bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time reconstruction and visualisation towards dynamic feedback control during time-resolved tomography experiments at TOMCAT
Authors: Buurlage Jan-Willem , Marone Federica , Pelt Daniël M. , Palenstijn Willem Jan , Stampanoni Marco , Batenburg K. Joost , Schlepütz Christian M. 
Published: December 2019

AbstractTomographic X-ray microscopy beamlines at synchrotron light sources worldwide have pushed the achievable time-resolution for dynamic 3-dimensional structural investigations down to a fraction of a second, allowing the study of quickly evolving systems. The large data rates involved impose heavy demands on computational resources, making it difficult to readily process and interrogate the resulting volumes. The data acquisition is thus performed essentially blindly. Such a sequential process makes it hard to notice problems with the measurement protocol or sample conditions, potentially rendering the acquired data unusable, and it keeps the user from optimizing the experimental parameters of the imaging task at hand. We present an efficient approach to address this issue based on the real-time reconstruction, visualisation and on-the-fly analysis of a small number of arbitrarily oriented slices. This solution, requiring only a single additional computing workstation, has been implemented at the TOMCAT beamline of the Swiss Light Source. The system is able to process multiple sets of slices per second, thus pushing the reconstruction throughput on the same level as the data acquisition. This enables the monitoring of dynamic processes as they occur and represents the next crucial step towards adaptive feedback control of time-resolved in situ tomographic experiments.
Visible light-induced thymine dimerisation based on large localised field gradient by non-uniform optical near-field
Authors: Tate Naoya , Yatsui Takashi 
Published: December 2019

AbstractThe localised excitations of several molecular reactions utilising optical irradiation have been studied in the field of molecular physics. In particular, deoxyribonucleic acid (DNA) strands organise the genetic information of all living matter. Therefore, artificial methods for freely controlling reactions using only light irradiation are highly desirable for reactions of these strands; this in regard with artificial protein synthesis, regional genetic curing, and stochastic analysis of several genetic expressions. Generally, DNA strands have strong absorption features in the deep ultra-violet (DUV) region, which are related to the degradation and reconstruction of the strand bonding structures. However, irradiation by DUV light unavoidably induces unintended molecular reactions which can damage and break the DNA strands. In this paper, we report a photo-induced molecular reaction initiated by the irradiation of DNA strands with visible light. We utilised photo-dissociation from the vibrational levels induced by non-uniform optical near-fields surrounding nanometric Au particles to which DNA strands were attached. The results were experimentally observed by a reduction in the DUV absorbance of the DNA strands during irradiation. There was a much higher yield of molecular reactions than expected due to the absorbance of visible light, and no defects were caused in the DNA strands.
Heterotopic Ossification in Orthopaedic and Trauma surgery: A Histopathological Ossification Score
Authors: Ohlmeier M. , Krenn V. , Thiesen D. M. , Sandiford N. A. , Gehrke T. , Citak M. 
Published: December 2019

AbstractHeterotopic Ossification (HO) is a potential long-term complication in orthopaedic surgery. It is commonly classified according to the Brooker classification, which is based on radiological findings. To our knowledge the correlation of histological features to the Brooker grade is unknown as is the association between HO and the indication for revision. The aim of this paper is to analyze the ossification grade of HO tissue in patients undergoing revision hip and knee arthroplasty and to propose a histologically based classification system for HO. We also assess the relationship between the grade of HO and the indication for revision (septic and aseptic revision). From January to May 2019 we collected 50 human HO samples from hip and knee revision arthroplasty cases. These tissue samples were double-blinded and sent for histopathological diagnostic. Based on these results, we developed a classification system for the progression of HO. The grade of ossification was based on three characteristics: Grade of heterotopic ossification (Grade 1–3), presence of necrosis (N0 or N1) and the presence of osteomyelitis (HOES-Score Type 1 to 5). Demographic data as well as surgical details and indication for surgery was prospectively collected from clinical records. Fifty tissue samples were harvested from 44 hips and 6 knee joints. Of these 33 exhibited Grade I ossifications (66%), followed by 11 Grade II (22%) and one Grade III (2%). Necrosis was noted in two tissue samples (4%) and 2 more had osteomyelitis findings according to HOES-Score. Six samples (12%) with radiologically suggestive of HO turned out to be wear-induced synovitis, SLIM Type 1. Of these cases 16 were septic (32%) and 34 aseptic (68%) revisions. Most of the HO tissue samples were classified as a low-grade. High-grade ossification-Score is rare. Higher grades of ossification seem to be associated with septic revision cases. Wear-induced synovitis potentially influences HO development. A histological scoring system for ossification grading can be derived from the data presented in this study.
Assessing the impact of global climate changes on irrigated wheat yields and water requirements in a semi-arid environment of Morocco
Authors: Bouras Elhoussaine , Jarlan Lionel , Khabba Said , Er-Raki Salah , Dezetter Alain , Sghir Fathallah , Tramblay Yves 
Published: December 2019

