bluuebunny/crossref_metadata_2025 huggingface dataset:
Geochemical Investigation of Selected Elements in an Agricultural Soil: Case Study in Sumani Watershed West Sumatera in Indonesia
Authors: Aflizar . , Muzakkir . , Afrizal Roni , Rahman Muhammad Azadur
Published: August 2018

This paper presents the geochemical study of agricultural soil and river sediments along Sumani watershed, West Sumatra in Indonesia. We examined the distribution and abundances of 16 elements (Pb, Zn, Cu, Ni, Cr,V, Sr, Rb, Ce, Th, Zr, Si, Ti, Fe Ca, and P) in vegetable soil, sawah soil =and river sediment sample, to evaluate the factors controlling their abundances, possible sources, and environmental implications. Average concentrations of Pb, Zn, Cu, Ni, Cr,V, Sr, Rb, Ce, Th, Zr at vegetable (1) soil were 38, 88.3, 38.7, 3, 8, 101, 96, 98, 87, 31 and 218 mg kg-1 , 26, 39.05, 8.8, 13.5, 31, 231.5, 37, 19, 78, 16 and 303.5 mg kg-1 at sawah soil (3, 4) and 30, 61.6, 35.7, 9, 22, 294, 65, 12, 78, 14 and 232 mg kg-1 at river sediment (2), respectively. The concentration of Pb, Rb, Th and Zr at upland vegetables, V and Zr at sawah soil and river sediment were mostly two time Sumatra BCSCST or BCC in several samples. Enrichment factor values showed low to moderate enrichment of Pb, Zn, Cu, Rb, Ce and Zr, whereas Th showed significant contamination at vegetables soil, suggesting contributions from anthropogenic sources. Anthropogenic contributions of most metals mainly originate from natural processes. However, Pb, Ce, Th and Zr ranges of 527–108, 41-89, 66-117 and 35-100%, respectively, at Vegetable and sawah soil and river sediment confirm their anthropogenic contribution. Factor analysis and correlation matrices suggested that elevated metal concentrations at agricultural soil in Sumaniwatershed might be controlled by pH, CEC, Fe-oxy-hydroxides. Deposition of metals at vegetable and sawah soil and river sediment might be controlled by non-ferrous metal (i.e., aluminosilicates), sediment grain size, or source rock composition (andesite, alluvial fan, undifferentiated volcanic material, granite and gneiss).Keyword: Agricultural soil, anthropogenic activities, enrichment factor, metals source, river sediment, watershed trace [How to Cite: Aflizar, Muzakkir, R Afrizal and MA Rahman. 2016. Geochemical Investigation of Selected Elements in an Agricultural Soil: Case Study in Sumani Watershed West Sumatera in Indonesia. J Trop Soils 21: 49-66. Doi: 10.5400/jts.2016.21.1.49]
Contingency Model of Multiple SNSs Running Strategy in Art and Cultural Institutions
Authors: Yum Joosun , Kim Kihwan , Mazzei Stephanie
Published: August 2018

Social Network Service (SNS) is getting popular among various organizations as a powerful tool for communication and promotion. Recently, cultural and art institutions began to employ multiple SNS platforms for a variety of applications such as marketing, communication, customer services, and even program development. It is a challenging task to run multiple SNSs platforms to execute many different applications. Although this is a more common trend, there have been few studies to explore the factors that might influence the successful running of multiple SNSs, in particular in the art and cultural institutions. As critical factors, our study considered three factors, 1) the applications of SNS use, 2) the features of SNS platform, and 3) the characteristics of SNS. From the perspective of contingency theory, we suggested the integrative model that when the fit among these three factors will result in the best outcomes. Using a case study method, we analyzed the case of Daelim museum in order to test our proposed model. We found that the fitness among the target audience, the selection of platform, and the purposes of usage lead to the increased number of audiences and the satisfaction with the services.
Management Control Systems and Integrated Reporting: Which Relationships? The Case of the Azienda Ospedaliero Universitaria Ospedali Riuniti Ancona
Authors: Gatti Marco , Chiucchi Maria Serena , Montemari Marco
Published: August 2018

This article explores the contribution that management accountants and management control systems can give to the design and the implementation of an integrated reporting system. In particular, the case of the Azienda Ospedaliero Universitaria Ospedali Riuniti Ancona is analysed in the aim of highlighting the role played by the management accountant in promoting the design and implementation of the integrated report in the specific context under investigation. The empirical evidence adds to the extant literature on this issue by showing the relevant role played by management control systems and by management accountants as well and, in particular, how the latter can significantly influence the whole design and implementation process at an organisational, technical, and motivational level.
Mir-186-5p Regulates WNT Signaling Pathway by Targeting TCF4 Transcription Factor
Authors: Bayat Zahra , Soltani Bahram M.
Published: August 2018

