bluuebunny/crossref_metadata_2025 huggingface dataset:
Devastating Consequences of Sex Trafficking on Women's Health
Authors: McTavish Fr. James
Published: November 2017

Sex trafficking has devastating consequences on the physical and mental well-being of millions of women around the world. These trafficking victims often come in contact with medical personnel, and these encounters with suitably prepared staff can be a step toward healing of the victims. The Catholic Church, especially through Pope Francis, is making strenuous efforts to curb the spread of sex trafficking. Same-sex feelings and behavior may arise post-trafficking in individuals, although this does not appear to be mentioned thus far in the literature. Here, we are most likely dealing with a type of “pseudo-lesbianism” post-trauma. The trafficking survivor can be helped to understand some of the likely roots of her feelings such as anti-male sentiments following abuse. She needs to be patiently, and expertly, accompanied to process the trauma she has experienced, and learn how to meet her genuine needs for female affection and affirmation in healthy, chaste, and non-erotic ways.

Around the world, millions of female victims of human trafficking are forced into sex “work,” often resulting in serious physical and mental-health problems. Healthcare staff should be alert to spot victims of sex trafficking and be ready to assist them. The Catholic Church, especially through Pope Francis, has been vocal in denouncing this form of modern slavery. Some female victims of sex trafficking may experience same-sex feelings afterward. Healing for such young women involves helping them to process their traumatic experiences, as well as patiently accompanying them as they seek to develop healthy, chaste friendships with other females and males.
Resisting Displacement amid Armed Conflict: Community-Level Conditions that Make People More Likely to Stay
Authors: Krakowski Krzysztof
Published: November 2017

The paper examines conditions under which communities threatened by armed groups amid the Colombian civil war are most likely to resist displacement. Using a game-theoretic framework and quantitative data, the paper shows that the threatened communities which expect rescue from an armed actor are more likely to resist displacement than those communities which expect no help. Community cohesion has a dual effect on displacement. The amount of peer support among community members reduces their chances to resist displacement, but the extent to which community members are involved in collective decision-making processes makes them less likely to displace. These findings reveal that both displaced communities and those that resisted displacement possess crucial social resources for their post-conflict recovery and development, such as cohesion and strong bonds of solidarity. The paper stresses the importance of local-level organisation coordinating collective decision-making to guarantee the most efficient use of these resources.
Investigation on the fiber based approach to estimate the axial load carrying capacity of the circular concrete filled steel tube (CFST)
Authors: Piscesa B , Attard M M , Suprobo P , Samani A K
Published: November 2017

External confining devices are often used to enhance the strength and ductility of reinforced concrete columns. Among the available external confining devices, steel tube is one of the most widely used in construction. However, steel tube has some drawbacks such as local buckling which needs to be considered when estimating the axial load carrying capacity of the concrete-filled-steel-tube (CFST) column. To tackle this problem in design, Eurocode 4 provided guidelines to estimate the effective yield strength of the steel tube material. To study the behavior of CFST column, in this paper, a non-linear analysis using a fiber-based approach was conducted. The use of the fiber-based approach allows the engineers to predict not only the axial load carrying capacity but also the complete load-deformation curve of the CFST columns for a known confining pressure. In the proposed fiber-based approach, an inverse analysis is used to estimate the constant confining pressure similar to design-oriented models. This paper also presents comparisons between the fiber-based approach model with the experimental results and the 3D non-linear finite element analysis.
Do Nutrient Management Plans Actually Manage Nutrients? Evidence from a Nationally‐Representative Survey of Hog Producers
Authors: Sneeringer Stacy , Key Nigel , Pon Shirley
Published: November 2017

A nutrient management plan (NMP) specifies recommended practices to match applied nutrients with crops’ uptake capacity. Because monitoring nutrient applications is difficult, regulators instead oversee NMP adoption. In this paper we examine whether having NMPs make hog farms more likely to adopt nutrient management practices. We estimate nutrient application and uptake rates to assess whether operations with NMPs are less likely to over‐apply nutrients. Using an endogenous treatment effects model to control for potential confounding and selection bias, we find that NMPs are positively correlated with the adoption of nutrient management practices, as well as with the reduced application of excess nutrients.
ThetaMater: Bayesian estimation of population size parameter θ from genomic data
Authors: Adams Richard H , Schield Drew R , Card Daren C , Corbin Andrew , Castoe Todd A
Published: November 2017

We describe ThetaMater, an open source R package comprising a suite of functions for efficient and scalable Bayesian estimation of the population size parameter θ from genomic data.

