bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential predictability of skipjack tuna (Katsuwonus pelamis) catches in the Western Central Pacific
Authors: Kim Jihwan , Na Hanna , Park Young-Gyu , Kim Young Ho
Published: February 2020

The Pacific Island countries have a substantial socio-economic dependency on fisheries. Skipjack tuna is one of the most important species in the Western Central Pacific (WCP) and its catches in this region exhibit a spatio-temporal variability influenced by ocean conditions, mainly the El Niño-Southern Oscillation (ENSO). This study investigates the relationship between skipjack tuna catch amounts and environmental variables in the equatorial Pacific during 1990–2014, and evaluates the potential predictability of the catches based on their statistical relationship. A series of regressed and reconstructed spatial patterns of upper-ocean temperature, salinity, currents and precipitation represent ENSO-like variability, and their principal component time series are used to estimate the predictability of skipjack tuna catches in the Federated States of Micronesia (FSM). ENSO-like variability depicted from 100 m temperature and 5 m salinity in the equatorial Pacific exhibit a significant predictability for the annual catch amount in the FSM for several years with a training period of > 20 years. This suggests that the subsurface temperature or near surface salinity can be a better predictor of ecosystem variability than widely used sea surface temperature. Applications of this result to other species could have broad implications for the fishery industry in the WCP.
The role of initial speed in projectile impacts into light granular media
Authors: Huang Kai , Hernández-Delfin Dariel , Rech Felix , Dichtl Valentin , Hidalgo Raúl Cruz
Published: February 2020

Projectile impact into a light granular material composed of expanded polypropylene (EPP) particles is investigated systematically with various impact velocities. Experimentally, the trajectory of an intruder moving inside the granular material is monitored with a recently developed non-invasive microwave radar system. Numerically, discrete element simulations together with coarse-graining techniques are employed to address both dynamics of the intruder and response of the granular bed. Our experimental and numerical results of the intruder dynamics agree with each other quantitatively and are in congruent with existing phenomenological model on granular drag. Stepping further, we explore the ‘microscopic’ origin of granular drag through characterizing the response of granular bed, including density, velocity and kinetic stress fields at the mean-field level. In addition, we find that the dynamics of cavity collapse behind the intruder changes significantly when increasing the initial speed . Moreover, the kinetic pressure ahead of the intruder decays exponentially in the co-moving system of the intruder. Its scaling gives rise to a characteristic length scale, which is in the order of intruder size. This finding is in perfect agreement with the long-scale inertial dissipation type that we find in all cases.
Light-induced silencing of neural activity in Rosa26 knock-in and BAC transgenic mice conditionally expressing the microbial halorhodopsin eNpHR3
Authors: Imayoshi Itaru , Tabuchi Sawako , Matsumoto Mami , Kitano Satsuki , Miyachi Hitoshi , Kageyama Ryoichiro , Yamanaka Akihiro
Published: February 2020

An engineered light-inducible chloride pump, Natronomonas pharaonis halorhodopsin 3 (eNpHR3) enables temporally and spatially precise inhibition of genetically defined cell populations in the intact nervous tissues. In this report, we show the generation of new mouse strains that express eNpHR3-EYFP fusion proteins after Cre- and/or Flp-mediated recombination to optically inhibit neuronal activity. In these mouse strains, Cre/Flp recombination induced high levels of opsin expression. We confirmed their light-induced activities by brain slice whole-cell patch clamp experiments. eNpHR3-expressing neurons were optically hyperpolarized and silenced from firing action potentials. In prolonged silencing of action potentials, eNpHR3 was superior to eNpHR2, a former version of the engineered pump. Thus, these eNpHR3 mouse strains offer reliable genetic tools for light-induced inhibiting of neuronal activity in defined sets of neurons.
Tailored for Real-World: A Whole Slide Image Classification System Validated on Uncurated Multi-Site Data Emulating the Prospective Pathology Workload
Authors: Ianni Julianna D. , Soans Rajath E. , Sankarapandian Sivaramakrishnan , Chamarthi Ramachandra Vikas , Ayyagari Devi , Olsen Thomas G. , Bonham Michael J. , Stavish Coleman C. , Motaparthi Kiran , Cockerell Clay J. , Feeser Theresa A. , Lee Jason B.
Published: February 2020

Standard of care diagnostic procedure for suspected skin cancer is microscopic examination of hematoxylin & eosin stained tissue by a pathologist. Areas of high inter-pathologist discordance and rising biopsy rates necessitate higher efficiency and diagnostic reproducibility. We present and validate a deep learning system which classifies digitized dermatopathology slides into 4 categories. The system is developed using 5,070 images from a single lab, and tested on an uncurated set of 13,537 images from 3 test labs, using whole slide scanners manufactured by 3 different vendors. The system’s use of deep-learning-based confidence scoring as a criterion to consider the result as accurate yields an accuracy of up to 98%, and makes it adoptable in a real-world setting. Without confidence scoring, the system achieved an accuracy of 78%. We anticipate that our deep learning system will serve as a foundation enabling faster diagnosis of skin cancer, identification of cases for specialist review, and targeted diagnostic classifications.
MultiFRAGing: Rapid and Simultaneous Genotyping of Multiple Alleles in a Single Reaction
Authors: Petree Cassidy , Varshney Gaurav K.
Published: February 2020