The evolutionarily conserved Wnt signaling pathway plays essential roles during embryonic development, tissue homeostasis and differentiation. This pathway is deregulated in many cancers especially colorectal cancer. MiRNAs are a class of small noncoding RNAs that may play a major role in post transcriptional regulation of many genes and signaling pathway such as WNT signaling pathway. Here, we intended to investigate if miR-186-5p is capable of regulating WNT signaling pathway wia suppression TCF4 gene expression. miR-186-5p was bioinformatically predicted as a candidate regulator of TCF4 gene expression and then, in this experimental study, miR-186-5p was overexpressed in SW480 cell line and its increased expression was detected through quantitative reverse transcription polymerase chain reaction (RT-qPCR). The effect of miR-186-5p on WNT pathway was analysied with TOP/FOP flash assay in SW480 cell line. Finally, flow cytometery was used to inves tigate the effect of miR-186-5p overexpression on cell cycle progression in SW480 cell line. miR-186-5p was overexpressed in the SW480 cell line and its overexpression resulted in significant reduction of the TCF4 mRNA level. TOP/FOP flash assay, confirmed the negative effect of miR-186-5p on the Wnt pathway in SW480 cells. Finally, Overexpression of miR186-5p in SW480 cells resulted in cell cycle arrest in subG1 phase, detected by flow cytometry. Overall, accumulative results indi-cated that miR-186-5p by targeting TCF4 is potentially one of the regulators of the WNT signaling pathway.
THE NATIONAL HOUSING PROGRAM AS A MAIN NORMATIVE DOCUMENT DEFINING THE AMENDED STATE HOUSING POLICY
Authors: Gołębiowska Anna , Prokopowicz Dariusz
Published: August 2018

At the end of 2016, the Polish government began to implement its Program “Mieszkanie Plus” by publishing the elaborated strategic and program document called the National Housing Program. The “Mieszkanie Plus: program, should fulfill important functions of the housing policy and improve the housing situation in terms of reducing the social stratification of families in Poland. The main objective of the “Mieszkanie Plus” program is to increase significantly the availability of housing, especially cheap rented flats, with the option to purchase property after 20-30 years of use. Considering the housing situation in Poland, one of the main goals of the housing policy that is currently underway is to create conditions for the effective development of the low-cost housing sector to improve the standards of housing availability in Poland in the next medium-term segment and in the segment of the lower middle class. Therefore, the housing policy in the National Housing Program was defined with an indication of the housing needs of citizens and adaptation of domestic housing standards in Poland to the statistical average situation in this respect in the European Union. The “Mieszkanie Plus” program was finalized in a document called the National Housing Program. In the this program the housing policy of the state was defined and adopted for the purpose of implementation in September 2016 by the government in Poland.
Making computer science results reproducible - A case study using Gradle and Docker
Authors: Elmenreich Wilfried , Moll Philipp , Theuermann Sebastian , Lux Mathias
Published: August 2018

This paper addresses two questions related to reproducibility within the context of research related to computer science. First, requirements on reproducibility are analyzed based on a survey addressed to researchers in the academic and private sector. The survey indicates a strong need for open but also easily accessible results, thus reproducing an experiment should not require too much effort. The results from the survey are then used to formulate general guidelines for making research results reproducible. In addition, this paper explores a number of existing software tools that could bring forward reproducibility in research results. After a general analysis of tools a further investigation is done via three case studies based on actual research projects which are used to evaluate the previously introduced tools. Results indicate that due to conflicting requirements, none of the presented solutions fulfills all intended goals perfectly. However, we present requirements and guidelines for making research reproducible. While the main focus of this paper is on reproducibility in computer science, the results of this paper are still valid for other fields using computation as a tool.
Gradient-reading and mechano-effector machinery for netrin-1-induced axon guidance
Authors: Baba Kentarou , Yoshida Wataru , Toriyama Michinori , Shimada Tadayuki , Manning Colleen F , Saito Michiko , Kohno Kenji , Trimmer James S , Watanabe Rikiya , Inagaki Naoyuki
Published: August 2018

Growth cones navigate axonal projection in response to guidance cues. However, it is unclear how they can decide the migratory direction by transducing the local spatial cues into protrusive forces. Here we show that knockout mice of Shootin1 display abnormal projection of the forebrain commissural axons, a phenotype similar to that of the axon guidance molecule netrin-1. Shallow gradients of netrin-1 elicited highly polarized Pak1-mediated phosphorylation of shootin1 within growth cones. We demonstrate that netrin-1–elicited shootin1 phosphorylation increases shootin1 interaction with the cell adhesion molecule L1-CAM; this, in turn, promotes F-actin–adhesion coupling and concomitant generation of forces for growth cone migration. Moreover, the spatially regulated shootin1 phosphorylation within growth cones is required for axon turning induced by netrin-1 gradients. Our study defines a mechano-effector for netrin-1 signaling and demonstrates that shootin1 phosphorylation is a critical readout for netrin-1 gradients that results in a directional mechanoresponse for axon guidance.
The songs of male pied flycatchers: exploring the legacy of the fathers
Authors: Labra Antonieta , Lampe Helene M.
Published: August 2018

Singing is a key element of songbirds’ behavioral repertoire, particularly for males, which sing during the breeding season to defend resources against other males and to attract females. Different song traits may convey honest information about males’ qualities or conditions, which may be used by females to select their mates. Traits under strong sexual selection have an important component of additive genetic variation (i.e., the main genetic inheritance from parents), and so relatively high heritability; therefore, it can be expected that song traits also do. Although the act of singing is an innate behavior, and thus, genetically determined, songbirds need to learn their songs and therefore the genetic contribution to song traits may be reduced by the effect of environmental factors. We tested this hypothesis in seven song traits recorded in the long-distance migratory bird, the pied flycatcher (Ficedula hypoleuca). From a 23-year database (1992–2015), we obtained songs for 28 father–son pairs, and for each song trait we applied parent–offspring regressions to estimate heritability. The type of syllables sung are learned from tutors, and here we also determined the cultural contribution of fathers to the song repertoires of their sons, by quantifying the percentage of syllables that sons shared with their fathers, and compared this with what sons shared with other males in the population (e.g., neighbors). The heritabilities of song traits were highly variable (ranging from −0.22 to 0.56), but most of these were around zero and none of them were significant. These results indicate that the seven song traits are most likely determined by environmental factors. Sons shared more syllables with their fathers than with neighbors (21% vs. 3%), suggesting that fathers are important song tutors during the nestling period. We conclude that there is a cultural inheritance from fathers to their sons’ syllable repertoires, but there is no strong evidence for a genetic contribution of fathers to the seven song traits studied.
piRNN: deep learning algorithm for piRNA prediction
Authors: Wang Kai , Hoeksema Joshua , Liang Chun
Published: August 2018

