bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-Dimensional Shear-Wave Elastography for Kidney Stiffness Assessment
Authors: Grosu Iulia , Bob Flaviu , Sporea Ioan , Popescu Alina , Sirli Roxana , Schiller Adalbert
Published: June 2019

This study aimed to analyze the utility of bidimensional shear-wave elastography for renal assessment and in the prediction of chronic kidney disease (CKD).

The study included 92 subjects: 50 healthy volunteers and 42 patients with different degrees of CKD (mean age, 57.5 ± 13.4; 50% were female), excluding those undergoing renal replacement therapies, obstructive pathology, or renal lithiasis. We performed kidney shear-wave velocity (KSWV) determinations in the midportion of the parenchyma of each kidney. The median values were expressed in meters per second.

We obtained successful assessments in 94% of the cases for the right kidney (RK) and 90.2% for the left kidney (LK), with an intraclass correlation coefficient of 0.96 (RK) and 0.91 (LK). We obtained significantly lower KSWV values in the CKD lot as opposed to the healthy volunteers: RK: 1.38 ± 0.1 versus 1.78 ± 0.1 m/s, P = 0.05; LK: 1.37 ± 0.1 m/s versus 1.72 ± 0.1 m/s. We could predict the presence of CKD with a sensitivity of 89.2% and a specificity of 76.9% for a KSWV of less than 1.47 m/s, with a tendency of KSWV to decrease with CKD progression.

Our study shows that KSWV measured using bidimensional shear-wave elastography decreases in patients with CKD compared with normal subjects, and that for a cutoff value of below 1.47 m/s we could predict, with a good sensitivity and specificity, the presence of CKD.
Effect of Mechanical Tension on the circRNA Expression Profile of Human Skin Tissue
Authors: Liu Zheng , Liu Wei , Fan Jincai , Liu Liqiang , Tian Jia , Gan Cheng , Jiao Hu , Yang Zengjie
Published: June 2019

Skin soft tissue dilatation has emerged as one of the most prominent methods to skin defects spanning large areas. However, effective expansion of additional skin tissue is still the most challenging problem. This study aimed to understand the potential role of circular RNAs (circRNAs) in gene regulation during skin regeneration via analysis of the circRNA expression profile of skin tissue during skin regeneration under mechanical tension. In total, 1039 circRNAs were identified, of which 126 were newly identified. Furthermore, 48 circRNAs were differentially expressed between the experimental and control groups, which were annotated with gene ontology and kyoto encyclopedia of genes and genomes functions, and the regulatory network of microRNA (miRNA)–circRNA was established. The present results provide a theoretical basis for future studies on the mechanism underlying skin regeneration.
A Rotational Flap Combined With a Mucosal Advancement Flap for the Lip Reconstruction
Authors: Kim Jeenam , Lee Yunhae , Choi Hyungon
Published: June 2019

The lips play an important role in both esthetics and oral functions, so it should be reconstructed in the light of both. The authors present a patient with the upper lateral lip defect after widely excising the basal cell carcinoma. The lip reconstruction was completed with a rotational flap combined with a mucosal advancement flap. By using 2 flaps simultaneously, the defect was covered with sufficient adjacent tissue without severe deformity and tension. At 2-month follow-up, the patient retained good aesthetic results as the scar was on the natural lines of the face. There was no noticeable deformity on the vermilion contour and oral commissure. Oral competence was also good.
Evolutionary trade-offs between baseline and plastic gene expression in two congeneric oyster species
Authors: Li Ao , Li Li , Wang Wei , Zhang Guofan
Published: June 2019

Organismal responses to environmental stresses are a determinant of the effect of climate change. These can occur through the regulation of gene expression, involving genetic adaptation and plastic changes as evolutionary strategy.Heat shock protein(hsp) family genes are extensively expanded and play important roles in thermal adaptation in oysters. We investigated expression of all heat-responsivehsps in two allopatric congeneric oyster species,Crassostrea gigasandC. angulata, which are respectively distributed along the northern and southern coasts of China, using common garden and reciprocal transplant experiments. Our results showed thathsps inC. gigashave evolved higher basal levels of expression under ambient conditions at each field site, with lower expression plasticity in response to heat stress in comparison toC. angulata, which exhibited lower baseline expression but higher expression plasticity. This pattern was fixed regardless of environmental disturbance, potentially implying genetic assimilation. Our findings indicate divergent adaptive strategies with underlying evolutionary trade-offs between genetic adaptation and plasticity at the molecular level in two oyster congeners in the face of rapid climate change.
An architectural understanding of natural sway frequencies in trees
Authors: Jackson T. , Shenkin A. , Moore J. , Bunce A. , van Emmerik T. , Kane B. , Burcham D. , James K. , Selker J. , Calders K. , Origo N. , Disney M. , Burt A. , Wilkes P. , Raumonen P. , Gonzalez de Tanago Menaca J. , Lau A. , Herold M. , Goodman R. C. , Fourcaud T. , Malhi Y.
Published: June 2019