Powerful and simple, RNA-guided CRISPR/Cas9 technology is a versatile genome editing tool that has revolutionized targeted mutagenesis. CRISPR-based genome editing has enabled large-scale functional genetic studies through the generation of gene knockouts in a variety of model organisms including zebrafish, and can be used to target multiple genes simultaneously. One of the challenges associated with the large scale application of this technique to zebrafish is the lack of a cost-effective method by which to identify mutants. To address this, we optimized the high-throughput, high-resolution fluorescent PCR-based fragment analysis method to develop MultiFRAGing - a robust and cost-effective method to genotype multiple targets in a single reaction. Our approach can identify indels in up to four targets from a single reaction, which represents a four-fold increase in genotyping throughput. This method can be used by any laboratory with access to capillary electrophoresis-based sequencing equipment.
Impaired motor skill learning and altered seizure susceptibility in mice with loss or gain of function of the Kcnt1 gene encoding Slack (KNa1.1) Na+-activated K+ channels
Authors: Quraishi Imran H. , Mercier Michael R. , McClure Heather , Couture Rachael L. , Schwartz Michael L. , Lukowski Robert , Ruth Peter , Kaczmarek Leonard K.
Published: February 2020

Gain-of-function mutations in KCNT1, the gene encoding Slack (KNa1.1) channels, result in epilepsy of infancy with migrating focal seizures (EIMFS) and several other forms of epilepsy associated with severe intellectual disability. We have generated a mouse model of this condition by replacing the wild type gene with one encoding Kcnt1R455H, a cytoplasmic C-terminal mutation homologous to a human R474H variant that results in EIMFS. We compared behavior patterns and seizure activity in these mice with those of wild type mice and Kcnt1−/− mice. Complete loss of Kcnt1 produced deficits in open field behavior and motor skill learning. Although their thresholds for electrically and chemically induced seizures were similar to those of wild type animals, Kcnt1−/− mice were significantly protected from death after maximum electroshock-induced seizures. In contrast, homozygous Kcnt1R455H/R455H mice were embryonic lethal. Video-EEG monitoring of heterozygous Kcnt1+/R455H animals revealed persistent interictal spikes, spontaneous seizures and a substantially decreased threshold for pentylenetetrazole-induced seizures. Surprisingly, Kcnt1+/R455H mice were not impaired in tasks of exploratory behavior or procedural motor learning. These findings provide an animal model for EIMFS and suggest that Slack channels are required for the development of procedural learning and of pathways that link cortical seizures to other regions required for animal survival.
The impermanent effect of waste incineration on children’s development from 6 months to 8 years: A Taiwan Birth Cohort Study
Authors: Lung For-Wey , Shu Bih-Ching , Chiang Tung-Liang , Lin Shio-Jean
Published: February 2020

Incineration is a solution to waste problems; however, it has adverse effects on human health. Our study aimed to investigate the direct and indirect effects of living near an incinerator and breastfeeding on children’s development at 6, 18, 36 and 66 months, and 8 years of age. The Taiwan Birth Cohort Study dataset used included randomized community data on 19,519 children from 6 months to 8 years old. The Taiwan Birth Cohort Study Developmental Instrument was used to measure children’s development at different developmental ages. The results of our study showed that living within 3 km of an incinerator had a negative effect on children’s 6-month development, however the effect dissipated after 18 months. Having been breastfed and living in the city had a more persistent and pervasive positive effect on children’s development. Conversely, living in the city had an adverse effect on children’s social-communication and emotional development when they were 8 years old; possibly due to the Chinese cultural characteristic of collectivism. Further follow-up of the long-term interactive effects of proximity to an incinerator and breastfeeding on children’s development and health is needed.
A randomised controlled trial to assess the feasibility of utilising virtual reality to facilitate analgesia during external cephalic version
Authors: Smith Vinayak , Warty Ritesh Rikain , Kashyap Ravi , Neil Peter , Adriaans Carol , Nair Amrish , Krishnan Sathya , Da Silva Costa Fabricio , Vollenhoven Beverley , Wallace Euan M.
Published: February 2020

External cephalic version (ECV) is associated with a moderate degree of pain. Virtual reality (VR) is a technology that has shown promise in offering procedural analgesia. We undertook a clinical pilot to assess the viability of VR to reduce pain during ECV. In an open randomised controlled trial (RCT), we randomised 50 women to either VR or standard care each (25 per group). Women receiving VR were administered VR content (Skylights) via a headset. Pre- and post-procedural measures of pain, anxiety, device experience and vital signs were measured. There were no significant differences between groups (VR/no VR) in pain scores (60.68 vs 49.76; p = 0.2), ECV success rates (80% vs 76%; p = 0.7) or anxiety levels. The women receiving VR had a significantly higher anticipation of pain pre-procedurally (70.0 vs 50.0; p = 0.03). 20 (80%) of the VR women indicated that they would use VR again and 22 (88%) indicated they would recommend it to a friend having ECV. There were no significant differences between groups for side effects encountered or changes in vital signs. We have shown that using VR during ECV is feasible and appears safe. Our results inform the design of future RCTs.
Temporal dynamics of muscle, spinal and cortical excitability and their association with kinematics during three minutes of maximal-rate finger tapping
Authors: Madinabeitia-Mancebo Elena , Madrid Antonio , Jácome Amalia , Cudeiro Javier , Arias Pablo
Published: February 2020

