bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound localization microscopy to image and assess microvasculature in a rat kidney
Authors: Foiret Josquin , Zhang Hua , Ilovitsh Tali , Mahakian Lisa , Tam Sarah , Ferrara Katherine W. 
Published: October 2017

AbstractThe recent development of ultrasound localization microscopy, where individual microbubbles (contrast agents) are detected and tracked within the vasculature, provides new opportunities for imaging the vasculature of entire organs with a spatial resolution below the diffraction limit. In stationary tissue, recent studies have demonstrated a theoretical resolution on the order of microns. In this work, single microbubbles were localized in vivo in a rat kidney using a dedicated high frame rate imaging sequence. Organ motion was tracked by assuming rigid motion (translation and rotation) and appropriate correction was applied. In contrast to previous work, coherence-based non-linear phase inversion processing was used to reject tissue echoes while maintaining echoes from very slowly moving microbubbles. Blood velocity in the small vessels was estimated by tracking microbubbles, demonstrating the potential of this technique to improve vascular characterization. Previous optical studies of microbubbles in vessels of approximately 20 microns have shown that expansion is constrained, suggesting that microbubble echoes would be difficult to detect in such regions. We therefore utilized the echoes from individual MBs as microscopic sensors of slow flow associated with such vessels and demonstrate that highly correlated, wideband echoes are detected from individual microbubbles in vessels with flow rates below 2 mm/s.
Characterization of serum miRNAs as molecular biomarkers for acute Stanford type A aortic dissection diagnosis
Authors: Xu Zhenjun , Wang Qiang , Pan Jun , Sheng Xia , Hou Dongxia , Chong Hoshun , Wei Zhe , Zheng Shasha , Xue Yunxing , Zhou Qing , Cao Hailong , Zhang Chen-Yu , Wang Dongjin , Jiang Xiaohong 
Published: October 2017

AbstractEarly and convenient diagnosis is urgently needed for acute Stanford type A aortic dissection (AAAD) patients due to its high mortality within the first 48 hours. Circulating microRNAs (miRNAs) are promising biomarkers of cardiovascular diseases, however, little is known about circulating miRNAs involved in AAAD. Here, the blood serum was sampled from 104 AAAD+ patients and 103 age-matched donors. Initial screening was conducted using the TaqMan Low Density Array followed by RT-qPCR confirmation. According to the two-phase selection and validation process, we found that miR-25, miR-29a and miR-155 were significantly elevated, while miR-26b was markedly decreased in AAAD+ serum samples compared with AAAD− individuals. Most importantly, for individuals with hypertension, which is a major contributor to AAAD, the 4-miRNA panel also showed high accuracy in predicting those who are more likely to develop AAAD. In the blind trial set, the panel correctly classified 93.33% AAAD+ patients and 86.67% controls from the hypertension cohort. Finally, the serum miRNA-based biomarker for early AAAD detection was supported by a retrospective analysis. Taken together, we identify a distinct profile of 4-miRNA that can serve as a noninvasive biomarker for AAAD diagnosis, especially for those with hypertension.
An optical Fourier transform coprocessor with direct phase determination
Authors: Macfaden Alexander J. , Gordon George S. D. , Wilkinson Timothy D. 
Published: October 2017

AbstractThe Fourier transform is a ubiquitous mathematical operation which arises naturally in optics. We propose and demonstrate a practical method to optically evaluate a complex-to-complex discrete Fourier transform. By implementing the Fourier transform optically we can overcome the limiting O(nlogn) complexity of fast Fourier transform algorithms. Efficiently extracting the phase from the well-known optical Fourier transform is challenging. By appropriately decomposing the input and exploiting symmetries of the Fourier transform we are able to determine the phase directly from straightforward intensity measurements, creating an optical Fourier transform with O(n) apparent complexity. Performing larger optical Fourier transforms requires higher resolution spatial light modulators, but the execution time remains unchanged. This method could unlock the potential of the optical Fourier transform to permit 2D complex-to-complex discrete Fourier transforms with a performance that is currently untenable, with applications across information processing and computational physics.
Evolving stability and pH-dependent activity of the high redox potential Botrytis aclada laccase for enzymatic fuel cells
Authors: Scheiblbrandner Stefan , Breslmayr Erik , Csarman Florian , Paukner Regina , Führer Johannes , Herzog Peter L. , Shleev Sergey V. , Osipov Evgeny M. , Tikhonova Tamara V. , Popov Vladimir O. , Haltrich Dietmar , Ludwig Roland , Kittl Roman 
Published: October 2017