The relationship between form and function in trees is the subject of a longstanding debate in forest ecology and provides the basis for theories concerning forest ecosystem structure and metabolism. Trees interact with the wind in a dynamic manner and exhibit natural sway frequencies and damping processes that are important in understanding wind damage. Tree-wind dynamics are related to tree architecture, but this relationship is not well understood. We present a comprehensive view of natural sway frequencies in trees by compiling a dataset of field measurement spanning conifers and broadleaves, tropical and temperate forests. The field data show that a cantilever beam approximation adequately predicts the fundamental frequency of conifers, but not that of broadleaf trees. We also use structurally detailed tree dynamics simulations to test fundamental assumptions underpinning models of natural frequencies in trees. We model the dynamic properties of greater than 1000 trees using a finite-element approach based on accurate three-dimensional model trees derived from terrestrial laser scanning data. We show that (1) residual variation, the variation not explained by the cantilever beam approximation, in fundamental frequencies of broadleaf trees is driven by their architecture; (2) slender trees behave like a simple pendulum, with a single natural frequency dominating their motion, which makes them vulnerable to wind damage and (3) the presence of leaves decreases both the fundamental frequency and the damping ratio. These findings demonstrate the value of new three-dimensional measurements for understanding wind impacts on trees and suggest new directions for improving our understanding of tree dynamics from conifer plantations to natural forests.
EmExplorer: a database for exploring time activation of gene expression in mammalian embryos
Authors: Hu Bosu , Zheng Lei , Long Chunshen , Song Mingmin , Li Tao , Yang Lei , Zuo Yongchun
Published: June 2019

Understanding early development offers a striking opportunity to investigate genetic disease, stem cell and assisted reproductive technology. Recent advances in high-throughput sequencing technology have led to the rising influx of omics data, which have rapidly boosted our understanding of mammalian developmental mechanisms. Here, we review the database EmExplorer (a database for exploring time activation of gene expression in mammalian embryos), which systematically organizes the genes from development-related pathways, and which we have already established and continue to update it. The current version of EmExplorer incorporates over 26 000 genes obtained from 306 functional pathways in five species. The function annotations of development-related genes were also integrated into EmExplorer. To facilitate data extraction, the database also contains the following information. (i) The dynamic expression values for each development stage are matched to the corresponding genes. (ii) A two-layer search tool which supports multi-option searching, such as by official symbol, pathway name and function annotation. The returned entries can directly link to the analysis results for the corresponding gene or pathway in the analysis module. (iii) The analysis module provides different gene comparisons at the multi-species level and functional pathway level, which shows the species specificity and stage specificity at the gene or pathway level. (iv) The analysis based on the hypergeometric distribution test reveals the enrichment of gene functions at a particular stage of one organism's pathway. (v) The browser is designed for users with ambiguous searching goals and greatly helps new users to get a general idea of the contents of the database. (vi) The experimentally validated pathways are manually curated and shown on the home page. EmExplorer will be helpful for elucidating early developmental mechanisms and exploring time activation genes. EmExplorer is freely available at
http://bioinfor.imu.edu.cn/emexplorer
.
Regulation of gene expression in trypanosomatids: living with polycistronic transcription
Authors: Clayton Christine
Published: June 2019

In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by
trans
-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
Experimental study of the supercritical CO
2
diffusion coefficient in porous media under reservoir conditions
Authors: Lv Junchen , Chi Yuan , Zhao Changzhong , Zhang Yi , Mu Hailin
Published: June 2019

Reliable measurement of the CO
2
diffusion coefficient in consolidated oil-saturated porous media is critical for the design and performance of CO
2
-enhanced oil recovery (EOR) and carbon capture and storage (CCS) projects. A thorough experimental investigation of the supercritical CO
2
diffusion in
n
-decane-saturated Berea cores with permeabilities of 50 and 100 mD was conducted in this study at elevated pressure (10–25 MPa) and temperature (333.15–373.15 K), which simulated actual reservoir conditions. The supercritical CO
2
diffusion coefficients in the Berea cores were calculated by a model appropriate for diffusion in porous media based on Fick's Law. The results show that the supercritical CO
2
diffusion coefficient increases as the pressure, temperature and permeability increase. The supercritical CO
2
diffusion coefficient first increases slowly at 10 MPa and then grows significantly with increasing pressure. The impact of the pressure decreases at elevated temperature. The effect of permeability remains steady despite the temperature change during the experiments. The effect of gas state and porous media on the supercritical CO
2
diffusion coefficient was further discussed by comparing the results of this study with previous study. Based on the experimental results, an empirical correlation for supercritical CO
2
diffusion coefficient in
n
-decane-saturated porous media was developed. The experimental results contribute to the study of supercritical CO
2
diffusion in compact porous media.
High-energy diet enhances spermatogenic function and increases sperm midpiece length in fallow deer (
Dama dama
) yearlings
Authors: Ros-Santaella José Luis , Kotrba Radim , Pintus Eliana
Published: June 2019