AbstractThe present work aims to quantify the impact of climate change (CC) on the grain yields of irrigated cereals and their water requirements in the Tensift region of Morocco. The Med-CORDEX (MEDiterranean COordinated Regional Climate Downscaling EXperiment) ensemble runs under scenarios RCP4.5 (Representative Concentration Pathway) and RCP8.5 are first evaluated and disaggregated using the quantile-quantile approach. The impact of CC on the duration of the main wheat phenological stages based on the degree-day approach is then analyzed. The results show that the rise in air temperature causes a shortening of the development cycle of up to 50 days. The impacts of rising temperature and changes in precipitation on wheat yields are next evaluated, based on the AquaCrop model, both with and without taking into account the fertilizing effect of CO2. As expected, optimal wheat yields will decrease on the order of 7 to 30% if CO2 concentration rise is not considered. The fertilizing effect of CO2 can counterbalance yield losses, since optimal yields could increase by 7% and 13% respectively at mid-century for the RCP4.5 and RCP8.5 scenarios. Finally, water requirements are expected to decrease by 13 to 42%, mainly in response to the shortening of the cycle. This decrease is associated with a change in temporal patterns, with the requirement peak coming two months earlier than under current conditions.
Adherence to guideline recommendations for coronary angiography in a poor South-East Asian setting: Impact on short- and medium-term clinical outcomes
Authors: Qanitha Andriany , Uiterwaal Cuno S. P. M. , Henriques Jose P. S. , Mappangara Idar , Amir Muzakkir , Saing Sumarsono G. , de Mol Bastianus A. J. M. 
Published: December 2019

AbstractIn South-East Asian populations and particularly in Indonesia, access to coronary angiography (CAG) is limited. We aimed to assess the adherence for undergoing CAG for indicated patients, according to the guideline recommendations. We then examined whether this adherence would have an impact on patients’ short- and medium-term mortality and morbidity. We consecutively enrolled 474 patients with acute and stable coronary artery disease who had indication for CAG at Makassar Cardiac Center, Indonesia from February 2013 to December 2014. We found that adherence to CAG recommendation in poor South-East Asian setting is low. Of 474 recommended patients, only 273 (57.6%) underwent the procedure. Factors for not undergoing CAG were: older age, female gender, low educational and socio-economic status, and insurance type. While reasons for patients refusing CAG and subsequent intervention included fear, symptoms reduction, and lack of trust concerning the procedure benefit. During follow-up (median 19 (IQR 6–39.3) months), 155 (32.7%) patients died, and 259 (54.6%) experienced at least one adverse event. Adherence to CAG recommendation was associated with a significantly lower short- and medium-term mortality, independent of revascularization and other potential confounders. In sub-group analysis, adhered patients “with revascularization” had significantly better outcomes compared to the “non-revascularization” and “not adhere” groups.
Seismic surveys reduce cetacean sightings across a large marine ecosystem
Authors: Kavanagh A. S. , Nykänen M. , Hunt W. , Richardson N. , Jessopp M. J. 
Published: December 2019