Availability and implementation

ThetaMater is available at GitHub (https://github.com/radamsRHA/ThetaMater).

Supplementary information

Supplementary data are available at Bioinformatics online.
Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies
Authors: Derkach Andriy , Zhang Haoyu , Chatterjee Nilanjan
Published: November 2017

Motivation

Genome-wide association studies are now shifting focus from analysis of common to rare variants. As power for association testing for individual rare variants may often be low, various aggregate level association tests have been proposed to detect genetic loci. Typically, power calculations for such tests require specification of large number of parameters, including effect sizes and allele frequencies of individual variants, making them difficult to use in practice. We propose to approximate power to a varying degree of accuracy using a smaller number of key parameters, including the total genetic variance explained by multiple variants within a locus.

Results

We perform extensive simulation studies to assess the accuracy of the proposed approximations in realistic settings. Using these simplified power calculations, we develop an analytic framework to obtain bounds on genetic architecture of an underlying trait given results from genome-wide association studies with rare variants. Finally, we provide insights into the required quality of annotation/functional information for identification of likely causal variants to make meaningful improvement in power.

Availability and implementation

A shiny application that allows a variety of Power Analysis of GEnetic AssociatioN Tests (PAGEANT), in R is made publicly available at https://andrewhaoyu.shinyapps.io/PAGEANT/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Capillary rarefaction from the kidney point of view
Authors: Afsar Baris , Afsar Rengin E , Dagel Tuncay , Kaya Ege , Erus Suat , Ortiz Alberto , Covic Adrian , Kanbay Mehmet
Published: November 2017

Capillary rarefaction is broadly defined as a reduction in vascular density. Capillary rarefaction in the kidneys is thought to promote hypoxia, impair hemodynamic responses and predispose to chronic kidney disease (CKD) progression and hypertension development. Various mechanisms have been suggested to play a role in the development of capillary rarefaction, including inflammation, an altered endothelial-tubular epithelial cell crosstalk, a relative deficiency in angiogenic growth factors, loss of pericytes, increased activity of Transforming growth factor -β1 and thrombospondin-1, vitamin D deficiency, a link to lymphatic neoangiogenesis and INK4a/ARF (Cylin-dependent kinase inhibitor 2a; CDKN2A). In this review, we summarize the tools available to monitor capillary rarefaction noninvasively in the clinic, the contribution of capillary rarefaction to CKD and hypertension, the known mechanisms of capillary rarefaction, and potential future strategies to attenuate capillary rarefaction and reduce its negative impact. Therapeutic strategies to be explored in more detail include optimization of antihypertensive therapy, vitamin D receptor activators, sirtuin 1 activators, Hypoxia inducible factor prolyl hydroxylase inhibitors and stem cell therapy.
Gender and cardiovascular disease: are sex-biased microRNA networks a driving force behind heart failure with preserved ejection fraction in women?
Authors: Florijn Barend W , Bijkerk Roel , van der Veer Eric P , van Zonneveld Anton Jan
Published: November 2017

Cardiovascular disease (CVD) is the primary cause of death among men and women worldwide. Nevertheless, our comprehension of how CVD progresses in women and elicits clinical outcomes is lacking, leading CVD to be under-diagnosed and under-treated in women. A clear example of this differential presentation of CVD pathophysiologies in females is the strikingly higher prevalence of heart failure with preserved ejection fraction (HFpEF). Women with a history of pre-eclampsia or those who present with co-morbidities such as obesity, hypertension, and diabetes mellitus are at increased risk of developing HFpEF. Long understood to be a critical CVD risk factor, our understanding of how gender differentially affects the development of CVD has been greatly expanded by extensive genomic and transcriptomic studies. These studies uncovered a pivotal role for differential microRNA (miRNA) expression in response to systemic inflammation, where their co-ordinated expression forms a post-transcriptional regulatory network that instigates microcirculation defects. Importantly, the potential sex-biased expression of the given miRNAs may explain sex-specific cardiovascular pathophysiologies in women, such as HFpEF. Sex-biased miRNAs are regulated by oestrogen (E2) in their transcription and processing or are expressed from loci on the X-chromosome due to incomplete X-chromosome inactivation. Interestingly, while E2-induced miRNAs predominantly appear to serve protective functions, it could be argued that many X-linked miRNAs have been found to challenge microvascular and myocardial integrity. Therefore, menopausal E2 deficiency, resulting in protective miRNA loss, and the augmentation of X-linked miRNA expression, may well contribute to the molecular mechanisms that underlie the female-specific cardiovascular aetiology in HFpEF.
HisgAtlas 1.0: a human immunosuppression gene database
Authors: Liu Yuan , He Mengqi , Wang Dan , Diao Lihong , Liu Jinying , Tang Li , Guo Shuzhen , He Fuchu , Li Dong
Published: November 2017