Nutrition is a major factor involved in the sexual development of livestock ruminants. In the male, a high-energy diet enhances the reproductive function, but its effects on the underlying processes such as spermatogenic efficiency are not yet defined. Moreover, the possible changes in sperm size due to a supplemented diet remain poorly investigated. The main goal of this study was to evaluate whether a high-energy diet affects the spermatogenic activity, epididymal sperm parameters (concentration, morphology, morphometry and acrosome integrity) and blood testosterone levels in fallow deer yearlings. For this purpose, 32 fallow deer were allocated into two groups according to their diet: control (pasture) and experimental (pasture and barley grain) groups. Fallow deer from the experimental group showed a significant increase in the Sertoli cell function and sperm midpiece length, together with a higher testicular mass, sperm concentration and percentage of normal spermatozoa than the control group (
p
< 0.05). We also found a tendency for higher blood testosterone levels in the animals fed with barley grain (
p
= 0.116). The better sperm quality found in the experimental group may be related to their higher efficiency of Sertoli cells and to an earlier onset of puberty. The results of the present work elucidate the mechanisms by which dietary supplementation enhances the male sexual development and might be useful for better practices of livestock management in seasonal breeders.
Non-contact respiration monitoring using impulse radio ultrawideband radar in neonates
Authors: Kim Jong Deok , Lee Won Hyuk , Lee Yonggu , Lee Hyun Ju , Cha Teahyen , Kim Seung Hyun , Song Ki-Min , Lim Young-Hyo , Cho Seok Hyun , Cho Sung Ho , Park Hyun-Kyung
Published: June 2019

Vital sign monitoring in neonates requires adhesive electrodes, which often damage fragile newborn skin. Because impulse radio ultrawideband (IR-UWB) radar has been reported to recognize chest movement without contact in adult humans, IR-UWB may be used to measure respiratory rates (RRs) in a non-contact fashion. We investigated the feasibility of radar sensors for respiration monitoring in neonates without any respiratory support to compare the accuracy and reliability of radar measurements with those of conventional impedance pneumography measurements. In the neonatal intensive care unit, RRs were measured using radar (RR
Rd
) and impedance pneumography (RR
IP
) simultaneously. The neonatal voluntary movements were measured using the radar sensor and categorized into three levels (low [M
0
], intermediate [M
1
] and high [M
2
]). RR
Rd
highly agreed with RR
IP
(
r
= 0.90; intraclass correlation coefficient [ICC] = 0.846 [0.835–0.856]). For the M
0
movement, there was good agreement between RR
Rd
and RR
IP
(ICC = 0.893; mean bias −0.15 [limits of agreement (LOA) −9.6 to 10.0]). However, the agreement was slightly lower for the M
1
(ICC = 0.833; mean bias = 0.95 [LOA −11.4 to 13.3]) and M
2
(ICC = 0.749; mean bias = 3.04 [LOA –9.30 to 15.4]) movements than for the M
0
movement. In conclusion, IR-UWB radar can provide accurate and reliable estimates of RR in neonates in a non-contact fashion. The performance of radar measurements could be affected by neonate movement.
Microwave-assisted synthesis of high thermal stability and colourless polyimides containing pyridine
Authors: Cheng Kai , Hu Jie-pin , Wu Yan-cheng , Shi Chu-qi , Chen Zhi-geng , Liu Shu-mei , Yuan Yan-chao , Mo Yue-qi , Zhao Jian-qing
Published: June 2019

A novel aromatic diamine containing pyridyl side group, 4-pyridine-4,4-bis(3,5-dimethyl-5-aminophenyl)methane (PyDPM), was successfully synthesized via electrophilic substitution reaction. The polyimides (PIs) containing pyridine were obtained via the microwave-assisted one-step polycondensation of the PyDPM with pyromellitic dianhydride (PMDA), 3,3′,4,4′-biphenyltetracarboxylic dianhydride (BPDA), 3,3′,4,4′-diphenylether tetracarboxylic dianhydride (ODPA) and 4,4′-(hexafluoroisopropylidene)diphthalic anhydride (6FDA). Contrarily to the reported similar PIs, these PIs exhibit much higher thermal stability or heat resistance, i.e. high glass transition temperatures (Tgs) in the range of 358–473°C, and the decomposition temperatures at 5% weight loss over 476°C under nitrogen. They can afford flexible and strong films with tensile strength of 82.1–93.3 MPa, elongation at break of 3.7%–15.2%, and Young's modulus of 3.3–3.8 GPa. Furthermore, The PI films exhibit good optical transparency with the cut-off wavelength at 313–366 nm and transmittance higher than 73% at 450 nm. The excellent thermal and optical transmittance can be attributed to synthesis method and the introduction of pyridine rings and ortho-methyl groups. The inherent viscosities of PIs via one-step method were found to be 0.58–1.12 dl g−1in DMAc, much higher than those via two-step method. These results indicate these PIs could be potential candidates for optical substrates of organic light emitting diodes (OLEDs).
Quantifying susceptibility of marine invertebrate biocomposites to dissolution in reduced pH
Authors: Chadwick Matthew , Harper Elizabeth M. , Lemasson Anaëlle , Spicer John I. , Peck Lloyd S.
Published: June 2019

