bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving bioreactor production of a recombinant glycoprotein in Escherichia coli: Effect of specific growth rate on protein glycosylation and specific productivity
Authors: Caillava Ana J. , Ortiz Gastón E. , Melli Luciano J. , Ugalde Juan E. , Ciocchini Andrés E. , Comerci Diego J. 
Published: February 2019

AbstractIn the last decades bacterial glycoengineering emerged as a new field as the result of the ability to transfer the Campylobacter jejuni N‐ glycosylation machinery into Escherichia coli for the production of recombinant glycoproteins that can be used as antigens for diagnosis, vaccines, and therapeutics. However, the identification of critical parameters implicated in the production process and its optimization to jump to a productive scale is still required. In this study, we developed a dual expression glycosylation vector for the production of the recombinant glycoprotein AcrA‐O157, a novel antigen that allows the serodiagnosis of the infection with enterohemorrhagic E. coli O157 in humans. Volumetric productivity was studied in different culture media and found that 2xYP had 6.9‐fold higher productivity than the extensively used LB. Subsequently, bioreactor batch and exponential‐fed‐batch cultures were designed to determine the influence of the specific growth rate (μ) on AcrA‐O157 glycosylation efficiency, production kinetics, and specific productivity. At μmax, AcrA glycosylation with O157‐polysaccharide and the specific synthesis rate were maximal, constituting the optimal physiological condition for AcrA‐O157 production. Our findings should be considered for the design, optimization, and scaling up of AcrA‐O157 production and other recombinant glycoproteins attractive for industrial applications.
Polymorphic Variants in NR1I3 and UGT2B7 Predict Taxane Neurotoxicity and Have Prognostic Relevance in Patients With Breast Cancer: A Case‐Control Study
Authors: Arbitrio Mariamena , Scionti Francesca , Altomare Emanuela , Di Martino Maria Teresa , Agapito Giuseppe , Galeano Teresa , Staropoli Nicoletta , Iuliano Eleonora , Grillone Francesco , Fabiani Fernanda , Caracciolo Daniele , Cannataro Mario , Arpino Grazia , Santini Daniele , Tassone Pierfrancesco , Tagliaferri Pierosandro 
Published: February 2019

Taxane‐related peripheral neuropathy (TrPN) is a dose‐limiting toxicity with important interindividual variability. Genetic polymorphisms in absorption, distribution, metabolism, and excretion (ADME) genes may account for variability in drug efficacy and/or toxicity. By the use of Affymetrix drug‐metabolizing enzyme and transporter microarray platform, in a retrospective case‐control study, the correlation between ADME polymorphic variants and grades ≥ 2−3‐TrPN was investigated. In a breast cancer (BC) training set, five single‐nucleotide polymorphisms in NR1I3 and UDP‐glucuronosyltransferase (UGT)2B7 genes were correlated to grades ≥ 2−3‐TrPN protection. By receiver operating characteristic curves, the grades ≥ 2−3‐TrPN‐related candidate biomarkers in an independent series of 54 patients with BC (17 cases and 37 controls) were validated. NR1I3 was correlated to paclitaxel‐TrPN and UGT2B7 to docetaxel‐TrPN. Moreover, a genetic signature of prognostic relevance for BC outcome was found. Our findings might have potential relevance for personalized management of patients with BC for prevention of treatment failure in ultrametabolizer genetic variants.
Media‐based single‐symbol generalized spatial modulation
Authors: Oladoyinbo Segun , Pillay Narushan , Xu Hongjun 
Published: February 2019

SummarySingle‐symbol generalized spatial modulation (GSM) improves upon the limitation of spatial modulation (SM) by reducing the number of required transmit antennas to achieve high data rates. In this paper, we investigate the application of media‐based modulation (MBM) based on radio frequency mirrors to single‐symbol GSM, with the aim of improving error performance. The theoretical average bit error probability of the proposed scheme is derived, employing a lower bound approach and used to validate the Monte Carlo simulation results. Finally, the effect of optimal and suboptimal mirror activation pattern selection employing Euclidean distance and channel amplitude coupled with antenna correlation is investigated for the proposed media‐based single‐symbol GSM system. The Monte Carlo simulation results obtained demonstrate a significant improvement over the conventional SM, GSM, and media‐based SM (MB‐SM) schemes in terms of error performance and spectral efficiency.
Box counting–based multifractal analysis of network to detect Domain Name Server attack
Authors: Rajakumareswaran Velusamy , Nithiyanandam Subramaniam 
Published: February 2019