Piwi-interacting RNAs (piRNAs) are the largest class of small non-coding RNAs discovered in germ cells. Identifying piRNAs from small RNA data is a challenging task due to the lack of conserved sequences and structural features of piRNAs. Many programs have been developed to identify piRNA from small RNA data. However, these programs have limitations. They either rely on extracting complicated features, or only demonstrate strong performance on transposon related piRNAs. Here we proposed a new program called piRNN for piRNA identification. For our software, we applied a convolutional neural network classifier that was trained on the datasets from four different species (Caenorhabditis elegans, Drosophila melanogaster, rat and human). A matrix of k-mer frequency values was used to represent each sequence. piRNN has great usability and shows better performance in comparison with other programs. It is freely available at https://github.com/bioinfolabmu/piRNN.
Reductive Transformation of Layered‐Double‐Hydroxide Nanosheets to Fe‐Based Heterostructures for Efficient Visible‐Light Photocatalytic Hydrogenation of CO
Authors: Zhao Yufei , Li Zhenhua , Li Mengzhu , Liu Jinjia , Liu Xingwu , Waterhouse Geoffrey I. N. , Wang Yuanshen , Zhao Jiaqing , Gao Wa , Zhang Zhaosheng , Long Run , Zhang Qinghua , Gu Lin , Liu Xi , Wen Xiaodong , Ma Ding , Wu Li‐Zhu , Tung Chen‐Ho , Zhang Tierui
Published: August 2018

Conversion of syngas (CO, H2) to hydrocarbons, commonly known as the Fischer–Tropsch (FT) synthesis, represents a fundamental pillar in today's chemical industry and is typically carried out under technically demanding conditions (1–3 MPa, 300–400 °C). Photocatalysis using sunlight offers an alternative and potentially more sustainable approach for the transformation of small molecules (H2O, CO, CO2, N2, etc.) to high‐valuable products, including hydrocarbons. Herein, a novel series of Fe‐based heterostructured photocatalysts (Fe‐x) is successfully fabricated via H2 reduction of ZnFeAl‐layered double hydroxide (LDH) nanosheets at temperatures (x) in the range 300–650 °C. At a reduction temperature of 500 °C, the heterostructured photocatalyst formed (Fe‐500) consists of Fe0 and FeOx nanoparticles supported by ZnO and amorphous Al2O3. Fe‐500 demonstrates remarkable CO hydrogenation performance with very high initial selectivities toward hydrocarbons (89%) and especially light olefins (42%), and a very low selectivity towards CO2 (11%). The intimate and abundant interfacial contacts between metallic Fe0 and FeOx in the Fe‐500 photocatalyst underpins its outstanding photocatalytic performance. The photocatalytic production of high‐value light olefins with suppressed CO2 selectivity from CO hydrogenation is demonstrated here.
High Performance and Stable All‐Inorganic Metal Halide Perovskite‐Based Photodetectors for Optical Communication Applications
Authors: Bao Chunxiong , Yang Jie , Bai Sai , Xu Weidong , Yan Zhibo , Xu Qingyu , Liu Junming , Zhang Wenjing , Gao Feng
Published: August 2018

Photodetectors are critical parts of an optical communication system for achieving efficient photoelectronic conversion of signals, and the response speed directly determines the bandwidth of the whole system. Metal halide perovskites, an emerging class of low‐cost solution‐processed semiconductors, exhibiting strong optical absorption, low trap states, and high carrier mobility, are widely investigated in photodetection applications. Herein, through optimizing the device engineering and film quality, high‐performance photodetectors based on all‐inorganic cesium lead halide perovskite (CsPbIxBr3–x), which simultaneously possess high sensitivity and fast response, are demonstrated. The optimized devices processed from CsPbIBr2 perovskite show a practically measured detectable limit of about 21.5 pW cm−2 and a fast response time of 20 ns, which are both among the highest reported device performance of perovskite‐based photodetectors. Moreover, the photodetectors exhibit outstanding long‐term environmental stability, with negligible degradation of the photoresponse property after 2000 h under ambient conditions. In addition, the resulting perovskite photodetector is successfully integrated into an optical communication system and its applications as an optical signal receiver on transmitting text and audio signals is demonstrated. The results suggest that all‐inorganic metal halide perovskite‐based photodetectors have great application potential for optical communication.
Regulation of Inflammatory Cytokines for Spinal Cord Injury Repair Through Local Delivery of Therapeutic Agents
Authors: Ren Hao , Chen Xuri , Tian Mengya , Zhou Jing , Ouyang Hongwei , Zhang Zhiyong
Published: August 2018