Ocean acidification threatens many ecologically and economically important marine calcifiers. The increase in shell dissolution under the resulting reduced pH is an important and increasingly recognized threat. The biocomposites that make up calcified hardparts have a range of taxon-specific compositions and microstructures, and it is evident that these may influence susceptibilities to dissolution. Here, we show how dissolution (thickness loss), under both ambient and predicted end-century pH (approx. 7.6), varies between seven different bivalve molluscs and one crustacean biocomposite and investigate how this relates to details of their microstructure and composition. Over 100 days, the dissolution of all microstructures was greater under the lower pH in the end-century conditions. Dissolution of lobster cuticle was greater than that of any bivalve microstructure, despite its calcite mineralogy, showing the importance of other microstructural characteristics besides carbonate polymorph. Organic content had the strongest positive correlation with dissolution when all microstructures were considered, and together with Mg/Ca ratio, explained 80–90% of the variance in dissolution. Organic content, Mg/Ca ratio, crystal density and mineralogy were all required to explain the maximum variance in dissolution within only bivalve microstructures, but still only explained 50–60% of the variation in dissolution.
N

ɛ

-acetyl lysine derivatives with zinc binding groups as novel HDAC inhibitors
Authors: Wang Fang , Wang Chun , Wang Jie , Zou Yefang , Chen Xiaoxue , Liu Ting , Li Yan , Zhao Yonglong , Li Yongjun , He Bin
Published: June 2019

HDAC inhibitors have been developed very rapidly in clinical trials and even in approvals for treating several cancers. However, there are few reported HDAC inhibitors designed from N

ɛ

-acetyl lysine. In the current study, we raised a novel design, which concerns N

ɛ

-acetyl lysine derivatives containing amide acetyl groups with the hybridization of ZBG groups as novel HDAC inhibitors.
A highly sensitive LC-MS/MS method to determine novel Bruton's tyrosine kinase inhibitor spebrutinib: application to metabolic stability evaluation
Authors: Abdelhameed Ali S. , Attwa Mohamed W. , Al-Shaklia Nasser S. , Kadi Adnan A.
Published: June 2019

Spebrutinib (SBT) is a Bruton's tyrosine kinase inhibitor. SBT is currently in phase II and phase I clinical trials for the management of rheumatoid arthritis and chronic lymphocytic leukaemia, respectively. We developed and validated a liquid chromatography tandem mass spectrometry analytical method to quantify SBT and investigate its metabolic stability. SBT and the naquotinib as internal standard were isocratically eluted on a C18 column. The linearity of the developed method is 5–500 ng ml
−1
(

r
2

≥ 0.9999) in the human liver microsomes (HLMs) matrix. Good sensitivity was approved by the very low limit of detection (0.39 ng ml
−1
). Inter- and intra-assay accuracy values of −1.41 to 12.44 and precision values of 0.71% to 4.78%, were obtained. SBT was found to have an
in vitro
half-life (82.52 min) and intrinsic clearance (8.4 µl min
−1
mg
−1
) as computed following its incubation with HLMs. The latter finding, hypothesize that SBT could be slowly excreted from the body unlike other related tyrosine kinase inhibitors. So, drug plasma level and kidney function should be monitored because of potential bioaccumulation. To the best of our knowledge, this is considered the first analytical method for SBT quantification using LC-MS/MS with application to metabolic stability evaluation.
Early-life lessons of the courtship dance in a dance-duetting songbird, the Java sparrow
Authors: Soma Masayo , Iwama Midori , Nakajima Ryoko , Endo Rika
Published: June 2019

Vocal learners, such as songbirds, must practise singing in a developmentally sensitive period to master songs. Yet, knowledge remains limited about the development of visual displays in birds, even when courtship includes well-coordinated vocalizations (songs) and body motions. The Java sparrow (
Lonchura oryzivora
) is a species of songbird that exhibits a courtship duet dancing exchange between the sexes, with this behaviour driving mating success. In this study, juvenile male Java sparrows were observed in captivity, showing that they repeatedly practise the courtship dance in their early life. We called it ‘practice’, as juvenile birds frequently dance towards family members or other juveniles well before sexual maturation. Based on our observation that dance motor performance increased with age, we propose that the practice is needed for motor learning. In addition, it could also be important for establishing vocal-motional coordination or socialization. Older juveniles gradually became capable of singing and dancing simultaneously, and participated in duet dancing more often. We also found that repeated encounters with the same individual promote dance movement. Though our results do not show how much social experiences account for the development of dance communication, early-life dance practising might influence future reproductive success, like song practising does.
A boundary layer analysis for the initiation of reactive shear bands
Authors: Timms Robert , Purvis Richard
Published: June 2019

