanalysis covering the period 1982–2012, the methodology illuminates the crucial impact on the upper ocean (top 100 m) reanalysis skill of both the atmospheric and oceanic observing network evolution, the former leading to a quicker skill increase. Conversely, the fundamental effect of the oceanic observing network below 100 m emerges from the study, as the assimilation‐free simulation shows no skill at any time in the comparison against observations.
Thermal free vibration behavior of FG‐CNT reinforced sandwich curved panel using finite element method
Authors: Mehar Kulmani , Kumar Panda Subrata
Published: January 2017

In this article, the vibration characteristics of carbon nanotube reinforced sandwich curved shell panel are investigated under the elevated thermal environment. The sandwich panel component (face and core layer) properties are assumed to be temperature‐dependent including various distribution of the carbon nanotube for the face sheets of the sandwich structure. The sandwich structural behavior has been modeled mathematically using the higher‐order shear deformation theory. The governing differential equation of motion of the free vibrated sandwich panel is obtained using the classical Hamilton's principle and transformed to the set of algebraic form with the help of suitable finite element steps. Further, fundamental frequencies of the curved sandwich shell panel are obtained numerically by means of a generalized computer code developed in MATLAB with the help of the present higher‐order mathematical model. The accuracy and the stability of the present numerical results have been checked through the proper convergence test. The model is again extended to work out the frequency responses for few more cases and compared with those available published results including the simulation responses (ANSYS). Finally, a wide variety of numerical examples have been solved for various design parameters (volume fraction of CNT, core to face thickness ratios, length to thickness ratios, aspect ratios, support conditions, curvature ratios, and types of grading) of CNT sandwich curved panel and underlined their effects in details under the uniform thermal load. POLYM. COMPOS., 39:2751–2764, 2018. © 2016 Society of Plastics Engineers
The sound absorption of sisal fiber and sisal fiber/polyethylene film sheets: Morphology and structure
Authors: Wang Ting , Ge Heyi , Wang Fujun
Published: January 2017

Sisal fiber (SF) and waterborne polyurethane adhesive were used to prepare SF‐based sound absorption material through hot press molding. SF with elastic polyethylene (PE) film interlayers was also fabricated as a new type of sound absorbing composite. The effects of SF treatment methods and PE film on sound absorption coefficient were evaluated. The alkaline‐treated SF composite had higher sound absorption as compared with the untreated SF composite when the sound wave was below 5500 Hz. The sound absorption peak of alkaline/oxidation‐treated SF composite moved towards low‐ and middle‐frequency regions. The SF/PE film composite showed that at low‐frequency the more layers of PE film inserted the better sound absorption property. The mass‐temperature relationship and FTIR of the composites were discussed. The SF surface and the cross section of the composites were observed by SEM, which showed the void structure and microfiber contributed to enhancing sound absorbing property. POLYM. COMPOS., 39:2812–2818, 2018. © 2016 Society of Plastics Engineers
Synthesis and characterization of transparent erbium–ytterbium co‐doped polymer nanocomposites for fabrication of polymer optical preform
Authors: Chinya Ipsita , Sen Ranjan , Dhar Anirban
Published: January 2017

Synthesis of polystyrene (PS) and poly (methylmethacrylate) (PMMA)‐grafted Er–Yb co‐doped transparent ternary nanocomposite is presented herein. Er–Yb co‐doped nanoparticles (NP) were synthesized from their nitrate precursors followed by surface modification using 3‐methacryloxypropyltrimethoxysilane (MPS) as surfactant. In situ polymerization of methylmethacrylate (MMA) was performed in presence of benzoyl peroxide as initiator in toluene. The synthesized NP–PMMA composite was blended with PS in tetrahydrofuran (THF). Different material characterizations of synthesized composite were performed to evaluate shape, size and chemical nature of developed composite. UV–visible spectra and DLS technique revealed that optimum particle size in the range of <25 nm is essential to achieve optical transparency of developed composite. Refractive index of synthesized composite was also measured (RIcore > 1.5 at 589 nm) and indicate their potential application as active core material for preparation of rare earth doped polymer optical preform (POP). The POF preform prepared using commercially available cladding tube containing Er–Yb transparent polymer nanocomposites as core material is found to have numerical aperture around 0.19. The photoluminescence (PL) spectrum was also measured and intensity of Er–Yb co‐doped composite found to be ten times greater than pure Er‐doped system.
Finite time control of robotic manipulators with position output feedback
Authors: Abooee Ali , Moravej Khorasani Masoud , Haeri Mohammad
Published: January 2017