AbstractNoise pollution is increasing globally, and as oceans are excellent conductors of sound, this is a major concern for marine species reliant on sound for key life functions. Loud, impulsive sounds from seismic surveys have been associated with impacts on many marine taxa including mammals, crustaceans, cephalopods, and fish. However, impacts across large spatial scales or multiple species are rarely considered. We modelled over 8,000 hours of cetacean survey data across a large marine ecosystem covering > 880,000 km2to investigate the effect of seismic surveys on baleen and toothed whales. We found a significant effect of seismic activity across multiple species and habitats, with an 88% (82–92%) decrease in sightings of baleen whales, and a 53% (41–63%) decrease in sightings of toothed whales during active seismic surveys when compared to control surveys. Significantly fewer sightings of toothed whales also occurred during active versus inactive airgun periods of seismic surveys, although some species-specific response to noise was observed. This study provides strong evidence of multi-species impacts from seismic survey noise on cetaceans. Given the global proliferation of seismic surveys and large propagation distances of airgun noise, our results highlight the large-scale impacts that marine species are currently facing.
Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing
Authors: Decio Pâmela , Ustaoglu Pinar , Roat Thaisa C. , Malaspina Osmar , Devaud Jean-Marc , Stöger Reinhard , Soller Matthias 
Published: December 2019

AbstractSecuring food supply for a growing population is a major challenge and heavily relies on the use of agrochemicals to maximize crop yield. It is increasingly recognized, that some neonicotinoid insecticides have a negative impact on non-target organisms, including important pollinators such as the European honeybeeApis mellifera. Toxicity of neonicotinoids may be enhanced through simultaneous exposure with additional pesticides, which could help explain, in part, the global decline of honeybee colonies. Here we examined whether exposure effects of the neonicotinoid thiamethoxam on bee viability are enhanced by the commonly used fungicide carbendazim and the herbicide glyphosate. We also analysed alternative splicing changes upon pesticide exposure in the honeybee. In particular, we examined transcripts of three genes: (i) the stress sensor geneX box binding protein-1(Xbp1), (ii) theDown Syndrome Cell Adhesion Molecule(Dscam)gene and iii) theembryonic lethal/abnormal visual system(elav)gene, which are important for neuronal function. Our results showed that acute thiamethoxam exposure is not enhanced by carbendazim, nor glyphosate. Toxicity of the compounds did not trigger stress-induced, alternative splicing in the analysed mRNAs, thereby leaving dormant a cellular response pathway to these man-made environmental perturbations.
Spatially Adjusted Time-varying Reproductive Numbers: Understanding the Geographical Expansion of Urban Dengue Outbreaks
Authors: Ng Ta-Chou , Wen Tzai-Hung 
Published: December 2019

AbstractThe basic reproductive number (R0) is a fundamental measure used to quantify the transmission potential of an epidemic in public health practice. However, R0 cannot reflect the time-varying nature of an epidemic. A time-varying effective reproductive number Rt can provide more information because it tracks the subsequent evolution of transmission. However, since it neglects individual-level geographical variations in exposure risk, Rt may smooth out interpersonal heterogeneous transmission potential, obscure high-risk spreaders, and hence hamper the effectiveness of control measures in spatial dimension. Therefore, this study proposes a new method for quantifying spatially adjusted (time-varying) reproductive numbers that reflects spatial heterogeneity in transmission potential among individuals. This new method estimates individual-level effective reproductive numbers (Rj) and a summarized indicator for population-level time-varying reproductive number (Rt). Data from the five most severe dengue outbreaks in southern Taiwan from 1998–2015 were used to demonstrate the ability of the method to highlight early spreaders contributing to the geographic expansion of dengue transmission. Our results show spatial heterogeneity in the transmission potential of dengue among individuals and identify the spreaders with the highest Rj during the epidemic period. The results also reveal that super-spreaders are usually early spreaders that locate at the edges of the epidemic foci, which means that these cases could be the drivers of the expansion of the outbreak. Therefore, our proposed method depicts a more detailed spatial-temporal dengue transmission process and identifies the significant role of the edges of the epidemic foci, which could be weak spots in disease control and prevention.
Modulation of the leptin receptors expression in breast cancer cell lines exposed to leptin and tamoxifen
Authors: Linares Rodolfo López , Benítez Jonnathan Guadalupe Santillán , Reynoso Mariana Ortiz , Romero Carlos González , Sandoval-Cabrera Antonio 
Published: December 2019