SummaryDomain Name Server (DNS) is a type of server used to maintain and process the IP addresses of all the domains in the Internet. It works by responding with corresponding IP addresses when a client requests with a domain name. The DNS can be attacked by redirecting all the incoming traffic to a fake server by returning fake IP address when requested by a client. In this work, a novel work has been employed to detect DNS attack using box‐counting method (BCM)–based multifractal analysis. A set of network features are selected and rules are created using CISCO's Flowspec model, and those features are analysed using BCM technique to find the attack in the network traffic. To the best of our knowledge, this is the first work that implements Flowspec‐based monitoring of DNS attack using fractal analysis.
Amino acids and proteomic acclimation of Staphylococcus aureus when incubated in a defined minimal medium supplemented with 5% sodium chloride
Authors: Alreshidi Mousa M. , Dunstan R. Hugh , Macdonald Margaret M. , Smith Nathan D. , Gottfries Johan , Roberts Tim K. 
Published: February 2019

AbstractStaphylococcus aureus is a versatile bacterium that can adapt to survive and grow in a wide range of salt concentrations. This study investigated whether the cells could mount a response to survive a challenge of 5% NaCl in a minimal incubation medium that would not support cell replication. Cells were grown in liquid culture, washed and then incubated for 90 min at 37°C in a medium that contained only glycine and glucose as substrates in PBS plus trace elements. The control cells were compared with a treatment group which was incubated with an additional 5% NaCl. Significantly more glycine was taken up by the cells exposed to 5% NaCl compared with control cells, and both groups consumed 99% of the glucose supplied. The NaCl treated cells had significantly higher cytoplasmic levels of proline and glutamic acid as well as lower levels of alanine and methionine compared with the controls (p < 0.05). The levels of the two major cytoplasmic amino acids, aspartic acid and glycine, remained constant in control and treated cells. Proteomic analyses revealed that 10 proteins showed differential responses between the control and treatment groups. The reductions in proteins were primarily associated with processes of protein biosynthesis, pathogenicity, and cell adhesion. Since cell numbers remained constant during the incubation period in minimal medium, it was concluded that there was no cell division to support population growth. The results provided evidence that the cells in the minimal medium exposed to the NaCl treatment underwent in situ homeostatic changes to adjust to the new environmental conditions. It was proposed that this represented a phenotypic shift to form cells akin to small colony variants, with lower metabolic rates and lower levels of key proteins associated with pathogenicity.
A Long-Term Analysis of Channel Morphology and Stream Substrates before and after Sediment Trap Construction in Michigan Trout Streams
Authors: Hessenauer Jan-Michael , Wills Todd C. , Zorn Troy G. 
Published: February 2019

Abstract
Sediment traps are commonly used to remove excess sand bedload from coldwater streams and to improve channel morphology and substrate conditions for salmonids in the Midwestern United States. However, few scientific evaluations of the rate and spatial extent of channel changes associated with sediment trapping efforts have occurred. We used a series of stream channel morphology measurements taken over a 10-year period in five Michigan streams to show that excavation of sediment traps had only small effects on mean channel bank-full depth, bank-full cross-sectional area, and bank-full width as well as substrate composition in the streams studied. When they did occur, changes in each of these metrics occurred both upstream and downstream of—and often in close proximity to—the sediment traps. While few positive effects of sediment traps were noted, there were also no negative effects to report. The construction of sediment traps did not lead to broad-scale widening of stream channels, and no excessive channel incision was observed in any of the study streams. Thus, concerns about typical sediment trap operations upsetting the stream-sediment equilibrium and creating excessive down-cutting appear to be unfounded for Michigan's low-gradient, naturally sandy stream channels. We conclude that sediment traps are unlikely to have any large-scale channel morphology or substrate effects that would be beneficial to stream salmonids when used as a stand-alone habitat treatment.
School‐based early intervention for anxiety and depression in older adolescents: A feasibility randomised controlled trial of a self‐referral stress management workshop programme (“DISCOVER”)
Authors: Brown June S.L. , Blackshaw Emily , Stahl Daniel , Fennelly Lisa , McKeague Lynn , Sclare Irene , Michelson Daniel 
Published: February 2019