This paper deals with the robust finite time tracking of desired trajectories for a wide group of robotic manipulators in spite of unknown disturbances, uncertainties, and saturations of actuators while only manipulator's positions are available and its velocities are not measurable physically. A new form of chattering‐free second order fast nonsingular terminal sliding mode control scheme is introduced to design input torques for fulfilling the determined tracking objective in the adjustable total finite settling time. The proposed control algorithm is incorporated with two nonlinear observers to estimate disturbances and velocities of joints within finite settling times. The global finite time stability of the closed‐loop manipulator is analytically proved. Finally, a numerical simulation is carried out to verify the effectiveness of the designed input torques. Copyright © 2017 John Wiley & Sons, Ltd.
Non‐GMO potato lines with an altered starch biosynthesis pathway confer increased‐amylose and resistant starch properties
Authors: Krunic Susanne L. , Skryhan Katsiaryna , Mikkelsen Lisbeth , Ruzanski Christian , Shaik Shahnoor S. , Kirk Hanne‐Grethe , Palcic Monica , Blennow Andreas
Published: January 2017

The lack of a gene marker directly affecting starch biosynthesis in the potato tuber is documented. The absence of a 454 bp amplified fragment length polymorphism (AFLP) Solanum tuberosum fragment was identified in the wild potato species Solanum sandemanii and its absence results in a combined increased‐amylose/high‐sugar tuber chemotype. The trait is recessive, termed IAm (Increased Amylose) and was transferred to modern tetraploid S. tuberosum potato cultivars by marker‐assisted crossing. Compared to controls, IAm plants had a larger number of stems and air exposed stolons, their tubers were smaller, elongated, and they were irregularly shaped. IAm starch had 28–59% higher amylose content than control starch, the starch granules were small and grossly misshaped, they had reduced crystallinity, swelling, and viscosity, reduced in vitro digestion rates with increased resistant starch fraction. The primary gene(s) responsible for the IAm phenotype is not known, but increased granule‐associated phosphorylase (Pho1) and reduced starch synthase (SS) protein and enzyme activity in the IAm plants might explain the effects on starch structure. The data support the establishment of non‐genetically modified crops with health‐related slowly digestible carbohydrate.
Is 2D speckle tracking echocardiography useful for detecting and monitoring myocardial dysfunction in adult m.3243A>G carriers? — a retrospective pilot study
Authors: Koene S. , Timmermans J. , Weijers G. , de Laat P. , de Korte C. L. , Smeitink J. A. M. , Janssen M. C. H. , Kapusta L.
Published: January 2017

Objectives

Cardiomyopathy is a common complication of mitochondrial disorders, associated with increased mortality. Two dimensional speckle tracking echocardiography (2DSTE) can be used to quantify myocardial deformation. Here, we aimed to determine the usefulness of 2DSTE in detecting and monitoring subtle changes in myocardial dysfunction in carriers of the 3243A>G mutation in mitochondrial DNA.

Methods

In this retrospective pilot study, 30 symptomatic and asymptomatic carriers of the mitochondrial 3243A>G mutation of whom two subsequent echocardiograms were available were included. We measured longitudinal, circumferential and radial strain using 2DSTE. Results were compared to published reference values.

Results

Speckle tracking was feasible in 90 % of the patients for longitudinal strain. Circumferential and radial strain showed low face validity (low number of images with sufficient quality; suboptimal tracking) and were therefore rejected for further analysis. Global longitudinal strain showed good face validity, and was abnormal in 56–70 % (depending on reference values used) of the carriers (n = 27). Reproducibility was good (mean difference of 0.83 for inter‐ and 0.40 for intra‐rater reproducibility; ICC 0.78 and 0.89, respectively). The difference between the first and the second measurement exceeded the measurement variance in 39 % of the cases (n = 23; feasibility of follow‐up 77 %).

Discussion

Even in data collected as part of clinical care, two‐dimensional strain echocardiography seems a feasible method to detect and monitor subtle changes in longitudinal myocardial deformation in adult carriers of the mitochondrial 3243A>G mutation. Based on our data and the reported accuracy of global longitudinal strain in other studies, we suggest the use of global longitudinal strain in a prospective follow‐up or intervention study.
Mortality after hematopoietic stem cell transplantation for severe mucopolysaccharidosis type I: the 30‐year University of Minnesota experience
Authors: Rodgers Nathan J. , Kaizer Alexander M. , Miller Weston P. , Rudser Kyle D. , Orchard Paul J. , Braunlin Elizabeth A.
Published: January 2017

Background and aim

Mucopolysaccharidosis IH (MPS IH, Hurler syndrome) naturally leads to death within the first decade of life, primarily from cardiac and pulmonary causes. To determine how hematopoietic stem cell transplantation (HSCT) has altered mortality, we analyzed our institution's 30‐year experience of patients with MPS IH undergoing HSCT.

Methods

Using chart review and the National Death Index, we determined survival status of 134 patients (males = 69) with MPS IH transplanted between 9/16/1983 and 7/25/2013 on 12/31/2013. Analysis included descriptive statistics, Kaplan‐Meier curves, and regression analysis by Cox proportional hazards model.