A one-dimensional model for the initiation of shear bands in a reactive material is developed, which accounts for thermal softening, strain hardening and strain-rate effects, and models the chemical reaction using an Arrhenius source term. An inhomogeneity in the heat flux is used as the stimulus for localized plastic deformation, and a solution is sought as a perturbation to the elastic solution. In the analysis, the thin zone of localization is identified as a boundary layer. It is found that the behaviour of the perturbations to the temperature, stress and strain hardening variable in the localization zone are governed by four dimensionless parameters which are known in terms of various material properties including density, the heat of reaction, strain-rate sensitivity, thermal sensitivity and strain sensitivity. The resulting equations are solved numerically and a criterion for the onset of shear banding is discussed. The analysis highlights key physical properties which control the reactive shear banding process and gives a deeper insight into how such a process may be understood as a mechanism for the accidental ignition of reactive materials.
Adaptive algorithm for electronic structure calculations using reduction of Gaussian mixtures
Authors: Beylkin Gregory , Monzón Lucas , Yang Xinshuo
Published: June 2019

We present a new adaptive method for electronic structure calculations based on novel fast algorithms for reduction of multivariate mixtures. In our calculations, spatial orbitals are maintained as Gaussian mixtures whose terms are selected in the process of solving equations. Using a fixed basis leads to the so-called basis error since orbitals may not lie entirely within the linear span of the basis. To avoid such an error, multiresolution bases are used in adaptive algorithms so that basis functions are selected from a fixed collection of functions, large enough to approximate solutions within any user-selected accuracy. Our new method achieves adaptivity without using a multiresolution basis. Instead, as part of an iteration to solve nonlinear equations, our algorithm selects the ‘best’ subset of linearly independent terms of a Gaussian mixture from a collection that is much larger than any possible basis since the locations and shapes of the Gaussian terms are not fixed in advance. Approximating an orbital within a given accuracy, our algorithm yields significantly fewer terms than methods using multiresolution bases. We demonstrate our approach by solving the Hartree–Fock equations for two diatomic molecules, HeH
+
and LiH, matching the accuracy previously obtained using multiwavelet bases.
Anomalous strain energy transformation pathways in mechanical metamaterials
Authors: Karpov Eduard G. , Danso Larry A. , Klein John T.
Published: June 2019

This discussion starts with a mechanics version of Parseval's energy theorem applicable to any discrete lattice material with periodic internal structure: a microtruss, grid, frame, origami or tessellation. It provides a simple relationship between the strain energy volumetric/usual and
spectral
distributions in the reciprocal space. The spectral energy distribution leads directly to a spectral entropy of lattice deformation (Shannon's type), whose variance with a material coordinate represents the decrease of information about surface loads in the material interior. Spectral entropy is also a basic measure of complexity of mechanical responses of metamaterials to surface and body loads. Considering transformation of the energy volumetric and spectral distributions with a material coordinate pointed away from a surface load, several interesting anomalies are seen even for simple lattice materials, when compared to continuum materials. These anomalies include selective filtering of surface Raleigh waves (sinusoidal pressure patterns), Saint–Venant effect inversion illustrated by energy spectral distribution contours, occurrence of ‘hiding pockets’ of low deformation, and redirection of strain energy maximum away from axis of a concentrated surface load. The latter phenomenon can be significant for impact protection applications of mechanical metamaterials.
Temperature and polarity based evolutionary model of the ribosomal complex in Thermus thermophilus and Escherichia coli
Authors: Tripathi Rashmi
Published: June 2019

The ribosome is considered a molecular fossil of the RNA world and is the oldest molecular machinery of living cells responsible for translating genetic information encoded by messenger RNA(mRNA) to proteins. Currently not much is known regarding how these proteins were assembled and the potential biogeochemical environment that could have shaped their evolution. In order to answer these questions, a comprehensive analysis of the amino acid frequencies of 30S and 50S ribosomal sub-units occurring in thermophile Thermus thermophilus and mesophile Escherichia coli was performed. The amino acid frequencies in proteins are believed to have been shaped by their pre-biotic abundances in the universe and by heavy bombardment of meteorites on planet earth (4.5-3.8 Ga). Absence of amino acid residues such as cysteine and tryptophan in T.thermophilus and E.coli proteins hints towards the evolution of small and large subunits prior to the origin of metabolic pathways of amino acid synthesis possibly under anoxic and sulphur free conditions. Moreover, an underrepresentation of readily oxidizable amino acids such as methionine, tyrosine and histidine, indicates that these proteins could have evolved in a more reducing environment as was prevalent on early earth. A comparison of amino acid biases with universal UNIPROT estimates, indicates arginine and lysine overrepresentation, linking a role of these amino acids in ribosomal RNA binding and stabilization corresponding to the RNA world hypothesis whereby RNA molecules drove the assembly of living systems. The continuing prevalence of these amino acid biases in modern proteins reflects the functional stability of ancient proteins constructed during billions of years of evolution and provides glimpses into the evolution of the ancient amino acid code. Step-wise accretion models involving increasing complexity of the amino acid code and the ribosomal sub-units are proposed for T.thermophilus and E.coli, providing potential insights regarding the origin of ribosomes in a temperature dependent and polar environment.
Memorability of photographs in subjective cognitive decline and mild cognitive impairment: implications for cognitive assessment
Authors: Bainbridge Wilma A. , Berron David , Schütze Hartmut , Cardenas-Blanco Arturo , Metzger Coraline , Dobisch Laura , Bittner Daniel , Glanz Wenzel , Spottke Annika , Rudolph Janna , Brosseron Frederic , Buerger Katharina , Janowitz Daniel , Fliessbach Klaus , Heneka Michael , Laske Christoph , Buchmann Martina , Peters Oliver , Diesing Dominik , Li Siyao , Priller Josef , Spruth Eike Jakob , Altenstein Slawek , Schneider Anja , Kofler Barbara , Teipel Stefan , Kilimann Ingo , Wiltfang Jens , Bartels Claudia , Wolfsgruber Steffen , Wagner Michael , Jessen Frank , Baker Chris , Düzel Emrah
Published: June 2019