We tested peripheral, spinal and cortical excitability during 3 minutes of unresisted finger tapping at the maximal possible rate, which induced fatigue. Subsequently, we studied the temporal dynamics of muscle fatigue, expressed in the tapping movement profile, and its relationship to neural systems using mixed model analyses. The tapping rate decreased by 40% over the duration of the task. The change in the amplitude of the range of motion was not significant. The excitability of the flexor and extensor muscles of the index finger was tested via evoked potentials obtained with various types of stimulation at various levels of the motor system. The change in spinal excitability with time was evaluated considering the simultaneous changes in muscle excitability; we also considered how spinal excitability changed over time to evaluate cortical excitability. Excitability in the flexor and extensor muscles at the different levels tested changed significantly, but similar excitability levels were observed at notably different tapping rates. Our results showed that only 33% of the decrease in the tapping rate was explained by changes in the excitability of the structures tested in the present work.
Speech Intonation Induces Enhanced Face Perception in Infants
Authors: Sirri Louah , Linnert Szilvia , Reid Vincent , Parise Eugenio
Published: February 2020

Infants’ preference for faces with direct compared to averted eye gaze, and for infant-directed over adult-directed speech, reflects early sensitivity to social communication. Here, we studied whether infant-directed speech (IDS), could affect the processing of a face with direct gaze in 4-month-olds. In a new ERP paradigm, the word ‘hello’ was uttered either in IDS or adult-direct speech (ADS) followed by an upright or inverted face. We show that the face-specific N290 ERP component was larger when faces were preceded by IDS relative to ADS. Crucially, this effect is specific to upright faces, whereas inverted faces preceded by IDS elicited larger attention-related P1 and Nc. These results suggest that IDS generates communicative expectations in infants. When such expectations are met by a following social stimulus – an upright face – infants are already prepared to process it. When the stimulus is a non-social one –inverted face – IDS merely increases general attention.
Low doses of ionizing radiation enhance angiogenesis and consequently accelerate post-embryonic development but not regeneration in zebrafish
Authors: Marques Filipa G. , Carvalho Lara , Sousa Joana S. , Rino José , Diegues Isabel , Poli Esmeralda , Pina Filomena , Saúde Leonor , Constantino Rosa Santos Susana
Published: February 2020

Low doses of ionizing radiation (LDIR) activate endothelial cells inducing angiogenesis. In zebrafish, LDIR induce vessel formation in the sub-intestinal vessels during post-embryonic development and enhance the inter-ray vessel density in adult fin regeneration. Since angiogenesis is a crucial process involved in both post-embryonic development and regeneration, herein we aimed to understand whether LDIR accelerate these physiological conditions. Our data show that LDIR upregulate the gene expression of several pro-angiogenic molecules, such as flt1, kdr, angpt2a, tgfb2, fgf2 and cyr61in sorted endothelial cells from zebrafish larvae and this effect was abrogated by using a vascular endothelial growth factor receptor (VEGFR)-2 tyrosine kinase inhibitor. Irradiated zebrafish present normal indicators of developmental progress but, importantly LDIR accelerate post-embryonic development in a VEGFR-2 dependent signaling. Furthermore, our data show that LDIR do not accelerate regeneration after caudal fin amputation and the gene expression of the early stages markers of regeneration are not modulated by LDIR. Even though regeneration is considered as a recapitulation of embryonic development and LDIR induce angiogenesis in both conditions, our findings show that LDIR accelerate post-embryonic development but not regeneration. This highlights the importance of the physiological context for a specific phenotype promoted by LDIR.
miRNA Expression Profiles and Potential as Biomarkers in Nontuberculous Mycobacterial Pulmonary Disease
Authors: Han Sun Ae , Jhun Byung Woo , Kim Su-Young , Moon Seong Mi , Yang Bumhee , Kwon O. Jung , Daley Charles L. , Shin Sung Jae , Koh Won-Jung
Published: February 2020

Pulmonary disease (PD) due to nontuberculous mycobacteria (NTM) is increasing globally, but specific biomarkers for NTM-PD have not been established. As circulating miRNAs are promising biomarkers for various diseases, we investigated whether miRNAs have potential as NTM-PD biomarkers. Sera from 12 NTM-PD patients due toMycobacterium avium,M. intracellulare,M. abscessus, orM. massilienseand three healthy controls were initially evaluated via small RNA sequencing. Multiple miRNAs showed significant differences in expression in patients compared to in healthy controls, with some expression differences unique to PD caused by a specific mycobacterial species. Notably, 14 miRNAs exhibited significant expression differences in PD associated with all four mycobacteria. Validation by quantitative reverse-transcription-PCR in an additional 40 patients with NTM-PD and 40 healthy controls confirmed that four differentially expressed miRNAs (hsa-miR-484, hsa-miR-584-5p, hsa-miR-625-3p, and hsa-miR-4732-5p) showed significantly higher serum expressions in NTM-PD patients than in controls. Receiver operating characteristic curve analysis of these four miRNAs supported the discriminative potential for NTM-PD and their combination provided an improved diagnostic value for NTM-PD. Furthermore, bioinformatics analysis revealed their 125 target genes, which were mostly associated with immune responses. Collectively, this study identified four miRNAs as potential biomarkers for NTM-PD and provided insight into NTM-PD pathophysiology.
Kynurenine Pathway as a New Target of Cognitive Impairment Induced by Lead Toxicity During the Lactation
Authors: Ramirez Ortega Daniela , Ovalle Rodríguez Paulina , Pineda Benjamín , González Esquivel Dinora F. , Ramos Chávez Lucio Antonio , Vázquez Cervantes Gustavo I. , Roldán Roldán Gabriel , Pérez de la Cruz Gonzalo , Díaz Ruiz Araceli , Méndez Armenta Marisela , Marcial Quino Jaime , Gómez Manzo Saul , Ríos Camilo , Pérez de la Cruz Verónica
Published: February 2020