Results

Overall survival (95% CI) at one‐ and 25‐years was 70% (62–78%) and 37% (19–55%), respectively. From 2004 onward, overall survival at one‐ and 8‐years was 84% (73–96%) and 81% (69–94%), respectively, compared to 65% (55–74%) and 57% (47–67%) prior to 2004 (Log‐rank p = 0.032). Regardless of era, male survival was significantly better than female (HR 0.40, [95% CI: 0.21–0.74], p = 0.004). The cumulative incidence of death (95% CI) at 25 years was 63% (45–81%); incidence of pulmonary‐related death was the highest at 27% (10–41%) compared to 8% (0.3–16%) for cardiac, 12% (6–17%) for infectious disease, and 16% (3–27%) from other complications.

Conclusions

HSCT has increased survival in MPS IH beyond the third decade of life and decreased the incidence of cardiac mortality, but deaths after the third year post‐HSCT occur in excess of expected US mortality. It is important to determine if improved transplant strategies since 2004 result in better long‐term survival in the current patient population.
Inhibition of ghrelin-induced feeding in rats by pretreatment with a novel dual orexin receptor antagonist
Authors: So Mariko , Hashimoto Hirofumi , Saito Reiko , Yamamoto Yukiyo , Motojima Yasuhito , Ueno Hiromichi , Sonoda Satomi , Yoshimura Mitsuhiro , Maruyama Takashi , Kusuhara Koichi , Ueta Yoichi
Published: January 2017

Orexin-A and -B, and ghrelin are potent orexigenic peptides. The effects of ACT462206, a novel dual orexin receptor antagonist (DORA), on ghrelin-induced feeding were examined in adult male Wistar rats. Hyperphagia induced by the intracerebroventricular (icv) administration of ghrelin was significantly suppressed for at least 2 h by pretreatment with icv administration of DORA. A marked increase was observed in the number of neurons showing Fos immunoreactivity in the paraventricular nucleus, arcuate nucleus and lateral hypothalamic area (LHA), 90 min after icv administration of ghrelin. Pretreatment with DORA significantly decreased the number of Fos-immunoreactive (IR) neurons; however, Fos immunoreactivity remained significantly increased. Double-immunostaining for Fos and orexin-A showed that many orexin-A-IR neurons in the LHA coexisted with Fos immunoreactivity after icv administration of ghrelin, but their number was reduced significantly by DORA pretreatment. These results suggest that centrally administered ghrelin may activate the orexinergic and non-orexinergic pathways responsible for the regulation of feeding.
Age at Arrival and Life Chances Among Childhood Immigrants
Authors: Hermansen Are Skeie
Published: January 2017

This study examines the causal relationship between childhood immigrants’ age at arrival and their life chances as adults. I analyze panel data on siblings from Norwegian administrative registries, which enables me to disentangle the effect of age at arrival on adult socioeconomic outcomes from all fixed family-level conditions and endowments shared by siblings. Results from sibling fixed-effects models reveal a progressively stronger adverse influence of immigration at later stages of childhood on completed education, employment, adult earnings, occupational attainment, and social welfare assistance. The persistence of these relationships within families indicates that experiences related to the timing of childhood immigration have causal effects on later-life outcomes. These age-at-arrival effects are considerably stronger among children who arrive from geographically distant and economically less-developed origin regions than among children originating from developed countries. The age-at-arrival effects vary less by parental education and child gender. On the whole, the findings indicate that childhood immigration after an early-life formative period tends to constrain later human capital formation and economic opportunities over the life course.
Focal ablation for atrial tachycardia from the double‐exit of the Marshall bundle inducing atrial fibrillation
Authors: Chin Jung Yeon , Kim Jong Woo , Kang Ki‐Woon
Published: January 2017

Atrial fibrillation (AF) from the ligament/vein of Marshall (LOM/VOM) has previously been described. We report the case of a 23‐year‐old woman with an antiarrhythmic drug‐resistant AF induced by two distinct atrial tachycardias (ATs). Focal ablation of these ATs from the double‐exit of the Marshall bundle using a three‐dimensional map eliminated AF triggering, even though pulmonary vein electrical isolation is the cornerstone for paroxysmal AF. Such mechanisms are important as triggering factors to plan ablation for paroxysmal AF. Focal ablation for triggering and inducing AF, originating from the double‐exit of the Marshall bundle may be effective in eliminating AF in young patients.
Current use of direct oral anticoagulants for atrial fibrillation in Japan: Findings from the SAKURA AF Registry
Authors: Okumura Yasuo , Yokoyama Katsuaki , Matsumoto Naoya , Tachibana Eizo , Kuronuma Keiichiro , Oiwa Koji , Matsumoto Michiaki , Kojima Toshiaki , Hanada Shoji , Nomoto Kazumiki , Arima Ken , Takahashi Fumiyuki , Kotani Tomobumi , Ikeya Yukitoshi , Fukushima Seiji , Itoh Satoru , Kondo Kunio , Chiku Masaaki , Ohno Yasumi , Onikura Motoyuki , Hirayama Atsushi
Published: January 2017

Background

Large‐scale investigations on the use of oral anticoagulants including direct oral anticoagulants (DOACs) in patients with atrial fibrillation (AF) have not included Japanese patients.

