bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eigenschaften des Osteozytennetzwerks in gesundem und erkranktem Knochen
Authors: vom Scheidt A. , Busse B. 
Published: April 2018

ZusammenfassungHumaner Knochen ist von einem komplexen Netzwerk aus Lakunen und Kanalikuli durchzogen, welches von mechanosensitiven Osteozyten bevölkert wird. Durch Signalmoleküle und direkten Zellkontakt regulieren Osteozyten die Aktivität von Osteoblasten und Osteoklasten im Knochenumbau und modulieren so die mechanischen Eigenschaften des Knochens. Zusätzlich greifen Osteozyten in den Kalziumstoffwechsel ein und können lokal Kalzium resorbieren oder eine Mineralisierung beeinflussen. Wir diskutieren zwei Hauptfaktoren, welche die Mechanoresponsivität des Netzwerks schädigen: 1. Der Tod von Osteozyten, z. B. bei unphysiologischer Belastung, und der Mangel an Osteozyten im Alter verschlechtern die Auflösung des mechanosensitiven Netzwerk. Dies verhindert eine adäquate Instandhaltung der Gewebequalität und resultiert in gealtertem, höher mineralisiertem Knochen mit einer Häufung von Mikrorissen. 2. Der Verschluss von Lakunen mit Mineral verhindert zusätzlich den Nährstoffund Signalmolekülfluss im Netzwerk. So wird die Lebensfähigkeit anliegender Zellen behindert und die Mechanoresponsivität verringert. Da die regulierende Funktion der Osteozyten auf den Knochenumbau für eine hohe Fraktur resistenz essenziell ist, bietet sich hier ein großes Potenzial, durch Unterstützung der Osteozytenlebensfähigkeit therapeutisch und präventiv Frakturen zu bekämpfen.
Magnetic isotopes as a means to elucidate Earth and environmental chemistry
Authors: Buchachenko Anatoly L. 
Published: April 2018

In Earth and environmental chemistry, magnetic isotopes provide a universal means to identify reaction mechanisms. Mass-independent fractionation of isotopes as a signature of a mechanism occurs by two ways: first, via the magnetic isotope effect (MIE), which is controlled by magnetic, or hyperfine, coupling between unpaired electrons and magnetic nuclei in paramagnetic species (particularly, in radicals), and, second, via the nuclear volume effect (NVE), which is induced by the volume difference between isotopic nuclei. The MIE is the dependence of the reaction rates on the nuclear magnetic moment of reactants and fractionates magnetic and nonmagnetic isotopes, whereas NVE fractionates isotopes with different nuclear volumes. Both effects, MIE and NVE, are supposed to coexist in condensed phases. A decisive test for their differentiation is illustrated by the example of radical pairs with mercury nuclei. Namely, if isotope fractionation is controlled by MIE, the ratio Δ201Hg/Δ199Hg is expected to be in the range of 1.05–1.25 for isotopic enrichment and 0.80–0.92 for depletion. If isotope fractionation is controlled by NVE, this ratio is estimated to be in the range of 0.50–0.62. In contrast to MIE-induced bidirectional fractionation controlled by the direction of coherent spin conversion of the radical pair (triplet–singlet or vice versa), the NVE induces unidirectional, universal isotope fractionation, which is almost independent of the reaction mechanism. In contrast to MIE which exhibits inversion of the fractionation sign depending on the spin multiplicity of reactants, NVE is incompatible with the inversion of the fractionation sign. The MIE is an unambiguous indicator of the radical mechanisms and dominates in chemical reactions, whereas NVE prevails in nonchemical processes. Chemical scenarios of MIE-induced oxygen, sulfur, iron, silicon, tin, mercury, germanium and uranium isotope fractionation in photostimulated and dark reactions are analyzed in terms of reaction mechanisms including reactions in living organisms. In conclusion, some restrictions, uncertainties and problems in Earth and environmental chemistry are discussed.
The bibliography includes 92 references.
I would like to request for your attention
Authors: Hoffmann Sebastian 
Published: April 2018