The immature brain is especially vulnerable to lead (Pb2+) toxicity, which is considered an environmental neurotoxin. Pb2+ exposure during development compromises the cognitive and behavioral attributes which persist even later in adulthood, but the mechanisms involved in this effect are still unknown. On the other hand, the kynurenine pathway metabolites are modulators of different receptors and neurotransmitters related to cognition; specifically, high kynurenic acid levels has been involved with cognitive impairment, including deficits in spatial working memory and attention process. The aim of this study was to evaluate the relationship between the neurocognitive impairment induced by Pb2+ toxicity and the kynurenine pathway. The dams were divided in control group and Pb2+ group, which were given tap water or 500 ppm of lead acetate in drinking water ad libitum, respectively, from 0 to 23 postnatal day (PND). The poison was withdrawn, and tap water was given until 60 PND of the progeny. The locomotor activity in open field, redox environment, cellular function, kynurenic acid (KYNA) and 3-hydroxykynurenine (3-HK) levels as well as kynurenine aminotransferase (KAT) and kynurenine monooxygenase (KMO) activities were evaluated at both 23 and 60 PND. Additionally, learning and memory through buried food location test and expression of KAT and KMO, and cellular damage were evaluated at 60 PND. Pb2+ group showed redox environment alterations, cellular dysfunction and KYNA and 3-HK levels increased. No changes were observed in KAT activity. KMO activity increased at 23 PND and decreased at 60 PND. No changes in KAT and KMO expression in control and Pb2+ group were observed, however the number of positive cells expressing KMO and KAT increased in relation to control, which correlated with the loss of neuronal population. Cognitive impairment was observed in Pb2+ group which was correlated with KYNA levels. These results suggest that the increase in KYNA levels could be a mechanism by which Pb2+ induces cognitive impairment in adult mice, hence the modulation of kynurenine pathway represents a potential target to improve behavioural alterations produced by this environmental toxin.
Association of a new 99-bp indel of the CEL gene promoter region with phenotypic traits in chickens
Authors: Wang Xiangnan , Wang Xinlei , Chen Bingjie , Guo Yaping , Tang Hehe , Li Donghua , Liu Danli , Wang Yanbin , Li Guoxi , Kang Xiangtao , Li Zhuanjian , Han Ruili
Published: February 2020

Carboxyl ester lipase (CEL) encodes a cholesterol ester hydrolase that is secreted into the duodenum as a component of pancreatic juice. The objective of this study was to characterize the CEL gene, investigate the association between the CEL promoter variants and chicken phenotypic traits, and explore the CEL gene regulatory mechanism. An insertion/deletion (indel) caused by a 99-bp insertion fragment was shown for the first time in the chicken CEL promoter, and large differences in allelic frequency were found among commercial breeds, indigenous and feral birds. Association analysis demonstrated that this indel site had significant effects on shank length, shank girth, chest breadth at 8 weeks (p < 0.01), evisceration weight, sebum weight, breast muscle weight, and leg weight (p < 0.05). Tissue expression profiles showed extremely high levels of the CEL gene in pancreatic tissue. Moreover, the expression levels of the genes APOB, MTTP, APOV1 and SREBF1, which are involved in lipid transport, were significantly reduced by adding a 4% oxidized soybean oil diet treatment at the individual level and transfecting the embryonic primary hepatocytes with a CEL-overexpression vector. Interestingly, the results showed that the expression level of the II homozygous genotype was significantly higher than that of the ID and DD genotypes, while individuals with DD genotypes had higher phenotypic values. Therefore, these data suggested that the CEL gene might affect body growth by participating in hepatic lipoprotein metabolism and that the 99-bp indel polymorphism could be a potentially useful genetic marker for improving the economically important traits of chickens.
Assessing and mapping multi-hazard risk susceptibility using a machine learning technique
Authors: Pourghasemi Hamid Reza , Kariminejad Narges , Amiri Mahdis , Edalat Mohsen , Zarafshar Mehrdad , Blaschke Thomas , Cerda Artemio
Published: February 2020

The aim of the current study was to suggest a multi-hazard probability assessment in Fars Province, Shiraz City, and its four strategic watersheds. At first, we construct maps depicting the most effective factors on floods (12 factors), forest fires (10 factors), and landslides (10 factors), and used the Boruta algorithm to prioritize the impact of each respective factor on the occurrence of each hazard. Subsequently, flood, landslides, and forest fire susceptibility maps prepared using a Random Forest (RF) model in the R statistical software. Results indicate that 42.83% of the study area are not susceptible to any hazards, while 2.67% of the area is at risk of all three hazards. The results of the multi-hazard map in Shiraz City indicate that 25% of Shiraz city is very susceptible to flooding, while 16% is very susceptible to landslide occurrences. For four strategic watersheds, it is notable that in the Dorodzan Watershed, landslides and floods are the most important hazards; whereas, flood occurrences cover the largest area of the Maharlou Watershed. In contrast, the Tashk-Bakhtegan Watershed is so sensible to floods and landslides, respectively. Finally, in the Ghareaghaj Watershed, forest fire ranks as the strongest hazard, followed by floods. The validation results indicate an AUC of 0.834, 0.939, and 0.943 for the flood, landslide, and forest fire susceptibility maps, respectively. Also, other accuracy measures including, specificity, sensitivity, TSS, CCI, and Gini coefficient confirmed results of the AUC values. These results allow us to forecast the spatial behavior of such multi-hazard events, and researchers and stakeholders alike can apply them to evaluate hazards under various mitigation scenarios.
Author Correction: FQSqueezer: k-mer-based compression of sequencing data
Authors: Deorowicz Sebastian
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Freezing water at constant volume and under confinement
Authors: Powell-Palm Matthew J. , Rubinsky Boris , Sun Wenhao
Published: February 2020