Methods

We established the multicenter SAKURA AF Registry to support prospective observational research on the status of anticoagulation treatment, especially with DOAC, for AF in Japan. We enrolled 3266 AF patients treated with warfarin (n=1577) or any of 4 DOACs (n=1689) from 63 institutions (2 cardiovascular centers, 13 affiliated hospitals or community hospitals, and 48 private clinics) in the Tokyo area.

Results

We conducted our first analysis of the registry data, and although we found equivalent mean age between the DOAC and warfarin users (71.8±9.5 vs. 72.3±9.4 years, p=0.2117), we found a slightly lower risk of stroke (CHADS2 score of 0 or 1 [46.9% vs. 39.4%, p<0.0001]) and significantly better creatinine clearance in DOAC users (70.4±27 vs. 65.6±25.7 mL/min, p<0.0001). Importantly, we documented under‐dosing in 32% of warfarin users and inappropriate‐low‐dosing in 19.7–27.6% of DOAC users.

Conclusions

Our initial analysis of the SAKURA AF Registry data clarified the real‐world use of anticoagulants, which includes DOACs and warfarin in Japan. The DOAC users were at a lower risk for stroke than the warfarin users. In 20–30% of DOAC users, the dose was inappropriately reduced.
Is Ross Syndrome an Autoimmune Entity? A Case Series of 11 Patients
Authors: Mishra Ajay Kumar , Kharkongor Meban , Kuriakose Cijoy K , George Anu Anna , Peter Dincy , Carey Ronal Albert Benton , Mathew Vivek , Hansdak Samuel George
Published: January 2017

Background: Ross syndrome is diagnosed by the presence of segmental anhidrosis, areflexia, and tonic pupils. Fewer than 60 cases have been described in literature so far. There have been reports of presence of antibodies in such patients, suggesting an autoimmune pathogenesis. Methods: We describe the clinical profile in this case series of 11 patients with Ross syndrome and discuss the current status of autoimmunity in its pathogenesis and the management. Results: Of the 11 patients with Ross syndrome there was an almost equal sex distribution (male:female ratio was 1.17:1) and the mean age of onset of symptoms was 26 years. Patients took an average of 6 years to present to a tertiary center. Sixty-three percent of the patients presented with complaints of excessive sweating, whereas only 27% had complaints of decreased sweating over a particular area of the body. Only 45% of the patients had the complete triad of Ross syndrome, which included segmental anhidrosis, tonic pupil, and absent reflexes. Eighty-nine percent of the patients had documented absent sympathetic skin response on electromyography. The various markers of autoimmunity were negative in all patients who were investigated for the same in this series. Ninety percent of the patients were managed conservatively. Conclusions: These findings suggest that, in Ross syndrome, generalized injury to ganglion cells or their projections are not purely autoimmune-mediated.
Inertial fusion-assisted production of Plutonium 238
Authors: Winterberg F.
Published: January 2017

It is proposed to assist and substantially increase the production of Plutonium 238 by inertial fusion inside a pipe made of stainless steel passing through the core of a conventional nuclear fission reactor, by injecting a stream of pellets of Neptunium 237 encapsulated liquid deuterium–tritium (DT) under high pressure. Then, if from both ends of the pipe, a pulse of multi-megajoule intense relativistic electron beams are injected, they will compress the pellets and heat the liquid DT to reach ignition, leading to a smoldering thermonuclear burn, releasing a burst of 14 MeV neutrons, converting the Neptunium 237 into Neptunium 238, which after leaving the pipe outside the reactor, will by radioactive decay be converted into Plutonium 238. This strategy permits that the surplus of neutrons are not lost, because they are absorbed in the bulk of the fission reactor and not lost into the environment.
“Like the Pirate and the Slave Trader Before Him”: Precedent and Analogy in Contemporary Law and Literature
Authors: Martinez Jenny S. , Surwillo Lisa
Published: January 2017

“The Mediterranean, central to the development of human civilization and lovingly celebrated in Euro-American historiography, from the viewpoint of human oppression has been a veritable vortex of horror for all mankind, especially for the Slavic and African peoples. The relationship was in no way accidental.”
From the “Imperfect Illness” to the Possibility of Developing Good Internal Objects
Authors: Luiza de Mattos Fiore Maria , Lottenberg Semer Norma , Yazigi Latife
Published: January 2017

Abstract. This paper is about a psychoanalytic psychotherapy follow-up by the Rorschach Comprehensive System of Doralice, a 30-year-old, unemployed, single woman, with diagnosis of Major Depressive Disorder, recurrent, severe, with psychotic features (Axis-I); and Borderline Personality Disorder (Axis-II) in DSM IV. The Rorschach Comprehensive System was administered upon admission and also in five annual follow-ups. In this paper, the authors show the characteristics and the development of the dual therapeutic attachment that will be illustrated by the responses to the Rorschach cards II, III and VII, focusing mainly on the MOA scale on the four assessments. The authors will discuss the development of good internal objects over the years during the psychotherapeutic process with a turning point in the third year of treatment that is manifested in the Rorschach. The State of São Paulo Research Foundation, FAPESP, sponsored this study.
New Way to Gauge Lightning's Role in Ozone Formation
Authors: McQuate Sarah
Published: January 2017