INTRODUCTION

Impaired long-term memory is a defining feature of Mild Cognitive Impairment (MCI). We tested whether this impairment is item-specific, limited to some memoranda whereas some remain consistently memorable.

METHODS

We conducted item-based analyses of long-term visual recognition memory. 394 participants (healthy controls (HC), Subjective Cognitive Decline (SCD), and MCI) in the multicentric DZNE-Longitudinal Cognitive Impairment and Dementia Study (DELCODE) were tested with images from a pool of 835 photographs.

RESULTS

We observed consistent memorability for images in HCs, SCDs, and MCI, predictable by a neural network trained on another healthy sample. Looking at memorability differences between groups, we identified images that could successfully categorize group membership with higher success and a substantial image reduction than the original image set.

DISCUSSION

Individuals with SCD and MCI show consistent memorability for specific items, while other items show significant diagnosticity. Certain stimulus features could optimize diagnostic assessment, while others could support memory.
A set of endogenous control genes for use in quantitative real-time PCR experiments reveal that the wild-type formin Ldia2 is enriched in the early pond snail embryo
Authors: Johnson Harriet F. , Davison Angus
Published: June 2019

Although the pond snail Lymnaea stagnalis is an emerging model organism for molecular studies in a wide variety of fields including development, biomineralisation and neurophysiology, there are a limited number of verified endogenous control genes for use in quantitative real-time PCR (qRT-PCR). As part of larger study on snail chirality or left-right asymmetry, we wished to assay relative gene expression in pond snail embryos, so we evaluated six new candidate control genes, by comparing their expression in three tissues (ovotestis, foot, and embryo) and across three programs (geNorm, Normfinder and Bestkeeper). The specific utility of these control genes was then tested by investigating the relative expression of six experimental transcripts, including the formin Ldia2, a gene that has been associated with chirality in L. stagnalis. All six control genes were found to be suitable for use. Of the six experimental genes that were tested, it was found that all were relatively depleted in the early embryo compared with other tissues, except the formin gene Ldia2. Instead, transcripts of the wild type Ldia2dex were enriched in the embryo, whereas a non-functional frameshifted version Ldia2sin was severely depleted. These differences in Ldia2sin expression were less evident in the ovotestis and not evident in the foot tissue, suggesting that nonsense-mediated decay may be obscured in actively transcribing tissues. This work therefore provides a set of control genes that may be useful to the wider community, and shows how they may be used to assay differences in expression in the early embryo.
Cross-species regulatory sequence activity prediction
Authors: Kelley David R.
Published: June 2019

Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, model organisms have been less explored. Model organism genomes offer both additional training sequences and unique annotations describing tissue and cell states unavailable in humans. Here, we develop a strategy to train deep convolutional neural networks simultaneously on multiple genomes and apply it to learn sequence predictors for large compendia of human and mouse data. Training on both genomes improves gene expression prediction accuracy on held out sequences. We further demonstrate a novel and powerful transfer learning approach to use mouse regulatory models to analyze human genetic variants associated with molecular phenotypes and disease. Together these techniques unleash thousands of non-human epigenetic and transcriptional profiles toward more effective investigation of how gene regulation affects human disease.
Neural correlates of conscious visual perception lie outside the visual system: evidence from the double-drift illusion
Authors: Liu Sirui , Yu Qing , Tse Peter U. , Cavanagh Patrick
Published: June 2019

