bluuebunny/crossref_metadata_2025 huggingface dataset:
Philosophy of Molecular Biology
Authors: Brigandt Ingo
Published: June 2018

Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. Some major philosophical issues in molecular biology are as follows: First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on laws of nature and comports well with molecular discovery. Second, reductionism continues to be debated and increasingly rejected by scientists. Philosophers have likewise moved away from reduction towards integration across fields or integrative explanations covering several levels of organisation. Third, although the gene concept has undergone substantial transformation and even fragmentation, it still enjoys widespread use by molecular biologists, which has prompted philosophers to understand the empirical reasons for this. At the same time, it has been argued that the notion of ‘genetic information’ is largely an empty metaphor, which generates the illusion of explanatory understanding without offering an adequate explanation of molecular and developmental mechanisms.

Key Concepts

Mechanistic explanation yields a notion of explanation for molecular biology that does not have to invoke laws of nature.

Philosophical accounts of mechanistic explanation mesh well with how discovery in molecular biology works.

The idea that all biological knowledge can be reduced to one fundamental theory or that all explanations are reductive has largely been abandoned.

Reductionism tends to be replaced in favour of integration across fields or explanations combining features from different levels of organisation.

The concept of the gene has undergone substantial transformation throughout its history. Despite its more recent fragmentation, the gene concept is still widely used.

The notion of ‘genetic information’ is largely a metaphor, generating the illusion of explanatory understanding, and cannot be articulated in a manner conforming to mechanistic explanations of molecular and developmental processes.
Deconstructing Gene Function throughENUMutagenesis
Authors: Potter Paul K
Published: June 2018

A great majority of genes present in the human genome are also present in the mouse, thus making it an attractive mammalian model organism to study gene function and dysfunction. Over the past few decades, the ability to manipulate the mouse genome has been developed in a variety of ways. A complementary methodology to create mutations in the mouse is to use chemical mutagenesis.N‐ethyl‐N‐Nitrosourea (ENU) is the mutagen of choice for creating random point mutations model organisms. Advances in sequencing technologies have resulted in a rapid identification of the causative mutation. ENU mutagenesis is a powerful hypothesis‐generating approach to create new mouse models through both forward and reverse genetics approaches. Furthermore, the addition of challenges can identify mutations affecting specific pathways, and specific mutant lines or strains can be used to identify modifiers.

Key Concepts

ENU produces mainly point mutations randomly throughout the genome.

ENU mutagenesis can be used in both forward and reverse genetics approaches.

ENU phenotype‐driven screens do not require previous knowledge of the gene to create new mouse models or reveal gene function.

ENU phenotype‐driven screens can assign functions to specific protein domains.

ENU phenotype‐driven screens identify new mouse models by means of phenotyping.

High‐throughput sequencing technologies mean that the identification of the mutation underlying an observed phenotype is very rapid.

Phenotype‐driven screens can be applied along with specific challenges or mutations to reveal mutations affecting specific pathways or which modify existing phenotypes.
Activation‐Induced Deaminase
Authors: Petersen‐Mahrt Svend , Conticello Silvestro , Munagala Uday
Published: June 2018

Activation‐induced deaminase is a simple evolutionary tool that nature has utilised to create a very powerful immune system. Hydrolytic deamination is one of the most ancient of enzymatically catalysed reactions, and yet in the context of deoxyribonucleic acid (DNA) can lead to wanted mutations and chromosomal rearrangements in the humoral immune system, changes in the epigenome and inactivation of foreign DNA. While on the dark side, it can lead to oncogenic mutations and translocations across the whole genome and serve as a conduit for nonmutagenic compounds to become mutagenic.

Key Concepts

AID is the ancestor to APOBEC1, and unlike APOBEC1, AID's enzymatic activity is restricted to DNA.

AID does not act on cytidine (the RNA nucleoside); hence, it should be classified as activation‐induced deoxy‐cytosine deaminase, or simply activation‐induced deaminase (AID).

AID was the first enzyme discovered to actively induce DNA lesions as part of its physiological function.

Nearly 70% of all cancer mutations are derived from the AID/APOBEC family.

Environmental factors (e.g. oestrogen) can drive AID expression, allowing for nonmutagenic compounds to elicit oncogenic mutations.

AID can be expressed in various tissues and lead to local and global DNA instability.

AID's ability to deaminate 5‐methyl cytosine can lead to active DNA demethylation and epigenetic reprogramming.

The physiological mutation activity of AID can be harnessed in new tools of biotechnology for
in vivo
genome editing.
Genetics of the Retinal Dystrophies
Authors: Merepa Solomon S , Broadgate Suzanne , Sekaran Sumathi , Halford Stephanie
Published: June 2018

The inherited retinal dystrophies (IRDs) are a group of heterogeneous disorders that individually are rare, but collectively have an incidence of 1 in 2000–3000 affecting an estimated 2 million people worldwide. The main cause of vision loss is the death or dysfunction of the photoreceptors, the rods and cones, leading to either partial or total blindness. To date, over 260 genes underlying the monogenic forms of IRDs have been identified, but there are still many to find. These disorders exhibit a wide range of phenotypes with significant overlap, but they can be broadly subdivided on the basis of retinal cell type affected. Understanding the underlying genetic cause enables patients to get a definitive diagnosis and in turn allows the development of therapies targeted to a specific gene defect, with both gene therapy and gene‐editing techniques showing great potential and suggesting a promising future for people living with these conditions.