Water expands upon freezing. What happens when water is cooled below 0 °C in an undeformable, constant-volume container? This is a fundamental question in materials thermodynamics, and is also relevant in biological, geological, and technological applications in which ice forms under nano-, meso-, or macroscale confinement. Here, we analyze the phase-equilibria and kinetic behaviors of water and ice-1h in an isochoric (constant-volume) system. By making use of the Helmholtz potential F(temperature, volume), in contrast to the Gibbs potential G(temperature, pressure), we demonstrate significant changes in phase behavior when the specific volume of the container is constrained below that of ice-1h. We construct a T–V (temperature–volume) phase diagram for water and ice that features a broad two-phase equilibrium region, and we further derive an isochoric nucleation theory that reveals the existence of a critical confinement volume, on the order of microns, below which ice-1h is kinetically prohibited from forming.
Mechanism and malleability of glucose dehydration to HMF: entry points and water-induced diversions
Authors: Meier Sebastian
Published: February 2020

A water-enabled reaction to a polyester building block is found to widely occur in the conversion of glucose to HMF.
Copper accumulation and the effect of chelation treatment on cerebral amyloid angiopathy compared to parenchymal amyloid plaques
Authors: Zhu Xiayoue , Victor Tiffany W , Ambi Ashwin , Sullivan Joseph K , Hatfield Joshua , Xu Feng , Miller Lisa M , Van Nostrand William E
Published: February 2020

Accumulation of fibrillar amyloid β-protein (Aβ) in parenchymal plaques and in blood vessels of the brain, the latter condition known as cerebral amyloid angiopathy (CAA), are hallmark pathologies of Alzheimer’s disease (AD) and related disorders. Cerebral amyloid deposits have been reported to accumulate various metals, most notably copper and zinc. Here we show that, in human AD, copper is preferentially accumulated in amyloid-containing brain blood vessels compared to parenchymal amyloid plaques. In light of this observation, we evaluated the effects of reducing copper levels in Tg2576 mice, a transgenic model of AD amyloid pathologies. The copper chelator, tetrathiomolybdate (TTM), was administered to twelve month old Tg2576 mice for a period of five months. Copper chelation treatment significantly reduced both CAA and parenchymal plaque load in Tg2576 mice. Further, copper chelation reduced parenchymal plaque copper content but had no effect on CAA copper levels in this model. These findings indicate that copper is associated with both CAA deposits and parenchymal amyloid plaques in humans, but less in Tg2576 mice. TTM only reduces copper levels in plaques in Tg2576 mice. Reducing copper levels in the brain may beneficially lower amyloid pathologies associated with AD.
Ultra-dense, curved, grating optics determines peacock spider coloration
Authors: Wilts Bodo D. , Otto Jürgen , Stavenga Doekele G.
Published: February 2020

This study reports the optics of ultra-dense, nanoscopic gratings of peacock spiders that cause either angle-dependent or stable colours.
A novel αvβ3 integrin-targeted NIR-II nanoprobe for multimodal imaging-guided photothermal therapy of tumors in vivo
Authors: Zhao Meng , Ding Jianan , Mao Qiulian , Zhang Yuqi , Gao Yinjia , Ye Shuyue , Qin Hongni , Shi Haibin
Published: February 2020

A novel NIR-II probe QT-RGD consisting of a NIR-II fluorophore and two tumor-targeting cyclic-RGD peptides was reported. In vitro and in vivo studies show that it could be successfully used for multimodal NIR-II/PA/SPECT imaging and photothermal therapy of malignant tumor.
Half-metallicity in new Heusler alloys Mn2ScZ (Z = Si, Ge, Sn)
Authors: Ram Mahesh , Saxena Atul , Aly Abeer E. , Shankar Amit
Published: February 2020

Study of half-metallicity has been performed in a new series of Mn2ScZ (Z = Si, Ge and Sn) full Heusler alloys using density functional theory with the calculation and implementation of a Hubbard correction term (U).
Modeling rapid and selective capture of nNOS–PSD-95 uncouplers from Sanhuang Xiexin decoction by novel molecularly imprinted polymers based on metal–organic frameworks
Authors: Pan Linli , Ding Yingying , Ni Xiaoting , Wang Chong-Zhi , Jiang Bo , Zhang Yu , Jiang Nan , Tang Yulin , Chen Lina , Yuan Chun-Su
Published: February 2020

Novel MIL@MIPs were prepared to rapidly capture nNOS–PSD-95 uncouplers from Sanhuang Xiexin decoction, coupled with SPE and HPLC.
Testing the limits of radical-anionic CH-amination: a 10-million-fold decrease in basicity opens a new path to hydroxyisoindolinesviaa mixed C–N/C–O-forming cascade
Authors: Elliott Quintin , dos Passos Gomes Gabriel , Evoniuk Christopher J. , Alabugin Igor V.
Published: February 2020