The balance of inflammation is critical to the repair of spinal cord injury (SCI), which is one of the most devastating traumas in human beings. Inflammatory cytokines, the direct mediators of local inflammation, have differential influences on the repair of the injured spinal cord. Some inflammatory cytokines are demonstrated beneficial to spinal cord repair in SCI models, while some detrimental. Various animal researches have revealed that local delivery of therapeutic agents efficiently regulates inflammatory cytokines and promotes repair from SCI. Quite a few clinical studies have also shown the promotion of repair from SCI through regulation of inflammatory cytokines. However, local delivery of a single agent affects only a part of the inflammatory cytokines that need to be regulated. Meanwhile, different individuals have differential profiles of inflammatory cytokines. Therefore, future studies may aim to develop personalized strategies of locally delivered therapeutic agent cocktails for effective and precise regulation of inflammation, and substantial functional recovery from SCI.
Heavy Doping by Bromine to Improve the Thermoelectric Properties of n‐type Polycrystalline SnSe
Authors: Li Shan , Wang Yumei , Chen Chen , Li Xiaofang , Xue Wenhua , Wang Xinyu , Zhang Zongwei , Cao Feng , Sui Jiehe , Liu Xingjun , Zhang Qian
Published: August 2018

Single crystal tin selenide (SnSe) has attracted much attention for its excellent thermoelectric performance. However, polycrystalline SnSe exhibits unsatisfactory figure‐of‐merit due to the inferior electrical properties, especially for n‐type SnSe. In this work, a high concentration of Br doping (6–12 atm%) on the Se site effectively increases the Hall carrier concentration from 1.6 × 1017 cm−3 (p‐type) in undoped SnSe to 1.3 × 1019 cm−3 (n‐type) in Br‐doped SnSe0.88Br0.12, leading to an increased electrical conductivity close to that of a single crystal. Combined with the decreased lattice thermal conductivity due to the enhanced phonon scattering by composition fluctuation and dislocations, a peak ZT of ≈1.3 at 773 K, together with the enhanced average ZT is obtained in SnSe0.9Br0.1 along the hot pressing direction.
Multilevel Data Encryption Using Thermal‐Treatment Controlled Room Temperature Phosphorescence of Carbon Dot/Polyvinylalcohol Composites
Authors: Tian Zhen , Li Di , Ushakova Elena V. , Maslov Vladimir G. , Zhou Ding , Jing Pengtao , Shen Dezhen , Qu Songnan , Rogach Andrey L.
Published: August 2018

Thermal‐treatment controlled room temperature phosphorescence is realized by embedding either originally synthesized carbon dots (CDs) or 200 °C thermal‐treated CDs into a polyvinylalcohol (PVA) matrix through post‐synthetic thermal annealing at 200 or 150 °C. The thermal‐treatment controlled phosphorescence is attributed to the transfer of photoexcitation from the excited singlet state to the triplet state through intersystem crossing, followed by radiative transition to the ground state, which is due to decrease of quenchers (oxygen) in the CDs and suppression of the vibrational dissipations through the chemical bonding of CDs in the PVA matrix. Multilevel fluorescence/phosphorescence data encryption is demonstrated based on the thermal‐treatment controlled phosphorescence from CD@PVA composites.
Change in Prevalence of Orofacial Clefts in California between 1987 and 2010
Authors: Andrew Tom , Yang Wei , Bernstein Jonathan A. , Shaw Gary M.
Published: August 2018

Introduction

To extend the knowledge base about possible prevalence declines of specific orofacial cleft phenotypes, here we examine prevalence in a population base from California over a two‐decade period among numerous race/ethnic groups.

Methods

This population‐based study used vital statistics and birth defects registry data. Its population involved all births (~1.5 million births) in central California counties from 1987 to 2010. Orofacial clefts were defined as cleft lip with or without cleft palate (CLP, n=1766), and cleft palate (CP, n=922) only. The slope of prevalence of each cleft phenotype over the period 1987‐2010 was estimated using weighted least squares regression.

Results

Birth prevalence of CLP was 121/100,000 live births, and 63/100,000 live births for CP. The slope for CLP decreased by 1.2 (slope: ‐1.2; 95% CI: ‐1.9, ‐0.5), and for CP by 0.7 (slope: ‐0.7; 95% CI: ‐1.7, 0.2) for CP. Stratification by race/ethnicity or infant sex did not demonstrate a statistical difference in slopes.

Conclusions

We observed a decline in the prevalence in CLP in all ethnic groups, however did not observe the same amount of decline in CP, perhaps due to antenatal screening.
Characterization of a severe case of PIK3CA‐related overgrowth at autopsy by droplet digital polymerase chain reaction and report of PIK3CA sequencing in 22 patients
Authors: Piacitelli Andrew M. , Jensen Dana M. , Brandling‐Bennett Heather , Gray Megan Mariner , Batra Maneesh , Gust Juliane , Thaker Ameet , Paschal Catherine , Tsuchiya Karen , Pritchard Colin C. , Perkins Jonathan , Mirzaa Ghayda M. , Bennett James T.
Published: August 2018

PIK3CA‐related overgrowth spectrum (PROS) refers to a group of disorders of segmental overgrowth of a wide variety of tissues as well as venous and lymphatic malformations. Clinical and molecular diagnosis can be challenging due to phenotypic heterogeneity and difficulties detecting low‐level mosaicism using standard methods. Here, we report a patient with a severe presentation of PIK3CA‐related overgrowth with analysis of 27 posthumously collected tissues by droplet digital polymerase chain reaction (PCR) at autopsy. This patient had a complicated medical course, with coagulopathy, ischemic brain injury, and sepsis resulting in multi‐organ failure and death at age 2 months despite sirolimus therapy. Five of the 27 tissues analyzed possessed a mosaic PIK3CA mutation (p.E545K), with mutation levels ranging from 3 to 20% across affected tissues. We found no correlation between tissue‐specific disease severity and mutation levels, likely reflecting sampling limitations. We also tested a series of 22 individuals with somatic overgrowth and/or vascular‐lymphatic malformations using a targeted next generation sequencing panel and found PIK3CA mutations in nine individuals, identifying three novel PIK3CA variants. This report expands the clinical and molecular spectrum of PROS, emphasizes that different molecular methods can be complimentary in the diagnosis of these disorders, and highlights the risk of coagulopathy in a subset of patients with PIK3CA‐related overgrowth.
Photoredoxkatalytische organische Umwandlungen an heterogenen Kohlenstoffnitriden
Authors: Savateev Aleksandr , Ghosh Indrajit , König Burkhard , Antonietti Markus
Published: August 2018