Key Concepts

The retina is the photosensitive tissue that lines the inside of the eye; it is multilayered and is composed of highly specialised cells that receive and process light information.

The inherited retinal dystrophies are a group of diseases that individually are rare, but collectively affect approximately 2 million people worldwide.

The main cause of vision loss is the death or dysfunction of the photoreceptors, the rods and cones, leading to either partial or total blindness.

Most inherited retinal dystrophies have been found to be caused by monogenic mutations in genes, although more complex forms, such as age‐related macular degeneration (AMD), caused by an interplay of genetic, environmental and lifestyle factors, also exist.

To date, more than 260 genes have been identified that cause monogenic retinal degeneration in humans.

The most common inherited retinal degeneration is retinitis pigmentosa (RP). More than 70 genes have been found to cause RP and can be inherited in an X‐linked, autosomal dominant or autosomal recessive manner.

IRDs exhibit both genetic and phenotypic heterogeneity, meaning that different genes can cause the same disease, and the same mutation can cause different disease phenotypes in different individuals. This means that there is a significant overlap between disorders often making a clear‐cut diagnosis difficult.

Recent advances in molecular genetics have seen gene therapy trials show some success in patients, but most conditions remain without a cure; however, recent advances in molecular technology have improved our understanding of IRDs and will further aid development of therapies with gene‐editing techniques an exciting prospect.
Solution‐Processable Near‐Infrared–Responsive Composite of Perovskite Nanowires and Photon‐Upconversion Nanoparticles
Authors: Yang Bingxiao , Wang Yangbo , Wei Tian , Pan Yue , Zhou Enlong , Yuan Ze , Han Yingdong , Li Mengxue , Ling Xincan , Yin Lisha , Xie Xiaoji , Huang Ling
Published: June 2018

Organolead halide perovskites (OHPs) have shown unprecedented potentials in optoelectronics. However, the inherent large bandgap has restrained its working wavelength within 280–800 nm, while light at other regions, e.g., near‐infrared (NIR), may cause drastic thermal heating effect that goes against the duration of OHP devices, if not properly exploited. Herein, a solution processable and large‐scale synthesis of multifunctional OHP composites containing lanthanide‐doped upconversion nanoparticles (UCNPs) is reported. Upon NIR illumination, the upconverted photons from UCNPs at 520–550 nm can be efficiently absorbed by closely surrounded OHP nanowires (NWs) and photocurrent is subsequently generated. The narrow full width at half maximum of the absorption of rare earth ions (Yb3+ and Er3+) has ensured high‐selective NIR response. Lifetime characterizations have suggested that Förster resonance energy transfer with an efficiency of 28.5% should be responsible for the direct energy transfer from UCNPs to OHP NWs. The fabricated proof‐of‐concept device has showcased perfect response to NIR light at 980 and 1532 nm, which has paved new avenues for applications of such composites in remote control, distance measurement, and stealth materials.
Emerging Nonaqueous Aluminum‐Ion Batteries: Challenges, Status, and Perspectives
Authors: Zhang Yu , Liu Shiqi , Ji Yongjun , Ma Jianmin , Yu Haijun
Published: June 2018

Aluminum‐ion batteries (AIBs) are regarded as viable alternatives to lithium‐ion technology because of their high volumetric capacity, their low cost, and the rich abundance of aluminum. However, several serious drawbacks of aqueous systems (passive film formation, hydrogen evolution, anode corrosion, etc.) hinder the large‐scale application of these systems. Thus, nonaqueous AIBs show incomparable advantages for progress in large‐scale electrical energy storage. However, nonaqueous aluminum battery systems are still nascent, and various technical and scientific obstacles to designing AIBs with high capacity and long cycling life have not been resolved until now. Moreover, the aluminum cell is a complex device whose energy density is determined by various parameters, most of which are often ignored, resulting in failure to achieve the maximum performance of the cell. The purpose here is to discuss how to further develop reliable nonaqueous AIBs. First, the current status of nonaqueous AIBs is reviewed based on statistical data from the literature. The influence of parameters on energy density is analyzed, and the current situation and existing problems are summarized. Furthermore, possible solutions and concerns regarding the construction of reliable nonaqueous AIBs are comprehensively discussed. Finally, future research directions and prospects in the aluminum battery field are proposed.
Carbon‐Quantum‐Dots‐Loaded Ruthenium Nanoparticles as an Efficient Electrocatalyst for Hydrogen Production in Alkaline Media
Authors: Li Weidong , Liu Yuan , Wu Min , Feng Xiaolei , Redfern Simon A. T. , Shang Yuan , Yong Xue , Feng Tanglue , Wu Kaifeng , Liu Zhongyi , Li Baojun , Chen Zhimin , Tse John S. , Lu Siyu , Yang Bai
Published: June 2018

Highly active, stable, and cheap Pt‐free catalysts for the hydrogen evolution reaction (HER) are facing increasing demand as a result of their potential use in future energy‐conversion systems. However, the development of HER electrocatalysts with Pt‐like or even superior activity, in particular ones that can function under alkaline conditions, remains a significant challenge. Here, the synthesis of a novel carbon‐loaded ruthenium nanoparticle electrocatalyst (Ru@CQDs) for the HER, using carbon quantum dots (CQDs), is reported. Electrochemical tests reveal that, even under extremely alkaline conditions (1 m KOH), the as‐formed Ru@CQDs exhibits excellent catalytic behavior with an onset overpotential of 0 mV, a Tafel slope of 47 mV decade−1, and good durability. Most importantly, it only requires an overpotential of 10 mV to achieve the current density of 10 mA cm−2. Such catalytic characteristics are superior to the current commercial Pt/C and most noble metals, non‐noble metals, and nonmetallic catalysts under basic conditions. These findings open a new field for the application of CQDs and add to the growing family of metal@CQDs with high HER performance.
Remote Control over Underwater Dynamic Attachment/Detachment and Locomotion
Authors: Ma Yanfei , Ma Shuanhong , Wu Yang , Pei Xiaowei , Gorb Stanislav N. , Wang Zuankai , Liu Weimin , Zhou Feng
Published: June 2018