AbstractFungal high redox potential laccases are proposed as cathodic biocatalysts in implantable enzymatic fuel cells to generate high cell voltages. Their application is limited mainly through their acidic pH optimum and chloride inhibition. This work investigates evolutionary and engineering strategies to increase the pH optimum of a chloride-tolerant, high redox potential laccase from the ascomyceteBotrytis aclada. The laccase was subjected to two rounds of directed evolution and the clones screened for increased stability and activity at pH 6.5. Beneficial mutation sites were investigated by semi-rational and combinatorial mutagenesis. Fourteen variants were characterised in detail to evaluate changes of the kinetic constants. Mutations increasing thermostability were distributed over the entire structure. Among them, T383I showed a 2.6-fold increased half-life by preventing the loss of the T2 copper through unfolding of a loop. Mutations affecting the pH-dependence cluster around the T1 copper and categorise in three types of altered pH profiles: pH-type I changes the monotonic decreasing pH profile into a bell-shaped profile, pH-type II describes increased specific activity below pH 6.5, and pH-type III increased specific activity above pH 6.5. Specific activities of the best variants were up to 5-fold higher (13 U mg−1) thanBaL WT at pH 7.5.
Investigation of Melts of Polybutylcarbosilane Dendrimers by 1H NMR Spectroscopy
Authors: Matveev Vladimir V. , Markelov Denis A. , Dvinskikh Sergey V. , Shishkin Andrei N. , Tyutyukin Konstantin V. , Penkova Anastasia V. , Tatarinova Elena A. , Ignat’eva Galina M. , Milenin Sergey A. 
Published: October 2017

AbstractMelts of polybutylcarbosilane (PBC) dendrimers from third (G3) up to sixth (G6) generations are investigated by 1H NMR spectroscopy in a wide temperature range up to 493 K. At room temperature, NMR spectra of G3-G5 dendrimers exhibit resolved, solution-like spectra (“liquid” phase). In contrast, the spectrum of the G6 dendrimer is characterized by a single unresolved broad line at whole temperature range, which supports the presence of an anomalous phase state of G6 at temperatures higher than glass transition temperature. For the first time, an unexpected transition of G5 dendrimer from a molecular liquid state to an anomalous state/phase upon temperature increase has been detected using NMR data. Specifically, an additional wide background line appears in the G5 spectrum above 473 K, and this line corresponds to a G5 state characterized by restricted molecular mobility, i.e., a state similar to the “anomalous” phase of G6 melt. The fraction of the G5 dendrimers in “anomalous” phase at 493 K is approximately 40%. Analysis of the spectral shapes suggests that changes in the G5 dendrimers are reversible with temperature.
Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes
Authors: Weise Nicholas J. , Ahmed Syed T. , Parmeggiani Fabio , Galman James L. , Dunstan Mark S. , Charnock Simon J. , Leys David , Turner Nicholas J. 
Published: October 2017

AbstractThe suite of biological catalysts found in Nature has the potential to contribute immensely to scientific advancements, ranging from industrial biotechnology to innovations in bioenergy and medical intervention. The endeavour to obtain a catalyst of choice is, however, wrought with challenges. Herein we report the design of a structure-based annotation system for the identification of functionally similar enzymes from diverse sequence backgrounds. Focusing on an enzymatic activity with demonstrated synthetic and therapeutic relevance, five new phenylalanine ammonia lyase (PAL) enzymes were discovered and characterised with respect to their potential applications. The variation and novelty of various desirable traits seen in these previously uncharacterised enzymes demonstrates the importance of effective sequence annotation in unlocking the potential diversity that Nature provides in the search for tailored biological tools. This new method has commercial relevance as a strategy for assaying the ‘evolvability’ of certain enzyme features, thus streamlining and informing protein engineering efforts.
Main factor causing “faster-is-slower” phenomenon during evacuation: rodent experiment and simulation
Authors: Oh Hyejin , Park Junyoung 
Published: October 2017