An intramolecular C(sp3)–H amidation proceeds in the presence oft-BuOK, molecular oxygen, and DMF.
Modeling the dynamics of phospholipids in the fluid phase of liposomes
Authors: Gupta Sudipta , Schneider Gerald J.
Published: February 2020

We present the derivation of a new model to describe neutron spin echo spectroscopy and quasi-elastic neutron scattering data on liposomes.
Ruling out delamination in bismuth-enhanced polyimide electrochemical actuator with tunable active/passive layer thickness
Authors: Wang Si-Qi , Zhang Bin , Luo Xue-Mei , Liang Fei , Zhang Guang-Ping
Published: February 2020

The PI/Au/Bi actuator is driven by the redox of polyimide and enhanced by bismuth for fast response and long life.
Assessing the range of enzymatic and oxidative tunability for biosensor design
Authors: Schunk Hattie C. , Hernandez Derek S. , Austin Mariah J. , Dhada Kabir S. , Rosales Adrianne M. , Suggs Laura J.
Published: February 2020

This review aims to inspire novel biosensor design by addressing materials chemistries through the lense of enzymatic and oxidative susceptibility in the spectra of inflammatory disease biomarkers.
Binuclear O2 activation and hydrogen transfer mechanism for aerobic oxidation of alcohols
Authors: Hu Zhiyun , Ge Hongyu , Yang Xinzheng
Published: February 2020

Density functional theory calculations reveal a binuclear O2 activation and hydrogen transfer mechanism with spin-crossovers for aerobic oxidation of alcohols.
Surface softening in palladium nanoparticles: effects of a capping agent on vibrational properties
Authors: Rebuffi Luca , Mukherjee Binayak , Siboni Stefano , Young Allison P. , Williams Benjamin P. , Tsung Chia-Kuang , Scardi Paolo
Published: February 2020

The presence of a capping agent (CTAB) on Pd nanoparticles produces a strong static disorder in the surface region.
Phenylboronic acid-functionalized unimolecular micelles based on a star polyphosphoester random copolymer for tumor-targeted drug delivery
Authors: Zhang Li , Shi Dongjian , Gao Yunyun , Zhou Tianyang , Chen Mingqing
Published: February 2020

A phenylboronic acid-functionalized unimolecular micellar drug delivery system based on a star phosphoester random copolymer synthesized by a one-pot ring-opening polymerization strategy.
Exploration of the Relationship Between Gut Microbiota and Polycystic Ovary Syndrome (PCOS): a Review
Authors: Zhao Xiaoxuan , Jiang Yuepeng , Xi Hongyan , Chen Lu , Feng Xiaoling
Published: February 2020

Polycystic ovary syndrome (PCOS) is an endocrine and metabolic syndrome (MS) with a complex etiology, and its pathogenesis is not yet clear. In recent years, the correlation between gut microbiota (GM) and metabolic disease has become a hot topic in research, leading to a number of new ideas about the etiology and pathological mechanisms of PCOS. The literature shows that GM can cause insulin resistance, hyperandrogenism, chronic inflammation and metabolic syndrome (obesity, diabetes) and may contribute to the development of PCOS by influencing energy absorption, the pathways of short chain fatty acids (SCFA), lipopolysaccharides, choline and bile acids, intestinal permeability and the brain–gut axis. As part of the treatment of PCOS, fecal microbiota transplantation, supplementation with prebiotics and traditional Chinese medicine can be used to regulate GM and treat disorders. This article reviews possible mechanisms and treatment options for PCOS, based on methods which target the GM, and offers new ideas for the treatment of PCOS.
Molecular ring toss of circular BAC DNA using micropillar array for single-molecule studies
Authors: Dohi Daiki , Hirano Ken , Terao Kyohei
Published: February 2020

This paper reports a method for trapping circular DNA molecules and imaging the dynamics with high spatial resolution using a micropillar-array device. We successfully trapped circular bacterial artificial chromosome DNA molecules at a micropillar-based “ring toss” in the laminar flow of a microchannel under a fluorescence microscope and demonstrated the imaging of their extension by flow and condensation process induced by spermine solution. DNA molecules were visualized in an extended loop conformation, allowing high spatial resolution, and the results showed that the dynamics is induced by the microfluidic control of the surrounding chemical environment. The method is expected to lead to the elucidation of the physical characteristics and the dynamics of circular DNA molecules.
Simulation strategies for the Food and Drug Administration nozzle using Nek5000
Authors: Sánchez Abad Nour , Vinuesa Ricardo , Schlatter Philipp , Andersson Magnus , Karlsson Matts
Published: February 2020