Comparing satellite data on a key airborne ozone precursor to readings from a lightning sensor network reveals how much different types of lightning strokes affect atmospheric ozone chemistry.
Synthesis of single-crystal-like nanoporous carbon membranes and their application in overall water splitting
Authors: Wang Hong , Min Shixiong , Ma Chun , Liu Zhixiong , Zhang Weiyi , Wang Qiang , Li Debao , Li Yangyang , Turner Stuart , Han Yu , Zhu Haibo , Abou-hamad Edy , Hedhili Mohamed Nejib , Pan Jun , Yu Weili , Huang Kuo-Wei , Li Lain-Jong , Yuan Jiayin , Antonietti Markus , Wu Tom
Published: January 2017

Nanoporous graphitic carbon membranes with defined chemical composition and pore architecture are novel nanomaterials that are actively pursued. Compared with easy-to-make porous carbon powders that dominate the porous carbon research and applications in energy generation/conversion and environmental remediation, porous carbon membranes are synthetically more challenging though rather appealing from an application perspective due to their structural integrity, interconnectivity and purity. Here we report a simple bottom–up approach to fabricate large-size, freestanding and porous carbon membranes that feature an unusual single-crystal-like graphitic order and hierarchical pore architecture plus favourable nitrogen doping. When loaded with cobalt nanoparticles, such carbon membranes serve as high-performance carbon-based non-noble metal electrocatalyst for overall water splitting.
Vacancy-induced dislocations within grains for high-performance PbSe thermoelectrics
Authors: Chen Zhiwei , Ge Binghui , Li Wen , Lin Siqi , Shen Jiawen , Chang Yunjie , Hanus Riley , Snyder G. Jeffrey , Pei Yanzhong
Published: January 2017

To minimize the lattice thermal conductivity in thermoelectrics, strategies typically focus on the scattering of low-frequency phonons by interfaces and high-frequency phonons by point defects. In addition, scattering of mid-frequency phonons by dense dislocations, localized at the grain boundaries, has been shown to reduce the lattice thermal conductivity and improve the thermoelectric performance. Here we propose a vacancy engineering strategy to create dense dislocations in the grains. In Pb1−xSb2x/3Se solid solutions, cation vacancies are intentionally introduced, where after thermal annealing the vacancies can annihilate through a number of mechanisms creating the desired dislocations homogeneously distributed within the grains. This leads to a lattice thermal conductivity as low as 0.4 Wm−1 K−1 and a high thermoelectric figure of merit, which can be explained by a dislocation scattering model. The vacancy engineering strategy used here should be equally applicable for solid solution thermoelectrics and provides a strategy for improving zT.
One-dimensional organic lead halide perovskites with efficient bluish white-light emission
Authors: Yuan Zhao , Zhou Chenkun , Tian Yu , Shu Yu , Messier Joshua , Wang Jamie C. , van de Burgt Lambertus J. , Kountouriotis Konstantinos , Xin Yan , Holt Ethan , Schanze Kirk , Clark Ronald , Siegrist Theo , Ma Biwu
Published: January 2017

Organic-inorganic hybrid metal halide perovskites, an emerging class of solution processable photoactive materials, welcome a new member with a one-dimensional structure. Herein we report the synthesis, crystal structure and photophysical properties of one-dimensional organic lead bromide perovskites, C4N2H14PbBr4, in which the edge sharing octahedral lead bromide chains [PbBr4 2−]∞ are surrounded by the organic cations C4N2H14 2+ to form the bulk assembly of core-shell quantum wires. This unique one-dimensional structure enables strong quantum confinement with the formation of self-trapped excited states that give efficient bluish white-light emissions with photoluminescence quantum efficiencies of approximately 20% for the bulk single crystals and 12% for the microscale crystals. This work verifies once again that one-dimensional systems are favourable for exciton self-trapping to produce highly efficient below-gap broadband luminescence, and opens up a new route towards superior light emitters based on bulk quantum materials.
Investigation of phonon coherence and backscattering using silicon nanomeshes
Authors: Lee Jaeho , Lee Woochul , Wehmeyer Geoff , Dhuey Scott , Olynick Deirdre L. , Cabrini Stefano , Dames Chris , Urban Jeffrey J. , Yang Peidong
Published: January 2017