This paper employs a diachronic corpus of newspaper data to investigate the use of a range of semantically redundant verb-particle combinations (e.g. to request for) in Singapore English since the 1950s. The findings are interpreted as evidence for possible processes of innovation and structural nativization, as outlined in Schneider’s (2003, 2007) dynamic model of post-colonial Englishes. The paper also touches on the motivations for speakers to employ such structures (e.g. analogy with existing forms, transparency) and shows that the results of parallel developments can be observed in other New – but not in native – Englishes world-wide, thus suggesting that we are dealing with strategies that are specific to ESL (English as a second language) contexts.
Recent progress in the high-cycle fatigue behaviour of γ-TiAl alloys
Authors: Edwards T.E.J. 
Published: April 2018

The high-cycle fatigue (HCF) properties of γ-TiAl (gamma titanium aluminide) alloys are reviewed, particularly with regards to the deformation mechanisms active in the near-threshold cyclic loading regime. By examining the influence of lamellar orientation and thickness on the HCF threshold, in addition to more conventional microstructural considerations such as the grain size or the volume fraction of lamellar colonies, factors to improve the γ-TiAl microstructure for HCF are assessed. Finally, experimental methods and loading strategies are surveyed to identify techniques for improving HCF testing of γ-TiAl alloys. In this, we consider both the conservativism of differing approaches and the possibility to measure with suitable resolution the local mechanical behaviour under HCF of the lamellar γ-TiAl microstructure. This review was submitted as part of the 2018 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
A fragmentation study of isoflavones by IT-TOF-MS using biosynthesized isotopes
Authors: Nakata Ryu , Yoshinaga Naoko , Teraishi Masayoshi , Okumoto Yutaka , Huffaker Alisa , Schmelz Eric A , Mori Naoki 
Published: April 2018

ABSTRACT
To aid in the identification and quantification of biologically and agriculturally significant natural products, tandem mass spectrometry can provide accurate structural information with high selectivity and sensitivity. In this study, diagnostic fragmentation patterns of isoflavonoids were examined by liquid chromatography-ion trap-time of flight-mass spectrometry (LC-IT-TOF-MS). The fragmentation scheme for [M+H−2CO]+ ions derived from isoflavones and [M+H−B-ring−CO]+ ions derived from 5-hydroxyisoflavones, were investigated using different isotopically labeled isoflavones, specifically [1′,2′,3′,4′,5′,6′,2,3,4-13C9] and [2′,3′,5′,6′,2-D5] isoflavones. Specific isotopically labeled isoflavones were prepared through the biosynthetic incorporation of pharmacologically applied 13C- and D-labelled L-phenylalanine precursors in soybean plants following the application of insect elicitors. Using this approach, we empirically demonstrate that the [M+H−2CO]+ ion is generated by an intramolecular proton rearrangement during fragmentation. Furthermore, [M+H−B-ring−CO]+ ion is demonstrated to contain a C2H moiety derived from C-ring of 5-hydroxyisoflavones. A mechanistic understanding of characteristic isoflavone fragmentation patterns contributes to the efficacy and confidence in identifying related isoflavones by LC-MSn.
Wireless SAW passive tag temperature measurement in the collision case
Authors: Sorokin A. , Shepeta A. , Wattimena M. 
Published: April 2018

Abstract
This paper describes temperature measurement in the multisensor systems based on the radio-frequency identification SAW passive tags which are currently applied in the electric power systems and the switchgears. Different approaches of temperature measurement in the collision case are shown here. The study is based on the tag model with specific topology, which allows us to determine temperature through the response signal with time-frequency information. This research considers the collision case for several passive tags as the temperature sensors which are placed in the switchgear. This research proposal is to analyze the possibility of using several SAW passive sensors in the collision case. We consider the using of the different typical elements for passive surface acoustic wave tag which applies as an anticollision passive sensor. These wireless sensors based on the surface acoustic waves tags contain specifically coded structures. This topology makes possible the reliability of increasing tag identification and the temperature measurement in the collision case. As the results for this case we illustrate simultaneous measurement of at least six sensors.
JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions
Authors: Deng Wenping , Zhang Kui , Liu Sanzhen , Zhao Patrick X , Xu Shizhong , Wei Hairong 
Published: April 2018