Computational fluid dynamics (CFD) is currently a versatile tool used for flow characterization in diverse areas of industry and research; however, its application in medical devices is less developed due to high regulatory standards for safety purposes. In this context, the development of a rigorous and standardized CFD methodology is essential in order to improve the accuracy and ensure the reliability of biomedical applications. To that end, the Food and Drug Administration (FDA) proposed a benchmark model of an idealized medical device to provide a common ground for verification and validation processes. Previous studies have evaluated the potential of conventional turbulence models to predict the relevant flow features in the FDA nozzle but have also been deemed inaccurate or exhibited high dependency on the numerical scheme. Furthermore, validation of computational results relied on previous experiments performed with particle image velocimetry (PIV), which also exhibited noticeable uncertainties. Here, we perform direct numerical simulations (DNSs) of the flow through the FDA nozzle configuration, at Reynolds numbers based on the throat diameter Ret = 500, 2000, 3500, and 5000, using the spectral-element code Nek5000. The predictive capabilities of the synthetic-eddy method and parabolic-inflow conditions at the inlet were tested, and the results were compared with PIV data. Our results highlight the very high sensitivity of this flow case to the inflow conditions and the disturbances at the throat, particularly when predicting the laminar–turbulent jet breakdown. Due to this extreme sensitivity, any benchmark data of this geometry need to include a very detailed characterization of both the conditions at the inflow and the throat, in order to enable relevant comparisons.
Blue perovskite LEDs dependent on temperature optical properties
Authors: Mandel Savannah
Published: February 2020

Using an excitonic luminescence model, researchers analyze temperature-dependent optical properties of chlorine-based organometallic halide perovskite film in relation to blue luminescence.
Temperature dependency equation for chub mackerel (Scomber japonicus) identified by a laboratory rearing experiment and microscale analysis
Authors: Nakamura Masahiro , Yoneda Michio , Ishimura Toyoho , Shirai Kotaro , Tamamura Masaki , Nishida Kozue
Published: February 2020

In this study, juveniles of chub mackerel (Scomber japonicus) were reared from eggs in six different temperature treatments, and their otoliths were subjected to micromilling and microvolume stable oxygen isotope (δ18O) analysis. We determined the δ18O values of otoliths (δ18Ootolith) formed at mean temperatures of 16.3, 17.6, 18.3, 20.0, 24.0 and 26.5°C and identified a linear relationship between rearing water temperature (T, °C) and δ18Ootolith as follows: δ18Ootolith (VPDB) – δ18Owater (VSMOW) =–0.25 (±0.01)T+4.46 (±0.21) (R2=0.96, P<0.01), where VPDB is Vienna Peedee Belemnite, VSMOW is Vienna Standard Mean Ocean Water and the error values in parentheses are standard deviations. This species-specific temperature dependency equation for chub mackerel will enable accurate reconstruction of individual thermal histories and provide essential information for effective resource management.
Delocalization in two and three-dimensional Rydberg gases
Authors: Abumwis G , Eiles Matthew T , Eisfeld Alexander
Published: February 2020

As was recently shown in Abumwis et al (2020 Phys. Rev. Lett.
124 193401), many eigenstates of a random Rydberg gas with resonant dipole–dipole interactions are highly delocalized. Although the high degree of delocalization is generic to various types of power-law interactions and to both two and three-dimensional systems, in their detailed aspects the coherence distributions are sensitive to these parameters and vary dramatically between different systems. We calculate the eigenstates of both two and three-dimensional gases and quantify their delocalization throughout the atoms in the gas using a coherence measure. By contrasting the angular dependence of the dipole–dipole interaction with an isotropic interaction we obtain additional information about the generic physical principles underlying random interacting systems. We also investigate the density of states and microwave absorption spectra to obtain information about the types of measurements where these delocalized states play a role, and to check that these delocalized eigenstates are robust against various types of perturbation.
Locomotor transition: how squid jet from water to air
Authors: Hou T G , Yang X B , Wang T M , Liang J H , Li S W , Fan Y B
Published: February 2020

The amazing multi-modal locomotion of flying squid helps to achieve fast-speed migration and predator-escape behavior. Observation of flying squid has been rarely reported in recent years, since it is challenging to clearly record the flying squid’s aquatic-aerial locomotion in a marine environment. The existing reports of squid-flying events are rare and merely record the in-air motion. Therefore, the water-air locomotor transition of flying squid is still unknown. This paper proposes the idea of using CFD to simulate the process of the flying squid (Sthenoteuthis oualaniensis (S. oualaniensis)) launching from water into air. The results for the first time reveal the flow field information of squid in launching phase and show the kinematic parameters of flying squid in quantification. Both a trailing jet and pinch-off vortex rings are formed to generate launching thrust, and the formation number L

ω
/D

ω
is 5.22, demonstrating that the jet strategy is to produce greater time-averaged thrust rather than higher propulsion efficiency. The results also indicate that the maximum flying speed negatively correlates with the launch angle, indicating that a lower launch angle could result in a larger flying speed for the flying squid to escape. These findings explore the multi-modal locomotion of flying squid from a new perspective, helping to explain the trade-off strategy of water-to-air transition, and further enhance the performance of aquatic-aerial vehicles.
Perspectives on quantum transduction
Authors: Lauk Nikolai , Sinclair Neil , Barzanjeh Shabir , Covey Jacob P , Saffman Mark , Spiropulu Maria , Simon Christoph
Published: February 2020

Quantum transduction, the process of converting quantum signals from one form of energy to another, is an important area of quantum science and technology. The present perspective article reviews quantum transduction between microwave and optical photons, an area that has recently seen a lot of activity and progress because of its relevance for connecting superconducting quantum processors over long distances, among other applications. Our review covers the leading approaches to achieving such transduction, with an emphasis on those based on atomic ensembles, opto-electro-mechanics, and electro-optics. We briefly discuss relevant metrics from the point of view of different applications, as well as challenges for the future.
Guided patchwork kriging to develop highly transferable thermal conductivity prediction models
Authors: Juneja Rinkle , Singh Abhishek K
Published: February 2020