Despite extensive efforts to mimic the fascinating adhesion capability of geckos, the development of reversible adhesives underwater has long been lagging. The appearance of mussels‐inspired dopamine chemistry has provided the feasibility to fabricate underwater adhesives; however, for such a system, imitating the reversible and fast dynamic attachment/detachment mechanism of gecko feet still remains unsolved. Here, by synthesizing a thermoresponsive copolymer of poly(dopamine methacrylamide‐co‐methoxyethyl‐acrylate‐co‐N‐isopropyl acrylamide) and then decorating it onto mushroom‐shaped poly(dimethylsiloxane) pillar arrays, a novel underwater thermoresponsive gecko‐like adhesive (TRGA) can be fabricated, yielding high adhesion during the attachment state above the lower critical solution temperature (LCST) of the copolymer, yet low adhesion during the detachment state below the LCST of the copolymer. By integrating the Fe3O4 nanoparticles into the TRGA, TRGAs responsive to near‐infrared laser radiation can be engineered, which can be successfully used for rapid and reversible remote control over adhesion so as to capture and release heavy objects underwater because of the contrast force change of both the normal adhesion force and the lateral friction force. It is also demonstrated that the material can be assembled on the tracks of an underwater mobile device to realize controllable movement. This opens up the door for developing intelligent underwater gecko‐like locomotion with dynamic attachment/detachment ability.
Self‐Folded Gripper‐Like Architectures from Stimuli‐Responsive Bilayers
Authors: Abdullah Arif M. , Li Xiuling , Braun Paul V. , Rogers John A. , Hsia K. Jimmy
Published: June 2018

Self‐folding microgrippers are an emerging class of smart structures that have widespread applications in medicine and micro/nanomanipulation. To achieve their functionalities, these architectures rely on spatially patterned hinges to transform into 3D configurations in response to an external stimulus. Incorporating hinges into the devices requires the processing of multiple layers which eventually increases the fabrication costs and actuation complexities. The goal of this work is to demonstrate that it is possible to achieve gripper‐like configurations in an on‐demand manner from simple planar bilayers that do not require hinges for their actuation. Finite element modeling of bilayers is performed to understand the mechanics behind their stimuli‐responsive shape transformation behavior. The model predictions are then experimentally validated and axisymmetric gripper‐like shapes are realized using millimeter‐scale poly(dimethylsiloxane) bilayers that undergo differential swelling in organic solvents. Owing to the nature of the computational scheme which is independent of length scales and material properties, the guidelines reported here would be applicable to a diverse array of gripping systems and functional devices. Thus, this work not only demonstrates a simple route to fabricate functional microgrippers but also contributes to self‐assembly in general.
Defect‐Enhanced Charge Separation and Transfer within Protection Layer/Semiconductor Structure of Photoanodes
Authors: Zheng Jianyun , Lyu Yanhong , Xie Chao , Wang Ruilun , Tao Li , Wu Haibo , Zhou Huaijuan , Jiang Sanping , Wang Shuangyin
Published: June 2018

Silicon (Si) requires a protection layer to maintain stable and long‐time photoanodic reaction. However, poor charge separation and transfer are key constraint factors in protection layer/Si photoanodes that reduce their water‐splitting efficiency. Here, a simultaneous enhancement of charge separation and transfer in Nb‐doped NiOx/Ni/black‐Si photoanodes induced by plasma treatment is reported. The optimized photoanodes yield the highest charge‐separation efficiency (ηsep) of ≈81% at 1.23 V versus reversible hydrogen electrode, corresponding to the photocurrent density of ≈29.1 mA cm−2. On the basis of detailed characterizations, the concentration and species of oxygen defects in the NiOx‐based layer are adjusted by synergistic effect of Nb doping and plasma treatment, which are the dominating factors for forming suitable band structure and providing a favorable hole‐migration channel. This work elucidates the important role of oxygen defects on charge separation and transfer in the protection layer/Si‐based photoelectrochemical systems and is encouraging for application of this synergistic strategy to other candidate photoanodes.
A General Approach for Fluid Patterning and Application in Fabricating Microdevices
Authors: Huang Zhandong , Yang Qiang , Su Meng , Li Zheng , Hu Xiaotian , Li Yifan , Pan Qi , Ren Wanjie , Li Fengyu , Song Yanlin
Published: June 2018