Die klassische Photoredoxkatalyse, die homogene Übergangsmetall‐basierte Systeme, organische Farbstoffe und Halbleiter umfasst, hat sich zu einem universellen Werkzeug für die Katalyse einer Vielzahl chemischer Reaktionen entwickelt, die unter milden Bedingungen unter Einstrahlung von sichtbarem Licht mit hoher Selektivität ablaufen. Dieser Kurzaufsatz fasst jüngste Fortschritte der Photoredoxkatalyse zusammen, die durch heterogene Kohlenstoffnitrid‐Materialien wie mesoporöses graphitisches Kohlenstoffnitrid (mpg‐CN), polymeres Kohlenstoffnitrid und Kaliumpoly(heptazinimid) (K‐PHI) vermittelt wird. Aufgrund der hohen thermischen, chemischen und Photostabilität dieser Materialien, wie auch der vorteilhaften Leitungs‐ und Valenzbandlagen, erweitern Kohlenstoffnitride den Reaktionsumfang der Photokatalyse um zahlreiche neue Reaktionen, wie beispielsweise die photokatalytische Aktivierung von elementarem Schwefel, die einen einfachen chemischen Zugang zu Organoschwefelverbindungen ermöglicht.
Catalytic Alkyne Arylation Using Traceless Directing Groups
Authors: Park Jung‐Woo , Kang Bubwoong , Dong Vy M.
Published: August 2018

By using Pd0/Mandyphos, we achieved a three‐component aminoarylation of alkynes to generate enamines, which are then hydrolyzed to either α‐arylphenones or α,α‐diarylketones. This Pd‐catalyzed method overcomes established known pathways to enable the use of amines as traceless directing groups for C−C bond formation.
Asymmetric Synthesis of Tetrahydroindolizines by Bimetallic Relay Catalyzed Cycloaddition of Pyridinium Ylides
Authors: Zhang Dong , Lin Lili , Yang Jian , Liu Xiaohua , Feng Xiaoming
Published: August 2018

A highly enantioselective synthesis of tetrahydroindolizines by catalytic multicomponent cycloaddition reactions of diazoacetate, pyridine, and alkenyloxindole was developed. Under the relay catalysis, involving an achiral iron(III) catalyst and chiral N,N′‐dioxide‐scandium(III) complex, a series of tetrahydroindolizines bearing different substituents were obtained in moderate to high yields (up to 99 %) with excellent diastereo‐ and enantioselectivities (up to >19:1 d.r., 99 % ee).
Self‐Assembly of a 3D DNA Crystal Structure with Rationally Designed Six‐Fold Symmetry
Authors: Zhang Fei , Simmons Chad R. , Gates Jade , Liu Yan , Yan Hao
Published: August 2018

Programming self‐assembled designer DNA crystals with various lattices and functions is one of the most important goals for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that rely on crystalline lattices and cavities. Herein, we present a rationally designed and self‐assembled 3D DNA crystal lattice with hexagonal symmetry. In our design, two 21‐base oligonucleotides are used to form a duplex motif that further assembles into a 3D array. The interactions between the strands are programmed using Watson–Crick base‐pairing. The six‐fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal provides a new avenue that could create self‐assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure contains a highly organized array of well‐defined cavities that are suitable for future applications with immobilized guests.
Neuprogrammierung von humanem Siderocalin zur Neutralisierung von Petrobactin, dem essenziellen Eisenfänger des Milzbrand‐Bazillus
Authors: Dauner Martin , Eichinger Andreas , Lücking Genia , Scherer Siegfried , Skerra Arne
Published: August 2018

Bacillus anthracis verdankt seine ausgeprägte Virulenz – neben spezifischen Toxinen – einem doppelten Importmechanismus für FeIII‐Ionen. Das pathogene Bakterium sekretiert die Siderophore Bacillibactin (BB) und Petrobactin (PB), von denen nur BB von menschlichem Siderocalin, einem im Plasma vorherrschenden Lipocalin, neutralisiert wird. Wir beschreiben dessen Umgestaltung durch kombinatorisches Protein‐Design, um PB⋅FeIII anstelle von BB⋅FeIII zu binden, und dies sogar mit höherer Affinität (KD≈20 pm). Die Röntgen‐kristallographische Analyse des erhaltenen “Petrocalins” in Komplex mit PB⋅GaIII offenbart eine positiv geladene Ligandentasche, wobei die ausgedehnte schmetterlingsartige Konformation des gebundenen PB die fehlende Erkennung durch das natürliche Siderocalin erklärt. In mikrobiologischen Studien unterdrückte eine Kombination aus Petrocalin und Siderocalin das Wachstum eines BB+/PB+‐Stamms von Bacillus cereus unter eisenlimitierenden Kulturbedingungen. Das neuprogrammierte Lipocalin vermag daher neuartige Behandlungsmöglichkeiten für verheerende Infektionen durch B. anthracis zu eröffnen.
5‐(Alkynyl)dibenzothiophenium Triflates: Sulfur‐Based Reagents for Electrophilic Alkynylation
Authors: Waldecker Bernd , Kraft Finn , Golz Christopher , Alcarazo Manuel
Published: August 2018