AbstractUnderstanding crowd flow at bottlenecks is important for preventing accidents in emergencies. In this research, a crowd evacuation passing through a narrow exit connected with guide-walls is analysed using the discrete element method based on physical and psychological modelling in parallel with empirical rodent research. Results of rodent experiment and simulation demonstrate the faster-is-slower (FIS) effect, which is a well-known phenomenon in pedestrian dynamics. As the angle of the guide-walls increases, agents rapidly evacuate the room even though they have low velocity. The increase in this angle causes agents to form lanes. It is validated that ordered agents evacuate expeditiously with relatively low velocity despite expectations to the contrary. The extracted experimental and simulation data strongly suggest that the agents’ standard deviation of velocity can be a key factor causing the FIS effect. It is found that the FIS effect can be eliminated by controlling the standard deviation.
Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486
Authors: Song Yoseb , Shin Jongoh , Jeong Yujin , Jin Sangrak , Lee Jung-Kul , Kim Dong Rip , Kim Sun Chang , Cho Suhyung , Cho Byung-Kwan 
Published: October 2017

AbstractAutotrophic conversion of CO2 to value-added biochemicals has received considerable attention as a sustainable route to replace fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, an understanding of acetogenesis-related genes and their regulatory elements is required. Here, we completed the genome sequence of the syngas fermenting Eubacterium limosum ATCC 8486 and determined its transcription start sites (TSS). We constructed a 4.4 Mb long circular genome with a GC content of 47.2% and 4,090 protein encoding genes. To understand the transcriptional and translational regulation, the primary transcriptome was augmented, identifying 1,458 TSSs containing a high pyrimidine (T/C) and purine nucleotide (A/G) content at the −1 and +1 position, respectively, along with 1,253 5′-untranslated regions, and principal promoter elements such as −10 (TATAAT) and −35 (TTGACA), and Shine-Dalgarno motifs (GGAGR). Further analysis revealed 93 non-coding RNAs, including one for potential transcriptional regulation of the hydrogenase complex via interaction with molybdenum or tungsten cofactors, which in turn controls formate dehydrogenase activity of the initial step of Wood-Ljungdahl pathway. Our results provide comprehensive genomic information for strain engineering to enhance the syngas fermenting capacity of acetogenic bacteria.
Challenging FRET-based E-Cadherin force measurements in Drosophila
Authors: Eder Dominik , Basler Konrad , Aegerter Christof M. 
Published: October 2017

AbstractMechanical forces play a critical role during embryonic development. Cellular and tissue wide forces direct cell migration, drive tissue morphogenesis and regulate organ growth. Despite the relevance of mechanics for these processes, our knowledge of the dynamics of mechanical forces in living tissues remains scarce. Recent studies have tried to address this problem with the development of tension sensors based on Förster resonance energy transfer (FRET). These sensors are integrated into force bearing proteins and allow the measurement of mechanical tensions on subcellular structures. Here, we developed such a FRET-based sensor to measure E-Cadherin tensions in different Drosophila tissues in and ex vivo. Similar to previous studies, we integrated the sensor module into E-cadherin. We assessed the sensitivity of the sensor by measuring dynamic, developmental processes and mechanical modifications in three Drosophila tissues: the wing imaginal disc, the amnioserosa cells and the migrating border cells. However, these assays revealed that the sensor is not functional to measure the magnitude of tensions occurring in any of the three tissues. Moreover, we encountered technical problems with the measurement of FRET, which might represent more general pitfalls with FRET sensors in living tissues. These insights will help future studies to better design and control mechano-sensing experiments.
Recurrent water deficit causes epigenetic and hormonal changes in citrus plants
Authors: Neves Diana Matos , Almeida Lucas Aragão da Hora , Santana-Vieira Dayse Drielly Souza , Freschi Luciano , Ferreira Claudia Fortes , Soares Filho Walter dos Santos , Costa Marcio Gilberto Cardoso , Micheli Fabienne , Coelho Filho Maurício Antônio , Gesteira Abelmon da Silva 
Published: October 2017