Engineering the fluid interface such as the gas–liquid interface is of great significance for solvent processing applications including functional material assembly, inkjet printing, and high‐performance device fabrication. However, precisely controlling the fluid interface remains a great challenge owing to its flexibility and fluidity. Here, a general method to manipulate the fluid interface for fluid patterning using micropillars in the microchannel is reported. The principle of fluid patterning for immiscible fluid pairs including air, water, and oils is proposed. This understanding enables the preparation of programmable multiphase fluid patterns and assembly of multilayer functional materials to fabricate micro‐optoelectronic devices. This general strategy of fluid patterning provides a promising platform to study the fundamental processes occurring on the fluid interface, and benefits applications in many subjects, such as microfluidics, microbiology, chemical analysis and detection, material synthesis and assembly, device fabrication, etc.
A Micro‐Ark for Cells: Highly Open Porous Polyhydroxyalkanoate Microspheres as Injectable Scaffolds for Tissue Regeneration
Authors: Wei Dai‐Xu , Dao Jin‐Wei , Chen Guo‐Qiang
Published: June 2018

To avoid large open surgery using scaffold transplants, small‐sized cell carriers are employed to repair complexly shaped tissue defects. However, most cell carriers show poor cell adherences and viability. Therefore, polyhydroxyalkanoate (PHA), a natural biopolymer, is used to prepare highly open porous microspheres (OPMs) of 300–360 µm in diameter, combining the advantages of microspheres and scaffolds to serve as injectable carriers harboring proliferating stem cells. In addition to the convenient injection to a defected tissue, and in contrast to poor performances of OPMs made of polylactides (PLA OPMs) and traditional less porous hollow microspheres (PHA HMs), PHA OPMs present suitable surface pores of 10–60 µm and interconnected passages with an average size of 8.8 µm, leading to a high in vitro cell adhesion of 93.4%, continuous proliferation for 10 d and improved differentiation of human bone marrow mesenchymal stem cells (hMSCs). PHA OPMs also support stronger osteoblast‐regeneration compared with traditional PHA HMs, PLA OPMs, commercial hyaluronic acid hydrogels, and carrier‐free hMSCs in an ectopic bone‐formation mouse model. PHA OPMs protect cells against stresses during injection, allowing more living cells to proliferate and migrate to damaged tissues. They function like a micro‐Noah's Ark to safely transport cells to a defect tissue.
Local pH and Its Evolution Near Mg Alloy Surfaces Exposed to Simulated Body Fluids
Authors: Lamaka Sviatlana V. , Gonzalez Jorge , Mei Di , Feyerabend Frank , Willumeit‐Römer Regine , Zheludkevich Mikhail L.
Published: June 2018

Many reports are available on degradation rates and corrosion product characterization of magnesium alloys for implant application. Typically, the data are obtained ex situ, as post factum analysis of occurred degradation processes or in bulk electrolyte that does not fully reflect concentration gradients at the interface and in the diffusion layer. Meanwhile, these local conditions are essential for tissue‐implant compatibility. Only a limited number of studies employ the techniques that visualize ongoing degradation and are localized enough to observe the changes in the electrolyte layer directly adjacent to corroding magnesium. Here, local pH in Hank's solution is studied in operando, with potentiometric micro‐probes (d = 2 µm) located 10–50 µm above the surface of four Mg alloys potentially relevant for implant applications. A significant difference in local pH is observed for Mg in simple Hank's solution (near surface pH 9.9–10.5) or Hank's solution modified with 2.5 × 10−3
m Ca2+ (pH 7.8–8.5). The corresponding pH values are established during the first seconds of immersion. These findings indicate different degradation kinetics in electrolytes with or without Ca2+. The degradation rate of Mg alloys decreases by almost two times in Ca2+ containing Hank's solution. Calcium‐phosphate/carbonate protective layer stabilizes the surface pH below 8.5 controlling Mg degradation.
Recent Progress in Durable and Self‐Healing Super‐Nonwettable Fabrics
Authors: Zhou Hua , Wang Hongxia , Niu Haitao , Lin Tong
Published: June 2018

Considerable interest has been devoted to the development of super‐nonwettable (SNW) fabrics owing to their novel functions and enormous potential for applications in diverse fields. The key to practical applications of super‐nonwettable fabrics is durability against various damages. Novel strategies have been developed to improve the durability of SNW fabrics. To mimic regeneration ability of natural SNW surfaces, self‐healing is introduced. This review summarizes the recent research progress in super‐nonwettable fabrics. It summarizes commonly used SNW properties including superhydrophobic–superoleophilic, superhydrophobic–superoleophobic (i.e., superamphiphobic), superoleophobic–superhydrophilic, and underwater superoleophobic fabrics. Strategies to fabricate durable SNW coatings on fabrics are discussed. Special attention is paid toward self‐healing SNW fabrics. A perspective on the future development in this field is also provided.
Recent Advances in the Electrochemical α‐C–H Bond Functionalization of Carbonyl Compounds
Authors: Liang Sen , Xu Kun , Zeng Cheng‐Chu , Tian Hong‐Yu , Sun Bao‐Guo
Published: June 2018

The α‐C–H functionalization of carbonyl compounds represents a cornerstone of organic chemistry. Site‐selective α‐C−H bond functionalization of carbonyl compounds to afford more versatile functionalized groups has become a promising strategy for atom‐economical C−C and C−X bond formation. Organic electrosynthesis is revolutionizing the nature of organic synthesis, and this field has seen explosive growth in recent years. In this review, we discuss advances in the use of electrochemistry for the α‐C–H oxidative functionalization of carbonyl compounds published since 2000.