The machine learning models developed on a dataset comprising particular class of materials show poor transferability across different classes. The problem can be partially solved by increasing the variability in the dataset at the cost of prediction accuracy. To develop a model on a highly variable database, we propose a localized regression based patchwork kriging approach for capturing most of the complex details in the data. In this approach, the data is partitioned into smaller regions with shared patches of few datapoints across the neighboring boundaries. Local regression functions are developed in each partition with a constrain to give similar performance at the boundary. Out of 17 different properties tried for partitioning the data, the decomposition with respect to target output κ

l
gave local models with unprecedented accuracies. The partitioning with respect to κ

l
, however, requires its estimate for any unknown compound beforehand. To address this, we developed a global model for the entire database. The global model accurately predicts the order of magnitude of κ

l
for the compounds in the dataset and hence, directs them towards a particular partition for more accurate prediction. We define this stepwise approach as guided patchwork kriging, which can be applied to develop highly accurate transferable prediction models.
Essentiality-specific pathogenicity prioritization gene score to improve filtering of disease sequence data
Authors: Alyousfi Dareen , Baralle Diana , Collins Andrew
Published: February 2020

The causal genetic variants underlying more than 50% of single gene (monogenic) disorders are yet to be discovered. Many patients with conditions likely to have a monogenic basis do not receive a confirmed molecular diagnosis which has potential impacts on clinical management. We have developed a gene-specific score, essentiality-specific pathogenicity prioritization (ESPP), to guide the recognition of genes likely to underlie monogenic disease variation to assist in filtering of genome sequence data. When a patient genome is sequenced, there are frequently several plausibly pathogenic variants identified in different genes. Recognition of the single gene most likely to include pathogenic variation can guide the identification of a causal variant. The ESPP score integrates gene-level scores which are broadly related to gene essentiality. Previous work towards the recognition of monogenic disease genes proposed a model with increasing gene essentiality from ‘non-essential’ to ‘essential’ genes (for which pathogenic variation may be incompatible with survival) with genes liable to contain disease variation positioned between these two extremes. We demonstrate that the ESPP score is useful for recognizing genes with high potential for pathogenic disease-related variation. Genes classed as essential have particularly high scores, as do genes recently recognized as strong candidates for developmental disorders. Through the integration of individual gene-specific scores, which have different properties and assumptions, we demonstrate the utility of an essentiality-based gene score to improve sequence genome filtering.
Stability in fig tree–fig wasp mutualisms: how to be a cooperative fig wasp
Authors: Dunn Derek W
Published: February 2020

Fig tree–fig wasp mutualisms are diverse and underpin much biodiversity. The wasps (Agaonidae) are the sole pollinators of the trees (Ficus). Figs are enclosed inflorescences, each of which contains many small flowers. Female wasps (foundresses) enter receptive figs to spread pollen and to lay their eggs individually into fig flowers. As they oviposit, wasps also inject chemicals that transform individual flower ovaries into galls that will feed and house wasp offspring. For fig tree–fig wasp mutualisms to persist, the trees must set seed; therefore, the wasps have both to pollinate and to fail to gall all flower ovaries. However, wasps that avoid pollination costs and/or gall all flowers are predicted to outcompete more cooperative conspecifics, resulting in destabilisation of the mutualism. Here, I review the literature on why wasps pollinate by focusing on how trees reduce investment to unpollinated figs, resulting in ‘sanctions’ to wasps that fail to pollinate via reduced production of offspring. I also review the mechanisms that prevent wasps from galling all flowers, mainly those in monoecious Ficus, that also result in wasps predominantly galling longer flowers whilst leaving shorter flowers to become seeds. I make suggestions for future work and conclude by reaffirming why multiple processes promote stability in fig tree–fig wasp mutualisms.
Successful percutaneous occlusion of a large left circumflex coronary artery fistula draining into the coronary sinus using a ventricular septal defect occluder: a case report
Authors: Egorova Anastasia D , Ewert Peter , Hadamitzky Martin , Eicken Andreas
Published: February 2020

Background

Coronary artery fistula (CAF) is a congenital anomaly of the coronaries that can lead to significant intracardiac shunting and myocardial ischaemia.

Case summary

We describe the case of a 15-year-old male with an incidentally documented precordial cardiac murmur. An evidently dilated coronary sinus (CS) on transthoracic echocardiography prompted further investigation. A computed tomography (CT) revealed the presence of a large CAF from the left circumflex coronary artery to the CS. No other structural heart defects were detected. A haemodynamically significant intracardiac shunt was confirmed during cardiac catheterization, and it was decided to close the fistula. This was successfully performed using a ventricular septal defect (VSD) occluder (Konar 10-8, Lifetech Scientific) that was deployed through a 6 Fr right coronary guiding catheter. A partial thrombotic occlusion of the CS behind the closure device was noted during follow-up which led to anticoagulation in a higher target INR range and concomitant start of low dose carbasalate calcium to reduce further retrograde thrombus extension. Patient is doing well at over 1 year of follow-up, and no further thrombotic extension into the CS was seen on a recent CT.

Discussion

This report illustrates the diagnostic workup and a percutaneous treatment strategy of a CAF using a VSD occluder. We also describe a not previously reported complication, thrombotic CS occlusion. Improving transcatheter techniques and marketing of novel devices with a broad spectrum of applications can offer new opportunities for treating CAF and avoiding surgical correction often involving cardiopulmonary bypass, reserving this option for patients with complex anatomy or failed transcatheter closure.