The synthesis of a series of 5‐(alkynyl) dibenzothiophenium triflates, prepared from dibenzo[b,d]thiophene 5‐oxide and the corresponding trimethylsilyl‐substituted alkynes is reported. Their structures were determined by X‐ray crystallography, and their reactivities as electrophilic alkynylation reagents evaluated. Their broad substrate scope and functional‐group tolerance illustrate their potential to become an alternative to the broadly used EBX reagents. Isotope labeling studies reveal that alkynyldibenzothiophenium salts may undergo attack by nucleophiles at either the α‐ or β‐carbon atom depending on the nature of their substitution pattern. Subsequent elimination of the dibenzothiophene unit and 1,2‐migration of one of the groups (in case of β‐attack) affords the desired alkynes.
Achieving Lifeline Infrastructure Resilience Through an Adaptive and Risk‐Based Approach
Authors: Habibian Ahmad , Minaie Ehsan
Published: August 2018

Climate change and the consequent increasing occurrence and intensity of natural disasters highlight the need for improved infrastructure resilience; an adaptive and risk‐based approach is key.
Keeping Watch Over Our Vital Water Infrastructure
Authors: Jacobsen Laura B.
Published: August 2018

300 volunteers in AWWA's Engineering and Construction Division promote industry best practices and focus on improving delivery of critical framework, with an eye to the future.
Contracting Models Shift Dynamics of Engineering and Construction
Authors: Pedley Jean
Published: August 2018

Alternative project delivery models can potentially shorten a project's schedule and lower the overall project cost.
3D printing and modeling of congenital heart defects: A technical review
Authors: Townsend Kevin , Pietila Todd
Published: August 2018

Use of 3D printing technology is expanding in healthcare. One of the common applications is the creation of anatomical models of congenital heart defects (CHD) from medical image data. These patient‐specific models are being used for multiple purposes including visualization of anatomy, simulation of surgical procedures, patient education, and facilitating communication between clinical staff.

The process for creating CHD models begins with acquiring volumetric image data that is segmented using medical image processing software. A virtual 3D model is calculated based on the segmented data which can be further refined using computer‐aided design software. Last, the virtual model is transferred to a 3D printer for production.

By obtaining detailed knowledge on the process for creating patient‐specific CHD anatomical models, institutions can implement the technology in an efficient and cost‐effective manner.
Folate transporter expression in placenta from pregnancies complicated with birth defects
Authors: Reza‐López Sandra A. , Aguirre‐Chacón Edwin O. , Sánchez‐Ramírez Blanca , Guerrero‐Salgado Fabiola , Chávez‐Corral Dora V. , Levario‐Carrillo Margarita
Published: August 2018

Background

Folate plays a fundamental role for fetal development, participating in cell division, embryogenesis, and fetal growth. The fetus depends on maternal supply of folate across the placenta. The objective of this study was to compare the expression of Folate Receptor‐α (FR‐α), Reduced Folate Carrier (RFC), and Proton Coupled Folate Transporter (PCFT) in placentas from pregnancies complicated with birth defects (BD) and controls.

Methods

Case‐control study, including placentas of BD‐complicated pregnancies (n = 25) and a control group (n = 25). We determined the placental expression of FR‐α, RFC, and PCFT by immunohistochemistry. Optical density was measured to obtain a relative quantification of the expression.

Results

The expression of PCFT was greater in placentas from pregnancies complicated with BD than in those from the control group (p < .01). The expression of FR‐α and RFC was not different between groups.

Conclusion

The expression of PCFT in placentas from BD‐complicated pregnancies is increased, possibly as an adaptive response to increase the folate flux at the maternal‐fetal interface.
Model‐based analysis and optimization of a full‐scale industrial high‐rate anaerobic bioreactor
Authors: Feldman Hannah , Flores‐Alsina Xavier , Kjellberg Kasper , Jeppsson Ulf , Batstone Damien J. , Gernaey Krist V.
Published: August 2018

The objective of this paper is to present the model‐based optimization results of an anaerobic granular sludge internal circulation reactor. The International Water Association Anaerobic Digestion Model No. 1 extended with phosphorus (P), sulfur (S), and ethanol is used to describe the main biological and physico‐chemical processes. The high‐rate conditions within the reactor are simulated using a flow + reactor model comprised of a series of continuous stirred tank reactors followed by an ideal total suspended solids separation unit. Following parameter estimation by least squares on the measured data, the model had a relative mean error of 13 and 15% for data set #1 and data set #2, respectively. Response surfaces show that the reactor performance index (a metric combining energy recovery in the form of heat and electricity, as well as chemicals needed for pH control) could be improved by 45% when reactor pH is reduced down to 6.8. Model‐based results reveal that influent S does not impose sufficient negative impacts on energy recovery (+5.7%, in MWh/day,+0.20 M€/year when influent S is removed) to warrant the cost of its removal (3.58 M€/year). In fact, the process could handle even higher S loads (ensuring the same degree of conversion) as long as the pH is maintained above 6.8. Nevertheless, a higher S load substantially increases the amount of added NaOH to maintain the desired operational pH (>25%) due to the acidic behavior of HS
−. CO
2 stripping decreases the buffer capacity of the system and hence use of chemicals for pH control. Finally, the paper discusses the possibilities and limitations of the proposed approach, and how the results of this study will be put into practice.
Bioprocess decision support tool for scalable manufacture of extracellular vesicles
Authors: Ng Kelvin S. , Smith James A. , McAteer Matthew P. , Mead Benjamin E. , Ware Jamie , Jackson Felix O. , Carter Alison , Ferreira Lino , Bure Kim , Rowley Jon A. , Reeve Brock , Brindley David A. , Karp Jeffrey M.
Published: August 2018