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Training for Failure: A Simulation Program for Emergency Medicine Residents to Improve Communication Skills in Service Recovery
Authors: Frallicciardi Alise , Lotterman Seth , Ledford Matthew , Prenovitz Ilana , Meter Rochelle Van , Kuo Chia‐Ling , Nowicki Thomas , Fuller Robert
Published: June 2018

Objectives

Service failures such as long waits, testing delays, and medical errors are daily occurrences in every emergency department (ED). Service recovery refers to the immediate response of an organization or individual to resolve these failures. Effective service recovery can improve the experience of both the patient and the physician. This study investigated a simulation‐based program to improve service recovery skills in postgraduate year 1 emergency medicine (PGY‐1 EM) residents.

Methods

Eighteen PGY‐1 EM residents participated in six cases that simulated common ED service failures. The patient instructors (PIs) participating in each case and two independent emergency medicine (EM) faculty observers used the modified Master Interview Rating Scale to assess the communication skills of each resident in three simulation cases before and three simulation cases after a service recovery debriefing. For each resident, the mean scores of the first three cases and those of the last three cases were termed pre‐ and postintervention scores, respectively. The means and standard deviations of the pre‐ and postintervention scores were calculated by the type of rater and compared using paired t‐tests. Additionally, the mean scores of each case were summarized. In the framework of the linear mixed‐effects model, the variance in scores from the PIs and faculty observers was decomposed into variance contributed by PIs/cases, the program effect on individual residents, and the unexplained variance. In reliability analyses, the intraclass correlation coefficient between rater types and the 95% confidence interval were reported before and after the intervention.

Results

When rated by the PIs, the pre‐ and postintervention scores showed no difference (p = 0.852). In contrast, when scored by the faculty observers, the postintervention score was significantly improved compared to the preintervention score (p < 0.001). In addition, for the faculty observers, the program effect was a significant contributor to the variation in scores. Low intraclass correlation was observed between rater groups.

Conclusions

This innovative simulation‐based program was effective at teaching service recovery communication skills to residents as evaluated by EM faculty, but not PIs. This study supports further exploration into programs to teach and evaluate service recovery communication skills in EM residents.
Central Doping of a Foreign Atom into the Silver Cluster for Catalytic Conversion of CO2 toward C−C Bond Formation
Authors: Liu Yuanyuan , Chai Xiaoqi , Cai Xiao , Chen Mingyang , Jin Rongchao , Ding Weiping , Zhu Yan
Published: June 2018

Clusters with an exact number of atoms are of particular interest in catalysis. Their catalytic behaviors can be potentially altered with the addition or removal of a single atom. Now the effects of doping with a single foreign atom (Au, Pd, and Pt) into the core of an Ag cluster with 25 atoms on the catalytic properties are explored, where the foreign atom is protected by 24 Ag atoms (Au@Ag24, Pd@Ag24, and Pt@Ag24). The central doping of a single atom into the Ag25 cluster has a substantial influence on the catalytic performance in the carboxylation reaction of CO2 with terminal alkyne through C−C bond formation to produce propiolic acid. These studies reveal that the catalytic properties of the cluster catalysts can be dramatically changed with the subtle alteration by a single atom away from the active sites.
Internal transcribed spacer 2 (ITS2) barcodes: A useful tool for identifying Chinese Zanthoxylum
Authors: Zhao Li‐Li , Feng Shi‐Jing , Tian Jie‐Yun , Wei An‐Zhi , Yang Tu‐Xi
Published: June 2018

Premise of the Study

The genus Zanthoxylum in the Rutaceae family of trees and shrubs has a long history of domestication and cultivation in Asia for both economic and medicinal purposes. However, many Zanthoxylum species are morphologically similar and are easily confused. This often leads to false authentication of source materials and confusion in herbal markets, hindering their safe utilization and genetic resource conservation. DNA barcoding is a promising tool for identifying plant taxa.

Methods

We used three candidate DNA barcoding regions (ITS2, ETS, and trnH‐psbA) to identify 69 accessions representing 13 Chinese Zanthoxylum species. The discriminatory capabilities of these regions were evaluated in terms of PCR amplification success, intra‐ and interspecific divergence, DNA barcoding gaps, and identification efficiency using the BLAST and tree‐building methods.

Results

ITS2 proved the most useful for discriminating Chinese Zanthoxylum species, with a correct identification rate of 100%, and this region also exhibited significantly higher intra‐ and interspecific divergence.

Discussion

Phylogenetic analysis confirmed that ITS2 has a powerful discriminatory ability both at and below the species level. We confirmed that ITS2 is a powerful barcoding region for identifying Chinese Zanthoxylum species, and will be useful for analyzing and managing Chinese Zanthoxylum germplasm collections.
Application of the Hirsch Generic Convergence Statement to the Set‐Point Regulation of Excitable‐Transparent‐Monotone Systems
Authors: Agahi Hamed
Published: June 2018

Monotone systems are dynamical systems whose solutions preserve an ordering, relative to the initial data. This paper focuses on the set‐point regulation problem for excitable‐transparent‐monotone single‐input single‐output systems with well‐defined static characteristics. The suggested technique for designing a static feedback controller is inspired from the Hirsch Theorem for monotone autonomous systems. It is shown that the closed‐loop system is strongly monotone and its generic solution converges to the desired set‐point. A remark is given on the application of the suggested design methodology to delay systems, as well as to systems with reaction‐diffusion equations. A simulation example from the biological world demonstrates the effectiveness of the proposed control strategy in real applications.
Surveillance of microcephaly and selected brain anomalies in Argentina: Relationship with Zika virus and other congenital infections
Authors: Tellechea Ana Laura , Luppo Victoria , Morales María Alejandra , Groisman Boris , Baricalla Agustin , Fabbri Cintia , Sinchi Anabel , Alonso Alicia , Gonzalez Cecilia , Ledesma Bibiana , Masi Patricia , Silva María , Israilev Adriana , Rocha Marcela , Quaglia Marcela , Bidondo María Paz , Liascovich Rosa , Barbero Pablo ,   RENAC Task Force
Published: June 2018

Background

Zika virus (ZIKV) vertical transmission may lead to microcephaly and other congenital anomalies. In March and April 2016, the first outbreak of ZIKV occurred in Argentina. The objective was to describe the surveillance of newborns with microcephaly and other selected brain anomalies in Argentina, and evaluation different etiologies.