AbstractMotivationJoint reconstruction of multiple gene regulatory networks (GRNs) using gene expression data from multiple tissues/conditions is very important for understanding common and tissue/condition-specific regulation. However, there are currently no computational models and methods available for directly constructing such multiple GRNs that not only share some common hub genes but also possess tissue/condition-specific regulatory edges.ResultsIn this paper, we proposed a new graphic Gaussian model for joint reconstruction of multiple gene regulatory networks (JRmGRN), which highlighted hub genes, using gene expression data from several tissues/conditions. Under the framework of Gaussian graphical model, JRmGRN method constructs the GRNs through maximizing a penalized log likelihood function. We formulated it as a convex optimization problem, and then solved it with an alternating direction method of multipliers (ADMM) algorithm. The performance of JRmGRN was first evaluated with synthetic data and the results showed that JRmGRN outperformed several other methods for reconstruction of GRNs. We also applied our method to real Arabidopsis thaliana RNA-seq data from two light regime conditions in comparison with other methods, and both common hub genes and some conditions-specific hub genes were identified with higher accuracy and precision.Availability and implementationJRmGRN is available as a R program from: https://github.com/wenpingd.Supplementary informationSupplementary data are available at Bioinformatics online.
Efficient flexible backbone protein–protein docking for challenging targets
Authors: Marze Nicholas A , Roy Burman Shourya S , Sheffler William , Gray Jeffrey J 
Published: April 2018

Abstract

Motivation
Binding-induced conformational changes challenge current computational docking algorithms by exponentially increasing the conformational space to be explored. To restrict this search to relevant space, some computational docking algorithms exploit the inherent flexibility of the protein monomers to simulate conformational selection from pre-generated ensembles. As the ensemble size expands with increased flexibility, these methods struggle with efficiency and high false positive rates.

Results
Here, we develop and benchmark RosettaDock 4.0, which efficiently samples large conformational ensembles of flexible proteins and docks them using a novel, six-dimensional, coarse-grained score function. A strong discriminative ability allows an eight-fold higher enrichment of near-native candidate structures in the coarse-grained phase compared to RosettaDock 3.2. It adaptively samples 100 conformations each of the ligand and the receptor backbone while increasing computational time by only 20–80%. In local docking of a benchmark set of 88 proteins of varying degrees of flexibility, the expected success rate (defined as cases with ≥50% chance of achieving 3 near-native structures in the 5 top-ranked ones) for blind predictions after resampling is 77% for rigid complexes, 49% for moderately flexible complexes and 31% for highly flexible complexes. These success rates on flexible complexes are a substantial step forward from all existing methods. Additionally, for highly flexible proteins, we demonstrate that when a suitable conformer generation method exists, the method successfully docks the complex.

Availability and implementation
As a part of the Rosetta software suite, RosettaDock 4.0 is available at https://www.rosettacommons.org to all non-commercial users for free and to commercial users for a fee.

Supplementary information
Supplementary data are available at Bioinformatics online.
D3NER: biomedical named entity recognition using CRF-biLSTM improved with fine-tuned embeddings of various linguistic information
Authors: Dang Thanh Hai , Le Hoang-Quynh , Nguyen Trang M , Vu Sinh T 
Published: April 2018

Abstract

Motivation
Recognition of biomedical named entities in the textual literature is a highly challenging research topic with great interest, playing as the prerequisite for extracting huge amount of high-valued biomedical knowledge deposited in unstructured text and transforming them into well-structured formats. Long Short-Term Memory (LSTM) networks have recently been employed in various biomedical named entity recognition (NER) models with great success. They, however, often did not take advantages of all useful linguistic information and still have many aspects to be further improved for better performance.

Results
We propose D3NER, a novel biomedical named entity recognition (NER) model using conditional random fields and bidirectional long short-term memory improved with fine-tuned embeddings of various linguistic information. D3NER is thoroughly compared with seven very recent state-of-the-art NER models, of which two are even joint models with named entity normalization (NEN), which was proven to bring performance improvements to NER. Experimental results on benchmark datasets, i.e. the BioCreative V Chemical Disease Relation (BC5 CDR), the NCBI Disease and the FSU-PRGE gene/protein corpus, demonstrate the out-performance and stability of D3NER over all compared models for chemical, gene/protein NER and over all models (without NEN jointed, as D3NER) for disease NER, in almost all cases. On the BC5 CDR corpus, D3NER achieves F1 of 93.14 and 84.68% for the chemical and disease NER, respectively; while on the NCBI Disease corpus, its F1 for the disease NER is 84.41%. Its F1 for the gene/protein NER on FSU-PRGE is 87.62%.