When perception differs from the physical stimulus, as it does for visual illusions and binocular rivalry, the opportunity arises to localize where perception emerges in the visual processing hierarchy. Representations prior to that stage differ from the eventual conscious percept even though they provide input to it. Here we investigate where and how a remarkable misperception of position emerges in the brain. This “double-drift” illusion causes a dramatic mismatch between retinal and perceived location, producing a perceived path that can differ from its physical path by 45° or more [1]. The deviations in the perceived trajectory can accumulate over at least a second [1] whereas other motion-induced position shifts accumulate over only 80 to 100 ms before saturating [2]. Using fMRI and multivariate pattern analysis, we find that the illusory path does not share activity patterns with a matched physical path in any early visual areas. In contrast, a whole-brain searchlight analysis reveals a shared representation in more anterior regions of the brain. These higher-order areas would have the longer time constants required to accumulate the small moment-to-moment position offsets that presumably originate in early visual cortices, and then transform these sensory inputs into a final conscious percept. The dissociation between perception and the activity in early sensory cortex suggests that perceived position does not emerge in what is traditionally regarded as the visual system but emerges instead at a much higher level.
Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics
Authors: East Kyle W. , Newton Jocelyn C. , Morzan Uriel N. , Acharya Atanu , Skeens Erin , Jogl Gerwald , Batista Victor S. , Palermo Giulia , Lisi George P.
Published: June 2019

CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian accelerated Molecular Dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond timescale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome editing capability.

Abstract Figure
A generalin vitroassay to study enzymatic activities of the ubiquitin system
Authors: Zuo Yukun , Chong Boon Keat , Jiang Kun , Finley Daniel , Klenerman David , Ye Yu
Published: June 2019

The ubiquitin (Ub) system regulates a wide range of cellular signaling pathways. Several hundred E1, E2 and E3 enzymes are together responsible for protein ubiquitination, thereby controlling cellular activities. Due to the numerous enzymes and processes involved, studies on ubiquitination activities have been challenging. We here report a novel FRET-based assay to study thein vitrokinetics of ubiquitination. FRET is established between binding of fluorophore-labeled Ub to eGFP-tagged ZnUBP, a domain that exclusively binds unconjugated Ub. We name this assay the Free Ub Sensor System (FUSS). Using Uba1, UbcH5 and CHIP as model E1, E2 and E3 enzymes, respectively, we demonstrate that ubiquitination results in decreasing FRET efficiency, from which reaction rates can be determined. Further treatment with USP21, a deubiquitinase, leads to increased FRET efficiency, confirming the reversibility of the assay. We subsequently use this assay to show that increasing the concentration of CHIP or UbcH5 but not Uba1 enhances ubiquitination rates, and develop a novel machine learning approach to model ubiquitination. The overall ubiquitination activity is also increased upon incubation with tau, a substrate of CHIP. Our data together demonstrate the versatile applications of a novel ubiquitination assay that does not require labeling of E1, E2, E3 or substrates, and is thus likely compatible with any E1-E2-E3 combinations.
A Comprehensive Integrated Anatomical And Molecular Atlas Of Rodent Intrinsic Cardiac Nervous System
Authors: Achanta Sirisha , Gorky Jonathan , Leung Clara , Moss Alison , Robbins Shaina , Eisenman Leonard , Chen Jin , Tappan Susan , Heal Maci , Farahani Navid , Huffman Todd , England Steve , Cheng Zixi (Jack) , Vadigepalli Rajanikanth , Schwaber James S.
Published: June 2019

In this study, we developed, coordinated, and integrated several technologies including novel whole organ imaging, software development to support the very first precise 3D neuroanatomical mapping and molecular phenotyping of the intracardiac nervous system (ICN). While qualitative and gross anatomical descriptions of the anatomy of the ICN have been presented, we here bring forth the first comprehensive atlas at large scale of the entire ICN in rat at a single cell resolution. Our work for the first time provides a novel 3D model to precisely integrate anatomical, functional and molecular data in the 3D digitally reconstructed whole heart with high resolution at the micron scale. This work represents the cutting edge in a long history of attempts to understand the anatomical substrate upon which the neuronal control of cardiac function is built. To our knowledge, there has not yet been a comprehensive histological mapping to generate a neurocardiac atlas at cellular and molecular level for the whole heart of any species. We now display the full extent and the position of neuronal clusters on the base and posterior left atrium, and the distribution of molecular phenotypes in that context. In addition we display in this context distinct molecular phenotypes that are defined along the base-to-apex axis, and the present novel discovery of their phenotypical spatial gradients, have not been previously described. The development of these approaches needed to acquire these data has produced method pipelines which can not only achieve the goals of anatomical and molecular mapping of the heart, but also provide the method pipelines for mapping other organs (e.g., stomach, lung, kidney, and liver).
Multi-generational Analysis and Manipulation of Chromosomes in a Polyploid Cyanobacterium
Authors: Moore Kristin A. , Tay Jian Wei , Cameron Jeffrey C.
Published: June 2019

Faithful inheritance of genetic material from one generation to the next is an essential process for all life on earth. Much of what is known about microbial DNA replication and inheritance has been learned from a small number of bacterial species that share many common traits. Whether these pathways are conserved across the great diversity of the microbiome remains unclear. To address this question, we studied chromosome dynamics in a polyploid photosynthetic bacteria using single cell, time-lapse microscopy over multi-generation lineages in conjunction with inducible CRISPR-interference and fluorescent chromosome labeling. With this method we demonstrated the long-term consequences of manipulating parameters such as cell growth, cell division, and DNA replication and segregation on chromosome regulation in a polyploid bacterial species. We find that these bacteria are surprisingly resilient to chromosome disruption resulting in continued cell growth when DNA replication is inhibited and even in the complete absence of chromosomes.
The coupling mechanism of reassembly quality with uncertainty of remanufactured parts
Authors: Zhang Cuixia , Liu Conghu , Chen Jianqing , Li Qiang , He Kang , Gao Mengdi , Cai Wei
Published: June 2019

Purpose

The uncertainty of remanufacturing parts is a key factor affecting the quality of remanufactured products. Therefore, the purpose of this paper is to measure the uncertainty of remanufactured parts and study the coupling mechanism of reassembly quality.