Methods

Participants were enrolled between April 2016 and March 2017.

Cases

newborns from the National Network of Congenital Abnormalities of Argentina (RENAC) with head circumference lower than the 3rd percentile according to gestational age and sex, or selected brain anomalies. Blood and urine samples from cases and their mothers were tested for ZIKV by real‐time polymerase chain reaction (RT‐PCR), antigen‐specific Immunoglobulin M (MAC‐ELISA) and plaque‐reduction neutralization test (PRNT90). Toxoplasmosis, rubella, herpes simplex, syphilis, and cytomegalovirus (CMV) infection were also tested.

Results

A total of 104 cases were reported, with a prevalence of 6.9 per 10,000 [95% confidence interval (CI): 5.7–8.4], a significant increase when compared with the data prior to 2016, Prevalence Rate Ratio 1.7 (95% CI 1.2–2.3). In five cases positive serology for ZIKV (IgM and IgG by PRNT) was detected. The five cases presented microcephaly with craniofacial disproportion. We detected four cases of CMV infection, three cases of congenital toxoplasmosis, two cases of herpes simplex infection, and one case of congenital syphilis.

Conclusion

The prevalence of microcephaly was significantly higher when compared with the previous period. The system had the capacity to detect five cases with congenital ZIKV syndrome in a country with limited viral circulation.
Bone development in laboratory mammals used in developmental toxicity studies
Authors: DeSesso John M. , Scialli Anthony R.
Published: June 2018

Evaluation of the skeleton in laboratory animals is a standard component of developmental toxicology testing. Standard methods of performing the evaluation have been established, and modification of the evaluation using imaging technologies is under development. The embryology of the rodent, rabbit, and primate skeleton has been characterized in detail and summarized herein. The rich literature on variations and malformations in skeletal development that can occur in the offspring of normal animals and animals exposed to test articles in toxicology studies is reviewed. These perturbations of skeletal development include ossification delays, alterations in number, shape, and size of ossification centers, and alterations in numbers of ribs and vertebrae. Because the skeleton is undergoing developmental changes at the time fetuses are evaluated in most study designs, transient delays in development can produce apparent findings of abnormal skeletal structure. The determination of whether a finding represents a permanent change in embryo development with adverse consequences for the organism is important in study interpretation. Knowledge of embryological processes and schedules can assist in interpretation of skeletal findings.
Expression of genes encoding the luciferase from Photobacterium leiognathi in Escherichia coli Rosetta (DE3) and its application in NADH detection
Authors: Xuan Guanhua , Xiao Qilin , Wang Jingxue , Lin Hong , Pavase Tushar
Published: June 2018

Cloning of genes encoding the luciferase from Photobacterium leiognathi YL in Escherichia coli Rosetta (DE3) was performed successfully and the expressed forms of lux AB were purified to homogeneity. Experimental measurements revealed that luciferase from Photobacterium leiognathi YL has good thermal stability and a high residual activity at extreme pH values, which are extremely important for its various ecological, industrial and medical applications. Furthermore, we made a first attempt for quantitative detection of NADH by recombinant E. coli Rosetta (DE3) coupled enzyme system. A good linear relationship between luminescence intensity and NADH with low (1–12 nmol/L) and high (10–500 nmol/L) concentration was observed, whose standard curve was y = 772.97× + 4041.1, R2 = 0.9884 and y = 1710× + 4.99 × 105, R2 = 0.9727, respectively. Our results demonstrate a high sensitivity of recombinant E. coli coupled enzyme system to NADH on the basis of high soluble expression of recombinant luciferase and continuous and stable expression of some NAD(P)H‐dependent flavin mononucleotide (FMN) reductases.
Bimolecular fluorescence quenching reactions of the biologically active coumarin composite 2‐acetyl‐3H‐benzo[f]chromen‐3‐one in different solvents
Authors: Koppal V. V. , Melavanki R. M. , Kusanur R. A. , Patil N. R.
Published: June 2018

A study on fluorescence quenching was carried out for the coumarin derivative 2‐acetyl‐3H‐benzo[f]chromen‐3‐one (2AHBC) with aniline at room temperature. Efficient fluorescence quenching was observed and Stern–Volmer (S–V) plots showed upward curves from linearity in all solvents of different polarities. For the solute 2AHBC, ground state complex formation does not hold in our study. The kinetic distance (r) value was found to be greater than the encounter distance (R) and indicated that the quenching reaction was held within the sphere of action. Diffusion‐limited reactions were found to be more prominent in high polarity solvents, namely dimethyl sulfoxide (DMSO), DMF, ACN, methanol, ethanol, propanol and DCM. The relationships between quenching constant (KSV) and dielectric constants (ε) of the different solvents were studied.
Meta‐Analysis of Publicly Available Chinese Hamster Ovary (CHO) Cell Transcriptomic Datasets for Identifying Engineering Targets to Enhance Recombinant Protein Yields
Authors: Tamošaitis Linas , Smales Christopher Mark
Published: June 2018