Newly recognized as natural nanocarriers that deliver biological information between cells, extracellular vesicles (EVs), including exosomes and microvesicles, provide unprecedented therapeutic opportunities. Large‐scale and cost‐effective manufacturing is imperative for EV products to meet commercial and clinical demands; successful translation requires careful decisions that minimize financial and technological risks. Here, we develop a decision support tool (DST) that computes the most cost‐effective technologies for manufacturing EVs at different scales, by examining the costs of goods associated with using published protocols. The DST identifies costs of labor and consumables during EV harvest as key cost drivers, substantiating a need for larger‐scale, higher‐throughput, and automated technologies for harvesting EVs. Importantly, we highlight a lack of appropriate technologies for meeting clinical demands, and propose a potentially cost‐effective solution. This DST can facilitate decision‐making very early on in development and be used to predict, and better manage, the risk of process changes when commercializing EV products.
Activity – Stability Volcano Plots for the Investigation of Nano‐Sized Electrode Materials in Lithium‐Ion Batteries
Authors: Exner Kai S.
Published: August 2018

In the last two decades, materials design in lithium‐ion batteries (LIBs) based on first‐principles methods has been spurred mainly by computationally demanding investigations of diffusion pathways, redox mechanisms or activation barriers for lithium‐ion migration. However, hitherto an expeditious tool with conceptual simplicity that enables a priori computational screening based on thermodynamic considerations in order to propose potential candidates for the usage as electrode materials in LIBs is missing. Here, a novel method based on the application of Volcano plots from catalysis is introduced which allows assessing lithium intercalation in nano‐sized electrode materials of LIBs by means of both activity and stability.
The Multiple Hydrogen‐Bonding Networks of Polyol Ribitol
Authors: Peña Isabel , Sanz Maria Eugenia , Alonso Elena R. , Alonso José L.
Published: August 2018

Conformational flexibility and non‐covalent interactions determine the structure and activity of molecules in biological processes. In this work, the hydrogen bonding networks of the polyol ribitol have been determined for the first time using a combination of laser ablation and broadband rotational spectroscopy. Five conformations of ribitol have been identified, two with extended carbon chains and three with bent chains. All conformations are stabilized by sequential hydrogen bonding networks of either four or five intramolecular O−H⋅⋅⋅O bonds in a clockwise or counter‐clockwise arrangement. The hydrogen bonding patterns are related to the extended or bent‐chain conformations of ribitol, and involve 2OH−4OH or 2OH−5OH linkages, respectively. Interestingly, all hydrogen bonds wrap round the carbon backbone of ribitol rather than being located above or below it as it happens for other polyols and cyclic sugars.
Employing Photoredox Catalysis for DNA‐Encoded Chemistry: Decarboxylative Alkylation of α‐Amino Acids
Authors: Kölmel Dominik K. , Loach Richard P. , Knauber Thomas , Flanagan Mark E.
Published: August 2018

A new procedure for the photoredox‐mediated conjugate addition of radicals that can be conveniently generated from α‐amino acids to DNA‐tagged Michael acceptors and styrenes is presented. This C(sp3)−C(sp3) coupling tolerates a broad array of structurally diverse radical precursors, including all of the 20 proteinogenic amino acids. Importantly, this reaction proceeds under mild conditions and in DNA‐compatible aqueous media. Furthermore, the presented reaction conditions are compatible with DNA, making this reaction platform well suited for the construction of DNA‐encoded libraries. The scope and limitations of the chemistry are discussed herein along with proposals for how this methodology might be used to construct DNA‐encoded libraries.
Monitoring PARKIN RBR Ubiquitin Ligase Activation States with UbFluor
Authors: Foote Peter K. , Statsyuk Alexander V.
Published: August 2018

PARKIN is a RING‐Between‐RING (RBR) E3 ligase, which ubiquitinates mitochondrial proteins in response to mitochondrial damage. Ser65 of PARKIN is phosphorylated by kinase PINK1 (pPARKIN), which causes partial PARKIN activation. PINK1 also phosphorylates Ser65 of ubiquitin (pUb), which further activates pPARKIN. Due to the lack of precise and quantitative assays to quantify the activity of PARKIN, there were many conflicting reports on the role of pUb as a PARKIN activator, whether S65E PARKIN is a true phosphomimetic of pPARKIN, and the effect of substrate of PARKIN turnover was also not known. This protocol provides a step‐by‐step guide on the use of the UbFluor probe to precisely quantitate changes in the activity of PARKIN in response to phosphorylation, allosteric activation by pUb, protein substrates, and activating structural mutations. These results pave the way to discover PARKIN activators and to precisely quantify the activity of other RBR E3s. © 2018 by John Wiley & Sons, Inc.
AXC: A new format to perform the SpMV oriented to Intel Xeon Phi architecture in OpenCL
Authors: Coronado‐Barrientos E. , Indalecio G. , García‐Loureiro A.
Published: August 2018