Design/methodology/approach

First, uncertainty of remanufactured parts is analyzed, and the uncertainty measure model for remanufacturing parts based on entropy is constructed. Second, the nonlinear mapping model between the uncertainty and reassembly quality were studied using Gauss-Newton iterative method to reveal the coupling mechanism between uncertainty of remanufacturing parts and reassembly quality. Finally, the model is verified in the reassembly process of remanufacturing cylinder head.

Findings

The method can guide reassembly operations to improve the reassembly quality with uncertainty of remanufactured parts.

Originality/value

This study provides practical implications by developing a multivariate nonlinear mapping model for reassembly quality based on entropy to determine the uncertainty factors that affect the reassembly quality significantly and then correct the reassembly operation to better optimize the allocation of remanufacturing production resources. The study also theoretically contributes to reveal the coupling mechanism of reassembly quality with the uncertainty of remanufactured parts.
The optimal capital structure of Swiss dairy farms
Authors: Schorr Anke , Lips Markus
Published: June 2019

Purpose

The purpose of this paper is to propose a novel way of determining optimal capital structure, applied to sub-groups of Swiss dairy farms from 2003 to 2014. Optimization of capital structure is carried out with respect to two performance indicators from an economic value added perspective.

Design/methodology/approach

Optimal values of capital structure are obtained based on a minimization of correlation between economic performance indicators and a distance function of the debt-to-asset ratio distribution to its quantiles. The approach differs from existing approaches in relying solely on empirical data and in using fewer external parameters, which are difficult to estimate, such as risk aversion coefficients. An unbalanced panel data set from the Swiss Farm Accounting Network with almost 14,000 dairy farm observations serves as input data to the model.

Findings

Concise optimal values of capital structure result for regional and temporal sub-groups of Swiss dairy farms. Comparing the evolution of optimal values for these sub-groups with existing models of optimal capital structure, the authors infer that dairy farmers in the mountain region are less risk averse than their counterparts in the valley region and that falling interest rates increase the optimal value of debt-to-asset ratio.

Originality/value

The straightforward computation of optimal values for capital structure without intermediate parameters is useful and new. In addition, the authors’ model can be used as a tool for comparison and validation of previous models with the same aim, e.g. for comparison of risk aversion coefficients or qualitative behavior of optimal values for capital structure.
CEO power and corporate social responsibility
Authors: Harper Joel , Sun Li
Published: June 2019

Purpose

The purpose of this paper is to examine the impact of chief executive officer (CEO) power on corporate social responsibility (CSR) performance.

Design/methodology/approach

The authors use regression analysis to investigate the research question.

Findings

Using a 23-year panel sample with 1,574 unique US firms and 8,575 firm-year observations, the authors find a significant and negative relation between CEO power and CSR, suggesting that firms with more powerful CEOs engage in less CSR activities.

Originality/value

The results reveal that more powerful CEOs become less responsive to the needs of stakeholder groups, confirming the validity of the stakeholder theory of CSR.
Family businesses, corporate social responsibility, and websites
Authors: Iaia Lea , Vrontis Demetris , Maizza Amedeo , Fait Monica , Scorrano Paola , Cavallo Federica
Published: June 2019

Purpose

The purpose of this paper is to identify the distinctive elements of CSR communications that characterize the communications models of family businesses in the Italian wine industry, and to compare them with nonfamily businesses.

Design/methodology/approach

Using a case study approach, a sample of large and medium companies practicing corporate social responsibility was identified. The content of their websites was examined using content analysis and text mining (correspondence analysis techniques and word association analysis using the T-Lab software).

Findings

The analysis indicates that the ownership structure nature makes a difference in the online CSR communications process. The cultural identity in both family and nonfamily businesses is founded on intangible factors such as tradition; however, being a family business is a fundamental driver in the online CSR communications process, no longer forming a bond among players in the wine industry, but rather linking with other wine family businesses.

Research limitations/implications

One limitation of this work is the small size of the investigated sample. An added value it contributes is its focus on the Italian wine industry. The paper provides the essential elements that family and nonfamily wine businesses should consider in customizing their CSR communications with the brand’s specific details.

Originality/value

The authors highlighted the similarities and differences of family and nonfamily wine businesses in terms of their online CSR communications. The authors also observed how the family wine business identity, in its multidimensional construct, has common factors with what we call “familiness.” This research could establish a starting point for further work within this important sector.