AbstractThe present study evaluated the physiological, molecular and hormonal parameters from scion/rootstock interaction of citrus plants during recurrent water deficit. Responses of the Valencia (VO) scion variety grafted on two rootstocks with different soil water extraction capacities, Rangpur Lime (RL) and Sunki Maravilha (SM), during three successive periods of water deficit: plants exposed to a single episode of water deficit (WD1) and plants exposed to two (WD2) and three (WD3) recurrent periods of WD were compared. The combinations VO/RL and VO/SM presented polymorphic alterations of epigenetic marks and hormonal (i.e. abscisic acid, auxins and salicylicacid) profiles, which were particularly prominent when VO/SM plantswere exposed toWD3 treatment. Upon successive drought events, the VO/SM combination presented acclimatization characteristics that enable higher tolerance to water deficit by increasing transpiration (E), stomatal conductance (g
s
) and photosynthetic rate (A), which in turn may have facilitated the whole plant survival. Besides providing comprehensive data on the scion/rootstock interactions upon successive stress events, this study brings the first dataset suggesting that epigenetic alterations in citrus plants triggered by recurrent water deficit lead to improved drought tolerance in this crop species.
Impact of analytical and biological variations on classification of diabetes using fasting plasma glucose, oral glucose tolerance test and HbA1c
Authors: Chai Jia Hui , Ma Stefan , Heng Derick , Yoong Joanne , Lim Wei-Yen , Toh Sue-Anne , Loh Tze Ping 
Published: October 2017

AbstractHistorically, diabetes is diagnosed by measuring fasting (FPG) and two-hour post oral glucose load (OGTT) plasma concentration and interpreting it against recommended clinical thresholds of the patient. More recently, glycated haemoglobin A1c (HbA1c) has been included as a diagnostic criterion. Within-individual biological variation (CVi), analytical variation (CVa) and analytical bias of a test can impact on the accuracy and reproducibility of the classification of a disease. A test with large biological and analytical variation increases the likelihood of erroneous classification of the underlying disease state of a patient. Through numerical simulations based on the laboratory results generated from a large population health survey, we examined the impact of CVi, CVa and bias on the classification of diabetes using fasting plasma glucose (FPG), oral glucose tolerance test (OGTT) and HbA1c. From the results of the simulations, HbA1c has comparable performance to FPG and is better than OGTT in classifying subjects with diabetes, particularly when laboratory methods with smaller CVa are used. The use of the average of the results of the repeat laboratory tests has the effect of ameliorating the combined (analytical and biological) variation. The averaged result improves the consistency of the disease classification.
Electrodeposition of tin on Nafion-bonded carbon black as an active catalyst layer for efficient electroreduction of CO2 to formic acid
Authors: Wang Qinian , Wang Xinqi , Wu Chao , Cheng Yuanyuan , Sun Qingye , Dong Heng , Yu Hongbing 
Published: October 2017

AbstractElectroreduction of CO2 to formic acid (ERCF) based on gas diffusion electrodes (GDEs) has been considered as a promising method to convert CO2 into value-added chemicals. However, current GDEs for ERCF suffer from low efficiency of electron transfer. In this work, a novel Sn-based gas diffusion electrode (ESGDE) is prepared by electrodepositing Sn on Nafion-bonded carbon black as catalyst layer to enhance electron transfer and thus the efficiency of ERCF. The highest Faraday efficiency (73.01 ± 3.42%), current density (34.21 ± 1.14 mA cm−2) and production rate (1772.81 ± 59.08 μmol m−2 s−1) of formic acid are obtained by using the ESGDE with electrodeposition time of 90 s in 0.5 M KHCO3 solution, which are one of the highest values obtained from Sn-based gas diffusion electrodes under similar conditions. The notable efficiency of ERCF achieved here should be attributed to the enhancement in the reactants transfer as well as the three-dimensional reaction zone. This work will be helpful for the industrial application of GDEs in EFCF.
Investigating light curve modulation via kernel smoothing
Authors: Süveges Maria , Anderson Richard I. 
Published: October 2017