Immunosuppression is body’s state in which the activation or efficacy of immune system is weakened. It is associated with a wide spectrum of human diseases. In the last two decades, tremendous efforts have been made to elucidate the mechanism of hundreds of immunosuppression genes. Immunosuppression genes could be valuable drug targets or biomarkers for the immunotherapeutic treatment of different diseases. However, the information of all previously identified immunosuppression genes is dispersed in thousands of publications. Here, we provide the HisgAtlas database that collects 995 previously identified human immunosuppression genes using text mining and manual curation. We believe HisgAtlas will be a valuable resource to search human immunosuppression genes as well as to investigate their functions in further research.

Database URL: http://biokb.ncpsb.org/HisgAtlas/
The impact of architectural spaces’ geometric forms and construction materials on the users’ brainwaves and consciousness status
Authors: Elbaiuomy Eslam , Hegazy Ibrahim , Sheta Sherif
Published: November 2017

Biogeometry is the patented science of using the energy of shapes and forms to qualitatively make a balance between the biological energy systems and accommodate their interactions with the environment. Balancing the activities of daily life, attaining harmony with our environment, humanizing modern technology, and incorporating science and spirituality are the work of the science of biogeometry. The research in biogeometry was and still is mainly dedicated to the development of a new form of architecture that would improve the human biological system. In this context, the current study aims to develop a scientific approach to investigate the influence of the geometric forms and construction materials of the architectural spaces on the users’ brainwaves and then on their consciousness status which is considered as the main controlling factor in human bioenergy. Trying to consolidating the theoretical views of this effect to be measurable scientifically, the study is based on using a numerical analysis based on a computerized simulation. The results of this study show different influences based on geometric forms and construction materials. The study is carried out using CST Microwave Studio to identify the resonance frequency occurred inside different geometric forms with different construction materials, and then distinguish the related user’s brainwaves which influence his/her consciousness status. This may assist architects and designers in identifying appropriate geometric forms to suit the required uses and functions that need particular consciousness statuses.
Physiologic Modulators of Neural Injury After Brain and Spinal Cord Injury
Authors: Dietrich W. Dalton
Published: November 2017

Brain and spinal cord injury are leading causes of death and long-term disability, producing diverse burdens for the affected individuals, their families, and society. Such injuries, including traumatic brain injury, stroke, subarachnoid hemorrhage, and spinal cord injury, have common patterns of neuronal cell vulnerability that are associated with a complex cascade of pathologic processes that trigger the propagation of tissue damage beyond the acute injury. Secondary injury mechanisms, including oxidative stress, edema formation, changes in cerebral blood flow and vessel reactivity, metabolic and blood–brain barrier disruption, and neuroinflammation, are therefore important therapeutic targets. Several key physiological parameters require monitoring and intensive management during various phases of treatment to ameliorate secondary injury mechanisms and potentially protect against further neuronal injury. This chapter reviews the core physiological targets in the management of brain and spinal cord injury and relates them to secondary injury mechanisms and outcomes.
Neurophysiologic Monitoring and Neuroprotection
Authors: Alawi Aws , Reznik Michael , Claassen Jan
Published: November 2017

One of the main goals of monitoring neurologically ill patients is detection of secondary brain injury early enough to intervene to prevent permanent damage. In some patients with impaired levels of consciousness and those who require sedation, monitoring various brain physiologic parameters by invasive and noninvasive means has become an essential tool in the care of critically ill patients. Integration of multiple physiological parameters provides a more comprehensive physiological assessment of the injured brain and allows real-time, early detection of secondary cerebral injury and intervention to prevent permanent damage. Importantly, these modalities should be interpreted collectively and not in isolation in order to manage acute brain injuries, which are often complex and dynamic at the same time.
Assessment of Postoperative Cognitive Decline
Authors: Uysal Suzan , Reich David L.
Published: November 2017