Emerging new architectures used in High Performance Computing require new research to adapt and optimise algorithms to them. As part of this effort, we propose the new AXC format to improve the performance of the SpMV product for the Intel Xeon Phi coprocessor. The performance of the OpenCL kernel, based on our new format, is compared with three very different and high efficient sparse matrix formats, ie, CSR, ELLR‐T, and K1. We perform tests with most of the matrices from the Williams collection used to test SpMV kernels for GPUs architectures in several related works. The numerical results show that the AXC format is more robust to spatial indirections proper of sparse matrices and prefers matrices with low variability amongst their rows' population, very much like matrices originated by FEM codes. The Conjugate Gradient (CG) is implemented in OpenCL using all the formats in this work to expose strengths and weaknesses of the formats in a real application. The CG implementation shows that the AXC has the fastest conversion time and its coherent with the numerical results generated by the SpMV tests, and that the format has a slower memory operations time due to an extra step required by the format and its larger memory footprint.
On the use of HCM to develop a resource allocation algorithm for heterogeneous clusters
Authors: Marques Soares Thiago , Weber dos Santos Rodrigo , Lobosco Marcelo
Published: August 2018

This work presents a resource allocation algorithm that considers the characteristics of regular applications to choose the subset of processors, accelerators, and networks that minimize their parallel execution time in a small heterogeneous cluster environment. The resource allocation algorithm uses Heterogeneous Cluster Model (HCM) to estimate the execution time of the parallel applications. The experimental results have shown that, for applications with distinct behaviors, the resource allocation algorithm has successfully chosen the set of resources that minimizes their execution time.
First‐Principles Study of Electrocatalytically Reversible CO2 Capture on Graphene‐like C3N
Authors: Qin Gangqiang , Cui Qianyi , Wang Weihua , Li Ping , Du Aijun , Sun Qiao
Published: August 2018

Developing advanced materials and new technologies for efficient CO2 capture and gas separation can enormously alleviate its impact on global climate change. In this study, we report a comprehensive density functional theory investigation of N2, CH4, H2, and CO2 adsorption on a graphene‐like C3N monolayer. Our calculation results show that the four gas molecules are all physisorbed on the neutral C3N monolayer. However, the interaction between CO2 and C3N can be significantly boosted via the strategies of electrochemical methods such as introducing negative charge or applying external electric field to the system. While the adsorption of N2, CH4 and H2 on C3N monolayer is slightly influenced with the above strategies. Moreover, CO2 will release spontaneously from C3N monolayer once the extra charge or electric field is removed from the system. These results demonstrate that the CO2 capture, regeneration and separation on C3N monolayer can be controllable with the method of switching on/off the charge state or electric field during the adsorption. In addition, as a new synthesized 2D material (PNAS, 2016, 113, 7414–7419), C3N possesses an extremely narrow band gap of 0.39 eV, which guarantees applying negative charge or electric field to it can be easily realized in experiment by electrochemical methods.
Analysis of Mitochondrial Protein Synthesis: De Novo Translation, Steady‐State Levels, and Assembled OXPHOS Complexes
Authors: Hilander Taru , Konovalova Svetlana , Terzioglu Mügen , Tyynismaa Henna
Published: August 2018

Mitochondria are multifunctional organelles with their own genome and protein synthesis machinery. The 13 proteins encoded by mitochondrial DNA (mtDNA) are core subunits of the oxidative phosphorylation (OXPHOS) system producing the majority of cellular ATP. Yet most mitochondrial proteins are encoded by nuclear genes, synthesized by cytosolic ribosomes, and imported into mitochondria. Therefore, disturbances in cytosolic proteostasis have consequences on the gene expression and synthesis of mtDNA‐encoded proteins and overall on mitochondrial function. Internal and environmental factors such as mutations, aging, oxidative stress, and toxic agents can affect the translation and the stability of mitochondrial proteins and lead to OXPHOS dysfunction. Here, methods for analysis of mitochondrial translation rate and protein stability using radioactive and non‐radioactive technique as well as the methods for studying steady‐state levels and assembly of OXPHOS complexes are described. © 2018 by John Wiley & Sons, Inc.
Confined Redox Reactions of Iodide in Carbon Nanopores for Fast and Energy‐Efficient Desalination of Brackish Water and Seawater
Authors: Lee Juhan , Srimuk Pattarachai , Carpier Sidonie , Choi Jaehoon , Zornitta Rafael Linzmeyer , Kim Choonsoo , Aslan Mesut , Presser Volker
Published: August 2018

Faradaic deionization is a promising new seawater desalination technology with low energy consumption. One drawback is the low water production rate as a result of the limited kinetics of the ion intercalation and insertion processes. We introduce the redox activities of iodide confined in carbon nanopores for electrochemical desalination. A fast desalination process was enabled by diffusionless redox kinetics governed by thin‐layer electrochemistry. A cell was designed with an activated carbon cloth electrode in NaI aqueous solution, which was separated from the feedwater channel by a cation‐exchange membrane. Coupled with an activated carbon counter electrode and an anion‐exchange membrane, the half‐cell in NaI with a cation‐exchange membrane maintained performance even at a high current of 2.5 A g−1 (21 mA cm−2). The redox activities of iodide allowed a high desalination capacity of 69 mg g−1 (normalized by the mass of the working electrode) with stable performance over 120 cycles. Additionally, we provide a new analytical method for unique performance evaluation under single‐pass flow conditions regarding the water production rate and energy consumption. Our cell concept provides flexible performance for low and high salinity and, thus, enables the desalination of brackish water or seawater. Particularly, we found a low energy consumption (1.63 Wh L−1) for seawater desalination and a high water production rate (25 L m−2 h−1) for brackish water.