Phonons can display both wave-like and particle-like behaviour during thermal transport. While thermal transport in silicon nanomeshes has been previously interpreted by phonon wave effects due to interference with periodic structures, as well as phonon particle effects including backscattering, the dominant mechanism responsible for thermal conductivity reductions below classical predictions still remains unclear. Here we isolate the wave-related coherence effects by comparing periodic and aperiodic nanomeshes, and quantify the backscattering effect by comparing variable-pitch nanomeshes. We measure identical (within 6% uncertainty) thermal conductivities for periodic and aperiodic nanomeshes of the same average pitch, and reduced thermal conductivities for nanomeshes with smaller pitches. Ray tracing simulations support the measurement results. We conclude phonon coherence is unimportant for thermal transport in silicon nanomeshes with periodicities of 100 nm and higher and temperatures above 14 K, and phonon backscattering, as manifested in the classical size effect, is responsible for the thermal conductivity reduction.
Evolution of form in metal–organic frameworks
Authors: Lee Jiyoung , Kwak Ja Hun , Choe Wonyoung
Published: January 2017

Self-assembly has proven to be a widely successful synthetic strategy for functional materials, especially for metal–organic materials (MOMs), an emerging class of porous materials consisting of metal–organic frameworks (MOFs) and metal–organic polyhedra (MOPs). However, there are areas in MOM synthesis in which such self-assembly has not been fully utilized, such as controlling the interior of MOM crystals. Here we demonstrate sequential self-assembly strategy for synthesizing various forms of MOM crystals, including double-shell hollow MOMs, based on single-crystal to single-crystal transformation from MOP to MOF. Moreover, this synthetic strategy also yields other forms, such as solid, core-shell, double and triple matryoshka, and single-shell hollow MOMs, thereby exhibiting form evolution in MOMs. We anticipate that this synthetic approach might open up a new direction for the development of diverse forms in MOMs, with highly advanced areas such as sequential drug delivery/release and heterogeneous cascade catalysis targeted in the foreseeable future.
Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer
Authors: Feliubadaló Lídia , Tonda Raúl , Gausachs Mireia , Trotta Jean-Rémi , Castellanos Elisabeth , López-Doriga Adriana , Teulé Àlex , Tornero Eva , del Valle Jesús , Gel Bernat , Gut Marta , Pineda Marta , González Sara , Menéndez Mireia , Navarro Matilde , Capellá Gabriel , Gut Ivo , Serra Eduard , Brunet Joan , Beltran Sergi , Lázaro Conxi
Published: January 2017

Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eighty-three genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception ofMSH6c.255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (inATM,BARD1,CHEK2,ERCC3,FANCL,FANCM,MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes.
PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data
Authors: Deneke Carlus , Rentzsch Robert , Renard Bernhard Y.
Published: January 2017

The reliable detection of novel bacterial pathogens from next-generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from the reference database. Here we present the machine learning based approach PaPrBaG (Pathogenicity Prediction for Bacterial Genomes). PaPrBaG overcomes genetic divergence by training on a wide range of species with known pathogenicity phenotype. To that end we compiled a comprehensive list of pathogenic and non-pathogenic bacteria with human host, using various genome metadata in conjunction with a rule-based protocol. A detailed comparative study reveals that PaPrBaG has several advantages over sequence similarity approaches. Most importantly, it always provides a prediction whereas other approaches discard a large number of sequencing reads with low similarity to currently known reference genomes. Furthermore, PaPrBaG remains reliable even at very low genomic coverages. CombiningPaPrBaG with existing approaches further improves prediction results.
Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells
Authors: Kim Joseph J. , Bennett Neal K. , Devita Mitchel S. , Chahar Sanjay , Viswanath Satish , Lee Eunjee A. , Jung Giyoung , Shao Paul P. , Childers Erin P. , Liu Shichong , Kulesa Anthony , Garcia Benjamin A. , Becker Matthew L. , Hwang Nathaniel S. , Madabhushi Anant , Verzi Michael P. , Moghe Prabhas V.
Published: January 2017

While distinct stem cell phenotypes follow global changes in chromatin marks, single-cell chromatin technologies are unable to resolve or predict stem cell fates. We propose the first such use of optical high content nanoscopy of histone epigenetic marks (epi-marks) in stem cells to classify emergent cell states. By combining nanoscopy with epi-mark textural image informatics, we developed a novel approach, termed EDICTS (Epi-mark Descriptor Imaging of Cell Transitional States), to discern chromatin organizational changes, demarcate lineage gradations across a range of stem cell types and robustly track lineage restriction kinetics. We demonstrate the utility of EDICTS by predicting the lineage progression of stem cells cultured on biomaterial substrates with graded nanotopographies and mechanical stiffness, thus parsing the role of specific biophysical cues as sensitive epigenetic drivers. We also demonstrate the unique power of EDICTS to resolve cellular states based on epi-marks that cannot be detected via mass spectrometry based methods for quantifying the abundance of histone post-translational modifications. Overall, EDICTS represents a powerful new methodology to predict single cell lineage decisions by integrating high content super-resolution nanoscopy and imaging informatics of the nuclear organization of epi-marks.
Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach
Authors: Li Li , Greene Ilana , Readhead Benjamin , Menon Madhav C. , Kidd Brian A. , Uzilov Andrew V. , Wei Chengguo , Philippe Nimrod , Schroppel Bernd , He John Cijiang , Chen Rong , Dudley Joel T. , Murphy Barbara
Published: January 2017