Context.Recent studies have revealed a hitherto unknown complexity of Cepheid pulsations by discovering irregular modulated variability using photometry, radial velocities, and interferometry.Aims.We aim to perform a statistically rigorous search and characterization of such phenomena in continuous time, applying it to 53 classical Cepheids from the OGLE-III catalog.Methods.We have used local kernel regression to search for both period and amplitude modulations simultaneously in continuous time and to investigate their detectability. We determined confidence intervals using parametric and non-parametric bootstrap sampling to estimate significance, and investigated multi-periodicity using a modified pre-whitening approach that relies on time-dependent light curve parameters.Results.We find a wide variety of period and amplitude modulations and confirm that first overtone pulsators are less stable than fundamental mode Cepheids. Significant temporal variations in period are more frequently detected than those in amplitude. We find a range of modulation intensities, suggesting that both amplitude and period modulations are ubiquitous among Cepheids. Over the 12-year baseline offered by OGLE-III, we find that period changes are often nonlinear, sometimes cyclic, suggesting physical origins beyond secular evolution. Our method detects modulations (period and amplitude) more efficiently than conventional methods that are reliant on certain features in the Fourier spectrum, and pre-whitens time series more accurately than using constant light curve parameters, removing spurious secondary peaks effectively.Conclusions.Period and amplitude modulations appear to be ubiquitous among Cepheids. Current detectability is limited by observational cadence and photometric precision: detection of amplitude modulation below 3 mmag requires space-based facilities. Recent and ongoing space missions (K2, BRITE, MOST, CoRoT) as well as upcoming ones (TESS, PLATO) will significantly improve detectability of fast modulations, such as cycle-to-cycle variations, by providing high-cadence high-precision photometry. High-quality long-term ground-based photometric time series will remain crucial to study longer-term modulations and to disentangle random fluctuations from secular evolution.
Acupuncture for Infertility in Women with Polycystic Ovary Syndrome: What Does It Add?
Authors: Stener-Victorin Elisabet 
Published: October 2017

AbstractAcupuncture is a nonpharmacological therapy to induce ovulation in women with polycystic ovary syndrome (PCOS), but not until recently there has been a study reporting the live birth rate following ovulation induction by acupuncture or its potential as an adjuvant to pharmacological ovulation induction. Clomiphene citrate, the first-line treatment for ovulation induction in women with PCOS, was twice as effective at achieving live birth, with no effect of acupuncture alone or in combination with clomiphene. Thus, the findings from the recent randomized control trial do not support acupuncture as an infertility treatment, alone or in combination, in women with PCOS. The recent trial has important clinical implications not only for women with PCOS with an active wish for pregnancy but also for those with no active wish of pregnancy, as acupuncture induces ovulation to a higher degree than no treatment and also relieves other PCOS-related symptoms. This narrative review dissects possible mechanism of action of acupuncture on reproductive function, it discusses stimulation parameters, it discusses the recent findings on live birth, and it also discusses the control situation in potential future acupuncture trials.
Patellofemoral Cartilage Restoration: Indications, Techniques, and Outcomes of Autologous Chondrocytes Implantation, Matrix-Induced Chondrocyte Implantation, and Particulated Juvenile Allograft Cartilage
Authors: Hinckel Betina , Gomoll Andreas 
Published: October 2017

AbstractFocal chondral defects are common in the patellofemoral (PF) joint and can significantly impair the quality of life. The autologous chondrocytes implantation (ACI) technique has evolved over the past 20 years: the first-generation technique involves the use of a periosteal patch, the second-generation technique (collagen-cover) uses a type I/III collagen membrane, and the newest third-generation technique seeds and cultivates the collagen membrane with chondrocytes prior to implantation and is referred to as matrix-induced autologous chondrocyte implantation. Particulated juvenile allograft cartilage (PJAC) (DeNovo NT) is minced cartilage allograft from juvenile donors. A thorough physical exam is important, especially for issues affecting the PF joint, to isolate the location and source of pain, and to identify associated pathologies. Imaging studies allow further characterization of the lesions and identification of associated pathologies and alignment. Conservative management should be exhausted before proceeding with surgical treatment. Steps of surgical treatment are diagnostic arthroscopy and biopsy, chondrocytes culture and chondrocyte implantation for the three generations of ACI, and diagnostic arthroscopy and implantation for PJAC. The techniques and their outcomes will be discussed in this article.