ABSTRACTIntroductionSchools may provide a convenient intervention setting for young people with mental health problems generally, as well as for those who are unwilling or unable to access traditional clinic‐based mental health services. However, few studies focus on older adolescents, or those from ethnic minority groups. This study aims to assess the feasibility of a brief school‐based psychological intervention for self‐referred adolescents aged 16–19 years.MethodsA two‐arm cluster randomised controlled trial was conducted in 10 inner‐city schools with block randomisation of schools. The intervention comprised a one‐day CBT Stress management programme with telephone follow‐up (DISCOVER) delivered by 3 psychology (2 clinical and 1 assistant) staff. The control was a waitlist condition. Primary outcomes were depression (Mood and Feelings Questionnaire; MFQ) and anxiety (Revised Child Anxiety and Depression Scale; RCADS‐anxiety subscale). Data were analysed descriptively and quantitatively to assess feasibility.Results155 students were enrolled and 142 (91.6%) followed up after 3 months. Participants were predominantly female (81%) and the mean age was 17.3 years, with equal numbers enrolled from Year 12 and Year 13. Over half (55%) of students were from ethnic minority groups. Intraclass correlations were low. Variance estimates were calculated to estimate the sample size for a full RCT. Preliminary outcomes were encouraging, with reductions in depression (d = 0.27 CI‐0.49 to −0.04, p = 0.021) and anxiety (d = 0.25, CI‐0.46 to −0.04, p = 0.018) at follow‐up.ConclusionsResults support the feasibility of a school‐based, self‐referral intervention with older adolescents in a definitive future full‐scale trial (Trial no. ISRCTN88636606).
The components of the adolescent brain and its unique sensitivity to sexually explicit material
Authors: Brown Jennifer A. , Wisco Jonathan J. 
Published: February 2019

AbstractIntroductionThe focus of this brief literature review is to explore whether there is a relationship between the unique anatomical and physiological paradigms of the adolescent brain and an increased sensitivity to sexually explicit material.MethodsThe EBSCO Research Data bases were searched using the following key terms: adolescence, adolescent brain development, neuroplasticity, sexually explicit material, sexualization, and pornography.ResultsThe literature highlighted several components of the adolescent brain that are different than the mature brain. These include: an immature prefrontal cortex and over‐responsive limbic and striatal circuits, heightened period for neuroplasticity, overactive dopamine system, a pronounced HPA axis, augmented levels of testosterone, and the unique impact of steroid hormones. The physiological response to sexually explicit material is delineated. The overlap of key areas associated with the unique adolescent brain development and sexually explicit material is noteworthy. A working model summary that compares the response of the adult and adolescent brain to the same sexually explicit stimulus is outlined.ConclusionsThe literature suggests that the adolescent brain may indeed be more sensitive to sexually explicit material, but due to a lack of empirical studies this question cannot be answered definitively. Suggestions for future research are given to further advance the work in this applicable field of today.
When do peers matter? The moderating role of peer support in the relationship between environmental adversity, complex trauma, and adolescent psychopathology in socially disadvantaged adolescents
Authors: Yearwood Karen , Vliegen Nicole , Chau Cecilia , Corveleyn Jozef , Luyten Patrick 
Published: February 2019

AbstractIntroductionThis study examined the longitudinal associations between environmental adversity (defined in terms of exposure to violence in the neighborhood, school, and media), complex trauma (operationalized as experiences of abuse and neglect), and adolescents' internalizing and externalizing symptoms.MethodsUsing a cross‐lagged panel research design, we investigated the moderating role of peer support in these relationships in a sample of 644 adolescents from a severely disadvantaged district of Lima, Peru, who were followed up in a 1‐year prospective study.Results and conclusionsWe found significant unidirectional dynamic relations, where both types of adversity were associated with higher levels of internalizing and externalizing symptoms. Peer support significantly moderated this effect, but only for complex trauma, in that higher levels of peer support were associated with a decreased impact of complex trauma on internalizing and externalizing symptoms. These findings highlight the importance of social relations and the quality of peer relations in particular as factors that may mitigate the risk of early exposure to trauma.
The development of monoaminergic neurotransmitter systems in childhood and adolescence
Authors: Pitzer Martina 
Published: February 2019