Transcriptomics has been extensively applied to the investigation of the CHO cell platform for the production of recombinant biotherapeutic proteins to identify transcripts whose expression is regulated and correlated to (non)desirable CHO cell attributes. However, there have been few attempts to analyze the findings across these studies to identify conserved changes and generic targets for CHO cell platform engineering. Here, the authors have undertaken a meta‐analysis of CHO cell transcriptomic data and report on those genes most frequently identified as differentially expressed with regard to cell growth (μ) and productivity (Qp). By aggregating differentially expressed genes from publicly available transcriptomic datasets associated with μ and Qp, using a pathway enrichment analysis and combining it with the concordance of gene expression values, the authors have identified a refined target gene and pathway list while determining the overlap across CHO transcriptomic studies. The authors find that only the cell cycle and lysosome pathways show good concordance. By mapping out the contributing genes the authors have constructed a transcriptomic “fingerprint” of a high‐performing cell line. This study provides a starting resource for researchers who want to navigate the complex landscape of CHO transcriptomics and identify targets to undertake cell engineering for improved recombinant protein output.
Protective effects of timosaponin BII on oxidative stress damage in PC12 cells based on metabolomics
Authors: Xie Qinmei , Zhao Hongxia , Li Na , Su Li , Xu Xu , Hong Zhanying
Published: June 2018

Peroxide and oxygen free radicals are some of the causes of oxidative stress in brain tissue, and could lead to the change of brain structure and function. In addition, oxidative damage is one of the most important causes of the aging of the vast majority of tissues. The aim of this study is to investigate the protective effect of timosaponin BII on oxidative stress damage of PC12 induced by H2O2 using metabolomics based on the UHPLC‐Q‐TOF‐MS technique. Partial least‐squares discriminant analysis method was used to identify 35 metabolites as decisive marker compounds in a preliminary interpretation of the mechanism of the antioxidative effect of timosaponin BII. The majority of these metabolites are involved in the glutathione metabolism, amino acid metabolism, sphingolipid and glycerophospholipid metabolism. Our results suggest that timosaponin BII demonstrates systematic antioxidant effects in the PC12 oxidative damage cell model via the regulation of multiple metabolic pathways. These findings provide insight into the pathophysiological mechanisms underlying oxidative stress damage and suggest innovative and effective treatments for this disorder, providing a reliable basis for the development of novel therapeutic target in timosaponin BII treatment of oxidative stress.
Simple Route for the Synthesis of Highly Active Bimetallic Nanoparticle Catalysts with Immiscible Ru and Ni Combination by utilizing a TiO2 Support
Authors: Masuda Shinya , Mori Kohsuke , Sano Taiki , Miyawaki Kohei , Chiang Wei‐Hung , Yamashita Hiromi
Published: June 2018

TiO2 support was proven to be acted as an efficient platform for the synthesis of RuNi bimetallic alloy, which are essentially immiscible at most of equilibrium composition, by simple impregnation followed by H2 reduction at 300 °C. Characterization by means of HAADF‐STEM and EDX analysis confirmed the formation of RuNi bimetallic nanoparticles (NPs) with a mean diameter of 2.3 nm. H2‐TPR and in situ XAFS measurements suggested the intraparticle hydrogen spillover mechanism on the surface of TiO2, which originated from the improved reducibility of the Ni species and retarded reducibility of the Ru species in comparison with those for the monometallic samples. RuNi/TiO2 catalyst exhibits remarkably high catalytic activity for the dehydrogenation from ammonia borane (AB, NH3BH3) (TOF=914 min−1) compared with those prepared with other conventional supports. DFT calculation study also suggested the synergistic alloying effect due to the random distribution of Ru−Ni NPs plays a crucial role in the improvement of the adsorption energy of AB, which ultimately resulted in the exceptional catalytic performance.
Facile Synthesis of S‐Substituted L‐Cysteines with Nano‐sized Immobilized O‐Acetylserine Sulfhydrylase
Authors: Vahidi Akbar K. , Wang Zunsheng , Li Zhi
Published: June 2018

Many S‐substituted l‐cysteines are useful pharmaceutical intermediates but require a simple synthesis method. Here we developed enzymatic synthesis of several S‐aryl‐l‐cysteines and S‐benzyl‐l‐cysteine directly from O‐acetylserine (OAS) with immobilized O‐acetylserine sulfhydrylase CysM. Novel iron‐oxide magnetic nanoparticles (MNPs) with cobalt‐nitrilotriacetic acid function were prepared with a diameter of 80 nm in 75 % yield. Direct immobilization of His‐tagged CysM in the cell‐free extract on the MNPs via affinity attachment afforded stable nanobiocatalyst with 97 % enzyme loading efficiency and 93 % free enzyme activity. The immobilized enzyme catalyzed the biotransformation of benzylthiol and OAS to give S‐benzyl‐l‐cysteine in 88 % yield. The nanobiocatalyst also demonstrated high recyclability, retaining 95 % productivity in the fifth cycle. The immobilized CysM accepts various arylthiols to react with OAS, giving rise to a new synthesis route of several S‐substituted l‐cysteines in 60–96 % yield.
Direct Observation of Interfacial Charge Transfer between Rutile TiO2 and Ultrathin CuOx Film by Visible‐Light Illumination and Its Application for Efficient Photocatalysis
Authors: Osako Kazutaka , Matsuzaki Kosuke , Susaki Tomofumi , Ueda Shigenori , Yin Ge , Yamaguchi Akira , Hosono Hideo , Miyauchi Masahiro
Published: June 2018