Neurocognitive outcome studies are a potentially rich source of information for evidence-based approaches to neuroprotection. This chapter provides a critical examination of assessment methods for studying postoperative cognitive decline (POCD), with regard to definition of the phenomenon, the role of hypotheses regarding mechanisms and localization of neural injury, and psychometric considerations for the design of POCD assessment protocols. It also describes an approach to conducting clinical neuropsychological assessments outside of research contexts for patients who present with signs or symptoms of POCD when there are no preoperative baseline cognitive test data. The authors propose a set of guidelines for designing, conducting, interpreting, and evaluating cognitive outcome studies in surgical patients and performing clinical POCD assessments.
Neuroprotection for Cardiac Arrest
Authors: Pitcher Joseph H. , Seder David B
Published: November 2017

This chapter reviews the pathophysiology of brain injury after resuscitation from cardiac arrest and describes a pragmatic approach to neuroprotection. Common mechanisms of brain injury in the postresuscitation milieu are discussed and strategies for optimizing physiological variables such as blood pressure, oxygen, ventilation, and blood glucose in order to minimize secondary injury are presented. Neuroprotective therapies, such as targeted temperature management and pharmacologic neuroprotective agents, are covered in detail. Finally, the use of raw and processed electroencephalography and other diagnostic tools are described for the purposes of determining severity of brain injury, triaging patients to different treatment pathways, and for prognostic value.
Neuroprotection for Premature Birth and Neonatal Brain Injury
Authors: Chang Eugene
Published: November 2017

Preterm birth is associated with increased risk of perinatal brain injury. Although there has been little headway made in reducing preterm birth rates, survival of infants born prematurely has improved greatly. Because of this, the neurodevelopmental consequences related to prematurity have become significant issues, especially in those infants born at less than 32 weeks gestation. Hypoxic-ischemic encephalopathy commonly leads to neonatal brain injury both before and after delivery. While perinatal birth asphyxia accounts for a proportion of neonatal brain injury in neonates younger than 37 weeks, preterm birth is the more significant risk factor. This chapter explores the neurodevelopmental consequences associated with preterm birth, the pathophysiology of perinatal brain injury, and the imaging modalities used to assess the newborn brain. Finally, various neuroprotective interventions in clinical use and in development will be described.
Neuroprotection for General, Orthopedic, Peripheral Vascular, and ENT Surgery
Authors: Selim Magdy
Published: November 2017

Unlike stroke after cardiac and carotid surgery, stroke after general; orthopedic; peripheral vascular; and ear, nose, and throat surgery has not been investigated extensively. The incidence, predisposing factors, and etiological mechanisms of stroke in patients undergoing these procedures are reviewed. Recommendations to prevent, recognize, and treat stroke following these surgical procedures are provided to minimize postoperative stroke risk and its associated morbidity and disability. Although these recommendations can help to decrease the incidence of perioperative stroke, there is an unmet need to find novel and effective neuroprotective strategies that can be used pre- or intraoperatively to minimize the effects of stroke on brain tissue and resulting disability. Future studies should evaluate the potential usefulness of neuroprotective therapies or interventions, including various anesthetic agents that can be used prophylactically in the perioperative setting.
A Clinician's Guide to Learning Disabilities
Authors: Franz Carleen , Ascherman Lee , Shaftel Julia
Published: November 2017

A Clinician’s Guide to Learning Disabilities provides succinct descriptions of the various types of learning disabilities that affect educational achievement, illustrated with numerous case studies. Clear descriptions of educational assessment best practices and score reporting simplify the interpretation of psychoeducational reports. An entire chapter on historical context and legal framework describes obligatory supports for students with learning disabilities in all settings. Chapters on preschool assessment and the transition to post–high-school college and career expand the scope of the book beyond the school years. Clinicians who work in nonschool settings view learning disorders through the lens of DSM-5. They may be surprised at IDEA requirements and how the law works to identify and serve students with learning disabilities. Clinicians may not be aware that DSM-5 is not familiar in the school setting and that their diagnoses and recommendations may not have their intended effect. Through detailed examination of relevant special education requirements and procedures, this text addresses and clarifies the confusion that clinicians and families often experience about the lack of diagnostic congruence and differing terminology between DSM-5 and IDEA. No other book describes learning disorders and the psychoeducational evaluation process for mental health clinicians who work with these children and adolescents. A chapter on referral and collaboration will inform clinicians who seek deeper educational knowledge about their clients to better guide students and their families.
In-solution Y-chromosome capture-enrichment on ancient DNA libraries
Authors: Cruz-Dávalos Diana I , Nieves-Colón María A , Sockell Alexandra , David Poznik G , Schroeder Hannes , Stone Anne C , Bustamante Carlos D , Malaspinas Anna-Sapfo , Ávila-Arcos María C
Published: November 2017

Background

As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach – in-solution capture-enrichment – retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3,000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC+Y) versus non-enriched (pre-capture) libraries.