AbstractOne of the factors that has increased the incidence and worse prognosis of breast cancer is obesity. In this condition, high amounts of leptin are secreted, which have proliferative, mitogenic, antiapoptotic, and proinflammatory activity that may be antagonistic to treatment with tamoxifen, considered the first choice. The modulation evaluation of leptin receptor expression in the presence of leptin and tamoxifen stimuli was performed in breast cancer cell lines MCF 7, MDA MB 231 and HCC 1937 as a model of initial approach for the study of breast cancer subtypes and their behavior to the action response of adipokines and their possible relationship with the mechanism of resistance to chemotherapeutics such as tamoxifen in ER positive cell lines and triple negative marker. It was determined that leptin increases the proliferation of the three breast cancer cell lines and tamoxifen is able to exert an antiproliferative effect on them, however, it was identified that the ability of tamoxifen to decrease the proliferation of cancer cells is diminished in the presence of leptin, in addition to changes in the modulation of the expression of its receptor. It was determined that tamoxifen induces a greater modulation of the expression of ObRb in cell lines, which may be related to the decrease of its antiproliferative activity, while leptin generates a proliferative effect in the three cell lines and could participate in the tamoxifen treatment resistance mechanism.
Behavioral and neural evidence of enhanced long-term memory for untrustworthy faces
Authors: Weymar Mathias , Ventura-Bort Carlos , Wendt Julia , Lischke Alexander 
Published: December 2019

AbstractIn daily life, we automatically form impressions of other individuals on basis of subtle facial features that convey trustworthiness. Because these face-based judgements influence current and future social interactions, we investigated how perceived trustworthiness of faces affects long-term memory using event-related potentials (ERPs). In the current study, participants incidentally viewed 60 neutral faces differing in trustworthiness, and one week later, performed a surprise recognition memory task, in which the same old faces were presented intermixed with novel ones. We found that after one week untrustworthy faces were better recognized than trustworthy faces and that untrustworthy faces prompted early (350–550 ms) enhanced frontal ERP old/new differences (larger positivity for correctly remembered old faces, compared to novel ones) during recognition. Our findings point toward an enhanced long-lasting, likely familiarity-based, memory for untrustworthy faces. Even when trust judgments about a person do not necessarily need to be accurate, a fast access to memories predicting potential harm may be important to guide social behaviour in daily life.
Scoring disease in an animal model of multiple sclerosis using a novel infrared-based automated activity-monitoring system
Authors: Shahi Shailesh K. , Freedman Samantha N. , Dahl Rachel A. , Karandikar Nitin J. , Mangalam Ashutosh K. 
Published: December 2019

AbstractMultiple sclerosis (MS) is a chronic demyelinating disorder of the central nervous system (CNS). Its corresponding animal model, experimental autoimmune encephalomyelitis (EAE), is widely used to understand disease pathogenesis and test novel therapeutic agents. However, existing methods to score EAE disease severity are subjective and often vary between individual researchers, making it difficult to translate findings across different studies. An enhanced automated method of disease scoring would eliminate subjectivity and reduce operator-dependent errors. Here, we used an Infra-Red Activity Monitoring System (IRAMS) to measure murine locomotor activity as a surrogate measure of disease severity and compared it to standard EAE scoring methods. In mice immunized with CNS-specific myelin antigens, we observed an inverse correlation between disease severity and mouse activity, with the IRAMS showing enhanced disease scoring compared to standard EAE scoring methods. Relative to standard EAE scoring methods, IRAMS showed comparable measurement of disease relapses and remissions in the SJL/J-relapsing-remitting model of EAE, and could comparably assess the therapeutic efficiency of the MS drug, Copaxone (Glatiramer acetate-GA). Thus, the IRAMS is a method to measure disease severity in EAE without subjective bias and is a tool to consistently assess the efficacy of novel therapeutic agents for MS.
Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome)
Authors: Walsh Dana M. , Hokenstad Alexis N. , Chen Jun , Sung Jaeyun , Jenkins Gregory D. , Chia Nicholas , Nelson Heidi , Mariani Andrea , Walther-Antonio Marina R. S. 
Published: December 2019