Availability and implementation
Data and source code are available at: https://github.com/aidantee/D3NER.

Supplementary information
Supplementary data are available at Bioinformatics online.
Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study
Authors: Berkhout Daniel J C , van Keulen Britt J , Niemarkt Hendrik J , Bessem Jet R , de Boode Willem P , Cossey Veerle , Hoogenes Neil , Hulzebos Christiaan V , Klaver Ellen , Andriessen Peter , van Kaam Anton H , Kramer Boris W , van Lingen Richard A , Schouten Aaron , van Goudoever Johannes B , Vijlbrief Daniel C , van Weissenbruch Mirjam M , Wicaksono Alfian N , Covington James A , Benninga Marc A , de Boer Nanne K H , de Meij Tim G J 
Published: April 2018

Abstract

Background
The intestinal microbiota has increasingly been considered to play a role in the etiology of late-onset sepsis (LOS). We hypothesize that early alterations in fecal volatile organic compounds (VOCs), reflecting intestinal microbiota composition and function, allow for discrimination between infants developing LOS and controls in a preclinical stage.

Methods
In 9 neonatal intensive care units in the Netherlands and Belgium, fecal samples of preterm infants born at a gestational age ≤30 weeks were collected daily, up to the postnatal age of 28 days. Fecal VOC were measured by high-field asymmetric waveform ion mobility spectrometry (FAIMS). VOC profiles of LOS infants, up to 3 days prior to clinical LOS onset, were compared with profiles from matched controls.

Results
In total, 843 preterm born infants (gestational age ≤30 weeks) were included. From 127 LOS cases and 127 matched controls, fecal samples were analyzed by means of FAIMS. Fecal VOCs allowed for preclinical discrimination between LOS and control infants. Focusing on individual pathogens, fecal VOCs differed significantly between LOS cases and controls at all predefined time points. Highest accuracy rates were obtained for sepsis caused by Escherichia coli, followed by sepsis caused by Staphylococcus aureus and Staphylococcus epidermidis.

Conclusions
Fecal VOC analysis allowed for preclinical discrimination between infants developing LOS and matched controls. Early detection of LOS may provide clinicians a window of opportunity for timely initiation of individualized therapeutic strategies aimed at prevention of sepsis, possibly improving LOS-related morbidity and mortality.
Examining Risk Perceptions Among Daily Smokers Naïve to Reduced Nicotine Content Cigarettes
Authors: Mercincavage Melissa , Lochbuehler Kirsten , Villanti Andrea C , Wileyto E Paul , Audrain-McGovern Janet , Strasser Andrew A 
Published: April 2018

AbstractIntroductionThe U.S. Food and Drug Administration (FDA) has stated its interest in reducing the addictiveness of combustible cigarettes by lowering their nicotine content. Delineating risk perceptions of reduced nicotine content (RNC) cigarettes prior to federal regulation may inform the content of future educational campaigns accompanying this policy.MethodsFive hundred non–treatment-seeking, daily smokers naïve to RNC cigarettes (63.0% male, 51.6% nonWhite, mean [SD] cigarettes per day = 15.69 [7.58], age = 43.44 [11.46]) completed a 10-item RNC cigarette risk perception questionnaire at baseline in two, unrelated experimental studies. We used multinomial logistic regression models to identify demographic (eg, gender) and smoking-related (eg, nicotine dependence) correlates of RNC cigarette risk perceptions.ResultsAlthough the majority of participants did not misperceive RNC cigarettes as less harmful than regular or high nicotine cigarettes, a large portion of the sample held misperceptions about RNC cigarettes’ addictiveness (56.4%) and cessation aid potential (63.4%). More than 20% of the sample reported being unsure about RNC-related risks, especially tar content (51.8%). NonWhite smokers were 2.5 to 3 times more likely to be incorrect about multiple RNC cigarette risks (p = .002–.006).ConclusionsIf the FDA mandates a reduced nicotine content standard for cigarettes, educational campaigns will be needed to correct misperceptions about RNC cigarettes’ addictiveness and potential to aid cessation as well as inform consumers about their safety risks. Campaigns tailored toward nonWhite smokers may also be needed to correct misperceptions of RNC cigarette risks held by this subgroup.ImplicationsThe FDA has stated its interest in reducing cigarettes’ addictiveness by lowering their nicotine content, enabling smokers to quit. Our findings suggest that most smokers who have not used RNC cigarettes do not perceive these products as less addictive or as cessation tools, stressing a need for future educational campaigns to correct these misperceptions. Campaigns are also needed to educate uninformed smokers about RNC cigarettes and should consider targeting messages toward subgroups likely to hold misperceptions about the risks and benefits of using these products (eg, nonWhite smokers).
Using Patient Risk Factors to Identify Whether Carbapenem-Resistant Enterobacteriaceae Infections Are Caused by Carbapenemase-Producing Organisms
Authors: Simner Patricia J , Goodman Katherine E , Carroll Karen C , Harris Anthony D , Han Jennifer H , Tamma Pranita D 
Published: April 2018