Chronic allograft damage, defined by interstitial fibrosis and tubular atrophy (IF/TA), is a leading cause of allograft failure. Few effective therapeutic options are available to prevent the progression of IF/TA. We applied a meta-analysis approach on IF/TA molecular datasets in Gene Expression Omnibus to identify a robust 85-gene signature, which was used for computational drug repurposing analysis. Among the top ranked compounds predicted to be therapeutic for IF/TA were azathioprine, a drug to prevent acute rejection in renal transplantation, and kaempferol and esculetin, two drugs not previously described to have efficacy for IF/TA. We experimentally validated the anti-fibrosis effects of kaempferol and esculetin using renal tubular cellsin vitroandin vivoin a mouse Unilateral Ureteric Obstruction (UUO) model. Kaempferol significantly attenuated TGF-β1-mediated profibrotic pathwaysin vitroandin vivo, while esculetin significantly inhibited Wnt/β-catenin pathwayin vitro and in vivo. Histology confirmed significantly abrogated fibrosis by kaempferol and esculetinin vivo. We developed an integrative computational framework to identify kaempferol and esculetin as putatively novel therapies for IF/TA and provided experimental evidence for their therapeutic activitiesin vitroandin vivousing preclinical models. The findings suggest that both drugs might serve as therapeutic options for IF/TA.
A four-compartment PBPK heart model accounting for cardiac metabolism - model development and application
Authors: Tylutki Zofia , Polak Sebastian
Published: January 2017

In the field of cardiac drug efficacy and safety assessment, information on drug concentration in heart tissue is desirable. Because measuring drug concentrations in human cardiac tissue is challenging in healthy volunteers, mathematical models are used to cope with such limitations. With a goal of predicting drug concentration in cardiac tissue, we have developed a whole-body PBPK model consisting of seventeen perfusion-limited compartments. The proposed PBPK heart model consisted of four compartments: the epicardium, midmyocardium, endocardium, and pericardial fluid, and accounted for cardiac metabolism using CYP450. The model was written in R. The plasma:tissues partition coefficients (Kp) were calculated in Simcyp Simulator. The model was fitted to the concentrations of amitriptyline in plasma and the heart. The estimated parameters were as follows: 0.80 for the absorption rate [h−1], 52.6 for Kprest, 0.01 for the blood flow through the pericardial fluid [L/h], and 0.78 for the P-parameter describing the diffusion between the pericardial fluid and epicardium [L/h]. The total cardiac clearance of amitriptyline was calculated as 0.316 L/h. Although the model needs further improvement, the results support its feasibility, and it is a first attempt to provide an active drug concentration in various locations within heart tissue using a PBPK approach.
Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network
Authors: Yao Qianlan , Wu Leilei , Li Jia , Yang Li guang , Sun Yidi , Li Zhen , He Sheng , Feng Fangyoumin , Li Hong , Li Yixue
Published: January 2017

LncRNAs play pivotal roles in many important biological processes, but research on the functions of lncRNAs in human disease is still in its infancy. Therefore, it is urgent to prioritize lncRNAs that are potentially associated with diseases. In this work, we developed a novel algorithm, LncPriCNet, that uses a multi-level composite network to prioritize candidate lncRNAs associated with diseases. By integrating genes, lncRNAs, phenotypes and their associations, LncPriCNet achieves an overall performance superior to that of previous methods, with high AUC values of up to 0.93. Notably, LncPriCNet still performs well when information on known disease lncRNAs is lacking. When applied to breast cancer, LncPriCNet identified known breast cancer-related lncRNAs, revealed novel lncRNA candidates and inferred their functions via pathway analysis. We further constructed the human disease-lncRNA landscape, revealed the modularity of the disease-lncRNA network and identified several lncRNA hotspots. In summary, LncPriCNet is a useful tool for prioritizing disease-related lncRNAs and may facilitate understanding of the molecular mechanisms of human disease at the lncRNA level.
Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems
Authors: Maslov Sergei , Sneppen Kim
Published: January 2017

Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.
Ndfip1 restricts Th17 cell potency by limiting lineage stability and proinflammatory cytokine production
Authors: Layman Awo Akosua Kesewa , Sprout Stephanie L. , Phillips Dylan , Oliver Paula M.
Published: January 2017