AbstractIncidence rates for endometrial cancer (EC) are rising, particularly in postmenopausal and obese women. Previously, we showed that the uterine and vaginal microbiome distinguishes patients with EC from those without. Here, we sought to examine the impact of patient factors (such as menopause status, body mass index, and vaginal pH) in the microbiome in the absence of EC and how these might contribute to the microbiome signature in EC. We find that each factor independently alters the microbiome and identified postmenopausal status as the main driver of a polymicrobial network associated with EC (ECbiome). We identified Porphyromas somerae presence as the most predictive microbial marker of EC and we confirm this using targeted qPCR, which could be of use in detecting EC in high-risk, asymptomatic women. Given the established pathogenic behavior of P. somerae and accompanying network in tissue infections and ulcers, future investigation into their role in EC is warranted.
A muscular hypotonia-associated STIM1 mutant at R429 induces abnormalities in intracellular Ca2+ movement and extracellular Ca2+ entry in skeletal muscle
Authors: Choi Jun Hee , Huang Mei , Hyun Changdo , Oh Mi Ri , Lee Keon Jin , Cho Chung-Hyun , Lee Eun Hui 
Published: December 2019

AbstractStromal interaction molecule 1 (STIM1) mediates extracellular Ca2+entry into the cytosol through a store-operated Ca2+entry (SOCE) mechanism, which is involved in the physiological functions of various tissues, including skeletal muscle. STIM1 is also associated with skeletal muscle diseases, but its pathological mechanisms have not been well addressed. The present study focused on examining the pathological mechanism(s) of a mutant STIM1 (R429C) that causes human muscular hypotonia. R429C was expressed in mouse primary skeletal myotubes, and the properties of the skeletal myotubes were examined using single-cell Ca2+imaging of myotubes and transmission electron microscopy (TEM) along with biochemical approaches. R429C did not interfere with the terminal differentiation of myoblasts to myotubes. Unlike wild-type STIM1, there was no further increase of SOCE by R429C. R429C bound to endogenous STIM1 and slowed down the initial rate of SOCE that were mediated by endogenous STIM1. Moreover, R429C increased intracellular Ca2+movement in response to membrane depolarization by eliminating the attenuation on dihydropyridine receptor-ryanodine receptor (DHPR-RyR1) coupling by endogenous STIM1. The cytosolic Ca2+level was also increased due to the reduction in SR Ca2+level. In addition, R429C-expressing myotubes showed abnormalities in mitochondrial shape, a significant decrease in ATP levels, and the higher expression levels of mitochondrial fission-mediating proteins. Therefore, serial defects in SOCE, intracellular Ca2+movement, and cytosolic Ca2+level along with mitochondrial abnormalities in shape and ATP level could be a pathological mechanism of R429C for human skeletal muscular hypotonia. This study also suggests a novel clue that STIM1 in skeletal muscle could be related to mitochondria via regulating intra and extracellular Ca2+movements.
Imaging of X-Ray-Excited Emissions from Quantum Dots and Biological Tissue in Whole Mouse
Authors: Ryan Sean G. , Butler Matthew N. , Adeyemi Segun S. , Kalber Tammy , Patrick P. Stephen , Zaw Thin May , Harrison Ian F. , Stuckey Daniel J. , Pule Martin , Lythgoe Mark F. 
Published: December 2019

AbstractOptical imaging in clinical and preclinical settings can provide a wealth of biological information, particularly when coupled with targetted nanoparticles, but optical scattering and absorption limit the depth and resolution in both animal and human subjects. Two new hybrid approaches are presented, using the penetrating power of X-rays to increase the depth of optical imaging. Foremost, we demonstrate the excitation by X-rays of quantum-dots (QD) emitting in the near-infrared (NIR), using a clinical X-ray system to map the distribution of QDs at depth in whole mouse. We elicit a clear, spatially-resolved NIR signal from deep organs (brain, liver and kidney) with short (1 second) exposures and tolerable radiation doses that will permit future in vivo applications. Furthermore, X-ray-excited endogenous emission is also detected from whole mouse. The use of keV X-rays to excite emission from QDs and tissue represent novel biomedical imaging technologies, and exploit emerging QDs as optical probes for spatial-temporal molecular imaging at greater depth than previously possible.