Results

We recovered 17–4,152 times more targeted unique Y-chromosome sequences after capture, where 0.01-6.2% (WGC+Y) and 0.01-23.5% (YCC) of the sequence reads were on-target, compared to 0.0002-0.004% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC+Y) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, WGC+Y yielded greater enrichment than YCC alone. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.

Conclusions

We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC+Y enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture for low-complexity libraries, as clonality increases considerably with each round.
Pediatric Severe Sepsis Prediction Using Machine Learning
Authors: Desautels Thomas , Hoffman Jana , Barton Christopher , Mao Qingqing , Jay Melissa , Calvert Jacob , Das Ritankar
Published: November 2017

Early detection of pediatric severe sepsis is necessary in order to administer effective treatment. In this study, we assessed the efficacy of a machine-learning-based prediction algorithm applied to electronic healthcare record (EHR) data for the prediction of severe sepsis onset. The resulting prediction performance was compared with the Pediatric Logistic Organ Dysfunction score (PELOD-2) and pediatric Systemic Inflammatory Response Syndrome score (SIRS) using cross-validation and pairwise t-tests. EHR data were collected from a retrospective set of de-identified pediatric inpatient and emergency encounters drawn from the University of California San Francisco (UCSF) Medical Center, with encounter dates between June 2011 and March 2016. Patients (n = 11,127) were 2-17 years of age and 103 [0.93%] were labeled severely septic. In four-fold cross-validation evaluations, the machine learning algorithm achieved an AUROC of 0.912 for discrimination between severely septic and control pediatric patients at onset and AUROC of 0.727 four hours before onset. Under the same measure, the prediction algorithm also significantly outperformed PELOD-2 (p < 0.05) and SIRS (p < 0.05) in the prediction of severe sepsis four hours before onset. This machine learning algorithm has the potential to deliver high-performance severe sepsis detection and prediction for pediatric inpatients.
deepNF: Deep network fusion for protein function prediction
Authors: Gligorijević Vladimir , Barot Meet , Bonneau Richard
Published: November 2017

The prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provide a rich source of information for inferring functional annotations for genes and proteins. An important challenge has been to develop methods for combining these heterogeneous networks to extract useful protein feature representations for function prediction. Most of the existing approaches for network integration use shallow models that cannot capture complex and highly-nonlinear network structures. Thus, we propose deepNF, a network fusion method based on Multimodal Deep Autoencoders to extract high-level features of proteins from multiple heterogeneous interaction networks. We apply this method to combine STRING networks to construct a common low-dimensional representation containing high-level protein features. We use separate layers for different network types in the early stages of the multimodal autoencoder, later connecting all the layers into a single bottleneck layer from which we extract features to predict protein function. We compare the cross-validation and temporal holdout predictive performance of our method with state-of-the-art methods, including the recently proposed method Mashup. Our results show that our method outperforms previous methods for both human and yeast STRING networks. We also show substantial improvement in the performance of our method in predicting GO terms of varying type and specificity.

Availability

deepNF is freely available at: https://github.com/VGligorijevic/deepNF
Prediction of potential disease-associated microRNAs using structural perturbation method
Authors: Zeng Xiangxiang , Liu Li , Lü Linyuan , Zou Quan
Published: November 2017

Motivation

The identification of disease-related microRNAs(miRNAs) is an essential but challenging task in bioinformatics research. Similarity-based link prediction methods are often used to predict potential associations between miRNAs and diseases. In these methods, all unobserved associations are ranked by their similarity scores. Higher score indicates higher probability of existence. However, most previous studies mainly focus on designing advanced methods to improve the prediction accuracy while neglect to investigate the link predictability of the networks that present the miRNAs and diseases associations. In this work, we construct a bilayer network by integrating the miRNA–disease network, the miRNA similarity network and the disease similarity network. We use structural consistency as an indicator to estimate the link predictability of the related networks. On the basis of the indicator, a derivative algorithm, called structural perturbation method (SPM), is applied to predict potential associations between miRNAs and diseases.