While Th17 cells can protect against colonization by pathogenic organisms, they also have the potential to become pathogenic and promote autoimmune and inflammatory diseases. Mechanisms that control their pathogenic potential remain poorly understood. Here we show that Ndfip1, a co-activator of the E3 ubiquitin ligase Itch, restricts the frequency and pathogenicity of Th17 cells. Mice lacking Ndfip1 have increased numbers of Th17 cells, and this increase is cell intrinsic. We found that Ndfip1 restricts production of the proinflammatory cytokines in Th17 cells. Increased cytokine production correlated with reduced degradation and accumulation of RORγT. When transferredin vivo, Th17 cells lacking Ndfip1 were more likely to maintain their ability to make IL-17, were more potent proinflammatory cytokine producers, and were powerful inducers of colitis. Together our data support an essential role for Ndfip1 in degrading RORγT and suppressing Th17 lineage stability, proinflammatory cytokine production, and pathogenicity.
Prior knowledge is essential for the beneficial effect of targeted memory reactivation during sleep
Authors: Groch Sabine , Schreiner Thomas , Rasch Björn , Huber Reto , Wilhelm Ines
Published: January 2017

Prior knowledge speeds up system consolidation and accelerates integration of newly acquired memories into existing neocortical knowledge networks. By using targeted memory reactivations, we demonstrate that prior knowledge is also essential for successful reactivation and consolidation of memories during sleep, both on the behavioral and oscillatory level (i.e., theta and fast spindle activity). Thus, prior knowledge is a prerequisite for new memories to enter processes of system consolidation during sleep.
Distinct prognostic values of S100 mRNA expression in breast cancer
Authors: Zhang Shizhen , Wang Zhen , Liu Weiwei , Lei Rui , Shan Jinlan , Li Ling , Wang Xiaochen
Published: January 2017

S100 family genes encode low molecular weight, acidic-Ca2+ binding proteins implicating in a wide spectrum of biological processes. S100 family contains at least 20 members, most of which are frequently dysregulated in human malignancies including breast cancer. However, the prognostic roles of each individual S100, especially the mRNA level, in breast cancer patients remain elusive. In the current study, we used “The Kaplan-Meier plotter” (KM plotter) database to investigate the prognostic values of S100 mRNA expression in breast cancer. Our results indicated that high mRNA expression of S100A8, S100A9, S100A11 and S100P were found to be significantly correlated to worse outcome, while S100A1 and S100A6 were associated with better prognosis in all breast cancer patients. We further assessed the prognostic value of S100 in different intrinsic subtypes and clinicopathological features of breast cancer. The associated results will elucidate the role of S100 in breast cancer and may further lead the research to explore the S100-targeting reagents for treating breast cancer patients.
Electroacupuncture treatment partly promotes the recovery time of postoperative ileus by activating the vagus nerve but not regulating local inflammation
Authors: Fang Jun-fan , Fang Jian-qiao , Shao Xiao-mei , Du Jun-ying , Liang Yi , Wang Wen , Liu Zhe
Published: January 2017

Postoperative ileus (POI) after abdominal surgery significantly lowers the life quality of patients and increase hospital costs. However, few treatment strategies have successfully shortened the duration of POI. Electroacupuncture (EA) is a modern way of administering acupuncture and widely used in various gastrointestinal (GI) diseases in the world. Here, we studied the effect of EA on POI and its underlying mechanisms. Intestinal manipulation resulted in significant delays of GI transit, colonic transit and gastric emptying. Surgery also up-regulated c-fos in nucleus of the solitary tract (NTS) and induced inflammation response in the small intestine. Further, operation and inhale anesthesia inhibited NTS neuron excitation duration for the whole observation time. EA administered at ST36 indeed shortened the recovery time of GI and colonic transit, and significantly increased the gastric emptying. EA also significantly activated the NTS neurons after operation. However, there was no anti-inflammation effect of EA during the whole experiment. Finally, atropine blocked the regulatory effect of EA on GI function, when it was injected after surgery, but not before surgery. Thus, the regulatory effect of EA on POI was mainly mediated by exciting NTS neurons to improve the GI tract transit function but not by activating cholinergic anti-inflammatory pathway.
Ingroup/outgroup membership modulates fairness consideration: neural signatures from ERPs and EEG oscillations
Authors: Wang Yiwen , Zhang Zhen , Bai Liying , Lin Chongde , Osinsky Roman , Hewig Johannes
Published: January 2017

Previous studies have shown that ingroup/outgroup membership influences individual’s fairness considerations. However, it is not clear yet how group membership influences brain activity when a recipient evaluates the fairness of asset distribution. In this study, subjects participated as recipients in an Ultimatum Game with alleged members of both an experimentally induced ingroup and outgroup. They either received extremely unequal, moderately unequal, or equal offers from proposers while electroencephalogram was recorded. Behavioral results showed that the acceptance rates for unequal offers were higher when interacting with ingroup partners than with outgroup partners. Analyses of event related potentials revealed that proposers’ group membership modulated offer evaluation at earlier processing stages. Feedback-related negativity was more negative for extremely and moderately unequal offers compared to equal offers in the ingroup interaction whereas it did not show differential responses to different offers in the outgroup interaction. Analyses of event related oscillations revealed that the theta power (4–6 Hz) was larger for moderately unequal offers than equal offers in the ingroup interaction whereas it did not show differential responses to different offers in the outgroup interaction. Thus, early mechanisms of fairness evaluation are strongly modulated by the ingroup/outgroup membership of the interaction partner.