AbstractBrain maturation extends throughout adolescence well into early adulthood. Knowledge on developmental changes is crucial for age‐appropriate pharmacotherapy. This article reviews data on maturational processes with a focus on the noradrenergic, dopaminergic, and serotonergic neurotransmitter systems.The literature was searched with a focus on studies in humans. However, since data in humans are limited animal studies were also included. All reviewed neurotransmitter systems show age‐related development processes that differentiate child and adolescent brain function from those of adult brains. Unfortunately, the state of knowledge surrounding development‐related changes remains sufficiently sparse, There is a high need for more studies on pediatric psychopharmacology and its biological underpinnings. Safety and efficacy of psychopharmacological medicines cannot be readily extrapolated from adults.
Neural predictors and effects of cognitive behavioral therapy for depression: the role of emotional reactivity and regulation
Authors: Rubin-Falcone Harry , Weber Jochen , Kishon Ronit , Ochsner Kevin , Delaparte Lauren , Doré Bruce , Raman Sudha , Denny Bryan T. , Oquendo Maria A. , Mann J. John , Miller Jeffrey M. 
Published: February 2019

AbstractBackgroundCognitive behavioral therapy (CBT) is an effective treatment for many patients suffering from major depressive disorder (MDD), but predictors of treatment outcome are lacking, and little is known about its neural mechanisms. We recently identified longitudinal changes in neural correlates of conscious emotion regulation that scaled with clinical responses to CBT for MDD, using a negative autobiographical memory-based task.MethodsWe now examine the neural correlates of emotional reactivity and emotion regulation during viewing of emotionally salient images as predictors of treatment outcome with CBT for MDD, and the relationship between longitudinal change in functional magnetic resonance imaging (fMRI) responses and clinical outcomes. Thirty-two participants with current MDD underwent baseline MRI scanning followed by 14 sessions of CBT. The fMRI task measured emotional reactivity and emotion regulation on separate trials using standardized images from the International Affective Pictures System. Twenty-one participants completed post-treatment scanning. Last observation carried forward was used to estimate clinical outcome for non-completers.ResultsPre-treatment emotional reactivity Blood Oxygen Level-Dependent (BOLD) signal within hippocampus including CA1 predicted worse treatment outcome. In contrast, better treatment outcome was associated with increased down-regulation of BOLD activity during emotion regulation from time 1 to time 2 in precuneus, occipital cortex, and middle frontal gyrus.ConclusionsCBT may modulate the neural circuitry of emotion regulation. The neural correlates of emotional reactivity may be more strongly predictive of CBT outcome. The finding that treatment outcome was predicted by BOLD signal in CA1 may suggest overgeneralized memory as a negative prognostic factor in CBT outcome.
Out-domain Chinese new word detection with statistics-based character embedding
Authors: Liang Yuzhi , Yang Min , Zhu Jia , Yiu S. M. 
Published: February 2019

AbstractUnlike English and other Western languages, many Asian languages such as Chinese and Japanese do not delimit words by space. Word segmentation and new word detection are therefore key steps in processing these languages. Chinese word segmentation can be considered as a part-of-speech (POS)-tagging problem. We can segment corpus by assigning a label for each character which indicates the position of the character in a word (e.g., “B” for word beginning, and “E” for the end of the word, etc.). Chinese word segmentation seems to be well studied. Machine learning models such as conditional random field (CRF) and bi-directional long short-term memory (LSTM) have shown outstanding performances on this task. However, the segmentation accuracies drop significantly when applying the same approaches to out-domain cases, in which high-quality in-domain training data are not available. An example of out-domain applications is the new word detection in Chinese microblogs for which the availability of high-quality corpus is limited. In this paper, we focus on out-domain Chinese new word detection. We first design a new method Edge Likelihood (EL) for Chinese word boundary detection. Then we propose a domain-independent Chinese new word detector (DICND); each Chinese character is represented as a low-dimensional vector in the proposed framework, and segmentation-related features of the character are used as the values in the vector.
Energetics of magnetic transients in a solar active region plage
Authors: Chitta L. P. , Sukarmadji A. R. C. , Rouppe van der Voort L. , Peter H. 
Published: February 2019