Abstract
Evaluating all inpatient carbapenem-resistant Enterobacteriaceae (CRE) infections over a 1-year period, 47% were caused by carbapenemase-producing (CP) organisms. Compared with non-CP-CRE patients, patients with CP-CRE had an 18-fold greater odds of a recent stay in a foreign health care facility and a 3-fold greater odds of transfer from a post–acute care facility.
Incisional Hernia After Minimally Invasive Lateral Retroperitoneal Surgery: Case Series and Review of the Literature
Authors: Vivas Andrew C , Januszewski Jacob , Hajirawala Luv , Paluzzi Jason M , Gandhi Shashank V , Uribe Juan S 
Published: April 2018

Abstract

BACKGROUND
Minimally invasive lateral retroperitoneal (lateral-MIS) approaches to the spine involve traversing the lateral abdominal wall musculature and fascia. Incisional hernia is an uncommon approach-related complication.

OBJECTIVE
To review the incidence, treatment, and preventative measures of incisional hernia after lateral-MIS approaches.

METHODS
This is a retrospective review of cases performed by a single surgeon from 2011 to 2016. All patients who underwent lateral-MIS approaches at this institution were included. Patients with a postoperative diagnosis of lateral hernia on physical exam and corroborating advanced imaging findings were included in this study. Cases of flank bulge due to peripheral nerve injury were excluded.

RESULTS
Three-hundred three patients underwent lateral-MIS approaches to the spine. Three (1%) patients with incisional hernia were identified. Two patients presented with a clinically symptomatic incisional hernia, while 1 patient was diagnosed incidentally after a routine abdominal magnetic resonance imaging for an unrelated reason. No patients suffered bowel entrapment or strangulation.

CONCLUSION
Incisional hernia after lateral-MIS approaches is rare. Patients with incisional hernias may be susceptible to bowel incarceration and ischemia, though the incidence of this is probably low. Meticulous closure of the fascia is critical to avoiding this complication.
Alcohol Metabolism in the Progression of Human Nonalcoholic Steatohepatitis
Authors: Li Hui , Toth Erica , Cherrington Nathan J 
Published: April 2018

Abstract
Alcohol metabolism is a well-characterized biological process that is dominated by the alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) families. Nonalcoholic steatohepatitis (NASH) is the advanced inflammatory stage of nonalcoholic fatty liver disease (NAFLD) and is known to alter the metabolism and disposition of numerous drugs. The purpose of this study was to investigate the alterations in alcohol metabolism processes in response to human NASH progression. Expression and function of ADHs, ALDHs, and catalase were examined in normal, steatosis, NASH (fatty) and NASH (not fatty) human liver samples. ALDH4A1 mRNA was significantly decreased in both NASH groups, while no significant changes were observed in the mRNA levels of other alcohol-related enzymes. The protein levels of ADH1A, ADH1B, and ADH4 were each decreased in the NASH groups, which was consistent with a decreased overall ADH activity. The protein level of ALDH2 was significantly increased in both NASH groups, while ALDH1A1 and ALDH1B1 were only decreased in NASH (fatty) samples. ALDH activity represented by oxidation of acetaldehyde was decreased in the NASH (fatty) group. The protein level of catalase was decreased in both NASH groups, though activity was unchanged. Furthermore, the significant accumulation of 4-hydroxynonenal protein adduct in NASH indicated significant oxidative stress and a potential reduction in ALDH activity. Collectively, ADH and ALDH expression and function are profoundly altered in the progression of NASH, which may have a notable impact on ADH- and ALDH-associated cellular metabolism processes and lead to significant alterations in drug metabolism mediated by these enzymes.