A well‐defined interface between CuOx film and TiO2 is constructed as a model for elucidating the interfacial charge transfer (IFCT) process that occurs during photocatalysis. Spectroscopic analysis revealed strong blue light absorption at 2.7 eV in this film system. Based on photoemission spectroscopy and the UV‐visible absorption analysis, the band offset of CuOx and TiO2 was investigated, and the observed blue absorption at 2.7 eV could be explained by an IFCT process, in which electrons in the valence band of TiO2 were excited into the conduction band of the ultrathin CuOx film. Furthermore, the IFCT transition was found to strongly depend on the crystal face of TiO2, as the IFCT absorption was significantly increased in the ultrathin CuOx film coated over the rutile TiO2 (110) substrate. Probe reduction and oxidation reactions were also used to investigate the charge transport process and determine photocatalytic reaction sites, which were located around a few nanometers‐scale region from the edge of the ultrathin CuOx and TiO2. The present findings provide a powerful method for the development of efficient visible‐light sensitive photocatalysts based on the IFCT concept.
Oxygen Electroreduction on Pt Nanoparticles Deposited on Reduced Graphene Oxide and N‐doped Reduced Graphene Oxide Prepared by Plasma‐assisted Synthesis in Aqueous Solution
Authors: Hussain Sajid , Erikson Heiki , Kongi Nadezda , Treshchalov Alexey , Rähn Mihkel , Kook Mati , Merisalu Maido , Matisen Leonard , Sammelselg Väino , Tammeveski Kaido
Published: June 2018

Platinum nanoparticles were deposited on reduced graphene oxide (rGO) and nitrogen‐doped rGO (rGO−N) by He/H2 plasma jet treatment of H2PtCl6 aqueous solution for electroreduction of oxygen. Physical characterization of the prepared catalysts was performed by scanning electron microscopy, transmission electron microscopy and X‐ray photoelectron spectroscopy. Electrochemical characterization was carried out by cyclic voltammetry and CO‐stripping techniques. The oxygen reduction reaction (ORR) activity of the prepared Pt/rGO and Pt/rGO−N catalyst materials was investigated using the rotating disk electrode method in 0.1 M KOH and 0.05 M H2SO4. In both acidic and alkaline electrolytes, the catalyst materials prepared by the plasma jet method demonstrated superior electrocatalytic properties compared to that of commercial 20 wt% Pt/C catalyst. Specific activity values for the ORR in acid electrolyte were 2‐fold and in alkaline media more than 3‐fold higher than that obtained for commercial Pt/C catalyst.
Self‐Supported Hierarchical Shell@Core Ni3S2@Ni Foam Composite Electrocatalyst with High Efficiency and Long‐Term Stability for Methanol Oxidation
Authors: Yuan Gang , Niu Xiaopo , Chen Zhichao , Wang Li , Zhang Xiangwen , Wang Qingfa
Published: June 2018

Direct methanol fuel cells are promising renewable energy devices for automobiles and portable electronic devices. The development of high effciency, poison tolerance, long‐term stability, and noble metal‐free electrocatalysts for methanol oxidation is still a major challenge. Herein, we develop a noble metal‐free, 3D self‐supported, defect‐rich, hierarchical shell‐core structured Ni3S2 composite on Ni foam as electrocatalyst. This electrocatalyst shows a good activity, poison tolerance, and long‐term durability towards methanol oxidation in alkaline media. It shows the lowest onset potential (−340 mV vs. Hg/HgO) among all the Ni‐based catalysts reported up to date and a Pt‐level specific activity. The methanol oxidation peak current of the electrocatalyst retains more than 97.5 % even after 5,000 voltammetry cycles in 0.5 M KOH+1 M CH3OH. The morphology and composition of the electrocatalysts before and after stability test were characterized by SEM, TEM, XRD, and XPS. The high activity, poison tolerance, and stability are attributed to the binder‐free, directly grown Ni3S2 shell on the Ni foam backbone, the lattice defect sites, and the synergetic eﬀects between the in‐situ formed active NiOx core and Ni3S2 shell during methanol oxidation. This work indicates that the self‐supported hierarchical shell‐core Ni3S2@Ni foam electrocatalyst is a viable alternative for commercial Pt‐based electrocatalyst applied in fuel cells.
A similarity index for comparing coupled matrices
Authors: Indahl Ulf G. , Næs Tormod , Liland Kristian Hovde
Published: June 2018

Application of different multivariate measurement technologies to the same set of samples is an interesting challenge in many fields of applied data analysis. Our proposal is a 2‐stage similarity index framework for comparing 2 matrices in this type of situation. The first step is to identify factors (and associated subspaces) of the matrices by methods such as principal component analysis or partial least squares regression to provide good (low‐dimensional) summaries of their information content. Thereafter, statistical significances are assigned to the similarity values obtained at various factor subset combinations by considering orthogonal projections or Procrustes rotations and how to express the results compactly in corresponding summary plots. Applications of the methodology include the investigation of redundancy in spectroscopic data and the investigation of assessor consistency or deviations in sensory science. The proposed methodology is implemented in the R‐package “MatrixCorrelation” available online from CRAN.