Context. Densely packed coronal loops are rooted in photospheric plages in the vicinity of active regions on the Sun. The photospheric magnetic features underlying these plage areas are patches of mostly unidirectional magnetic field extending several arcsec on the solar surface.
Aims. We aim to explore the transient nature of the magnetic field, its mixed-polarity characteristics, and the associated energetics in the active region plage using high spatial resolution observations and numerical simulations.
Methods. We used photospheric Fe I 6173 Å spectropolarimetric observations of a decaying active region obtained from the Swedish 1-m Solar Telescope (SST). These data were inverted to retrieve the photospheric magnetic field underlying the plage as identified in the extreme-ultraviolet emission maps obtained from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO). To obtain better insight into the evolution of extended unidirectional magnetic field patches on the Sun, we performed 3D radiation magnetohydrodynamic simulations of magnetoconvection using the MURaM code.
Results. The observations show transient magnetic flux emergence and cancellation events within the extended predominantly unipolar patch on timescales of a few 100 s and on spatial scales comparable to granules. These transient events occur at the footpoints of active region plage loops. In one case the coronal response at the footpoints of these loops is clearly associated with the underlying transient. The numerical simulations also reveal similar magnetic flux emergence and cancellation events that extend to even smaller spatial and temporal scales. Individual simulated transient events transfer an energy flux in excess of 1 MW m−2 through the photosphere.
Conclusions. We suggest that the magnetic transients could play an important role in the energetics of active region plage. Both in observations and simulations, the opposite-polarity magnetic field brought up by transient flux emergence cancels with the surrounding plage field. Magnetic reconnection associated with such transient events likely conduits magnetic energy to power the overlying chromosphere and coronal loops.
Socru: Typing of genome level order and orientation in bacteria
Authors: Page Andrew J. , Langridge Gemma C. 
Published: February 2019

AbstractSummaryGenome rearrangements occur in bacteria between repeat sequences and impact growth and gene expression. Homologous recombination can occur between ribosomal operons, which are found in multiple copies in many bacteria. Inversion between indirect repeats and excision/translocation between direct repeats enable structural genome rearrangement. To identify what these rearrangements are by sequencing, reads of several thousand bases are required to span the ribosomal operons. With long read sequencing aiding the routine generation of complete bacterial assemblies, we have developed socru, a typing method for the order and orientation of genome fragments between ribosomal operons, defined against species-specific baselines. It allows for a single identifier to convey the order and orientation of genome level structure and 434 of the most common bacterial species are supported. Additionally, socru can be used to identify large scale misassemblies.Availability and implementationSocru is written in Python 3, runs on Linux and OSX systems and is available under the open source license GNU GPL 3 from https://github.com/quadram-institute-bioscience/socru.Contactgemma.langridge@quadram.ac.uk
Renal Localization of Plasmodium vivax and Zoonotic Monkey Parasite Plasmodium knowlesi in Malaria Associated Acute Kidney Injury
Authors: Acharya Pragyan , Pramanik Atreyi , Kaur Charandeep , Sinha Kalpana , Dinda Amit Kumar , Sankar Jhuma , Bagga Arvind , Agarwal Sanjay Kumar , Sinha Aditi , Singh Geetika 
Published: February 2019

ABSTRACTAcute kidney injury (AKI) is a frequent presentation in Plasmodium vivax (P. vivax) associated severe malaria. However, tissue presence of P. vivax parasites in the kidney has never been demonstrated. In the present study, we show that renal biopsies from malaria associated AKI patients harbor the human malaria parasite P. vivax and, in several cases, the zoonotic monkey malaria parasite P. knowlesi in addition to P. vivax. Presence of microvascular injury in a majority of the malaria associated AKI cases suggests vascular involvement of P. vivax and P. knowlesi. This study implicates Plasmodium species as a possible pathogenic mechanism for AKI, and suggests host renal tissue interaction of P. vivax and P. knowlesi.