Results

The link predictability of bilayer network is higher than that of miRNA–disease network, indicating that the prediction of potential miRNAs-diseases associations on bilayer network can achieve higher accuracy than based merely on the miRNA–disease network. A comparison between the SPM and other algorithms reveals the reliable performance of SPM which performed well in a 5-fold cross-validation. We test fifteen networks. TheAUCvalues of SPM are higher than some well-known methods, indicating that SPM could serve as a useful computational method for improving the identification accuracy of miRNA-disease associations. Moreover, in a case study on breast neoplasm, 80% of the top-20 predicted miRNAs have been manually confirmed by previous experimental studies.

Availability and Implementation

https://github.com/lecea/SPM-code.git

Contact

linyuan.lv@gmail.com,zouquan@nclab.net.

Supplementary information

Supplementary data are available atBioinformaticsonline.
Task-dependent modulation of spinal and transcortical stretch reflexes linked to motor learning rate
Authors: Dimitriou Michael
Published: November 2017

It is generally believed that task-dependent control of body configuration (‘posture’) is achieved by adjusting voluntary motor activity and transcortical ‘long-latency’ reflexes. Spinal monosynaptic circuits are thought not to be engaged in such task-level control. Similarly, being in a state of motor learning has been strongly associated only with an upregulation of feedback responses at transcortical latencies and beyond. In two separate experiments, the current study examined the task-dependent modulation of stretch reflexes by perturbing the hand of human subjects while they were waiting for a ‘Go’ signal to move at the different stages of a classic kinematic learning task (visuomotor rotation). Although the subjects had to resist all haptic perturbations equally, the study leveraged that task-dependent feedback controllers may already be ’loaded’ at the movement anticipation stage. In addition to an upregulation of short- and long-latency reflex gains during early exposure to the visual distortion, I found a relative inhibition of reflex responses in the ‘washout’ stage (sensory realignment state). For more distal muscles (brachioradialis), this inhibition also extended to the monosynaptic reflex response (‘R1’). These R1 gains reflected individual motor learning performance in the visuomotor task. The results demonstrate that the system’s ‘control policy’ in visuomotor adaptation can also include inhibition of proprioceptive reflexes, and that aspects of this policy can affect monosynaptic spinal circuits. The latter finding suggests a novel form of state-related control, probably realized by independent control of fusimotor neurons, through which segmental circuits can tune to higher-level features of a sensorimotor task.

Additional Information

Conflict of interest

The author declares no conflict of interest.

Author contributions

M.D. devised, designed and implemented the project, analyzed the data and wrote the manuscript. The author approves the final version of the manuscript and is fully accountable for all aspects of the work. The experiments were performed at the Department of Integrative Medical Biology, Umeå University, Sweden.

Funding

This work was financially supported through grants awarded to M.D. by the Kempe Foundation, the local Foundation for Medical Research (“Insamlingsstiftelsen”) and the Swedish Research Council (project 2016-02237).
Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor
Authors: Bucca Giselda , Pothi Radhika , Hesketh Andrew , Möller-Levet Carla , Hodgson David A. , Laing Emma E. , Stewart Graham R. , Smith Colin P.
Published: November 2017

Stress-induced adaptations require multiple levels of regulation in all organisms to repair cellular damage. In the present study we evaluated the genome-wide transcriptional and translational changes following heat stress exposure in the soil-dwelling model actinomycete bacterium, Streptomyces coelicolor. The combined analysis revealed an unprecedented level of translational control of gene expression, deduced through polysome profiling, in addition to transcriptional changes. Our data show little correlation between the transcriptome and ‘translatome’; while an obvious downward trend in genome wide transcription was observed, polysome associated transcripts following heat-shock showed an opposite upward trend. A handful of key protein players, including the major molecular chaperones and proteases were highly induced at both the transcriptional and translational level following heat-shock, a phenomenon known as ‘potentiation’. Many other transcripts encoding cold-shock proteins, ABC-transporter systems, multiple transcription factors were more highly polysome-associated following heat stress; interestingly, these protein families were not induced at the transcriptional level and therefore were not previously identified as part of the stress response. Thus, stress coping mechanisms at the level of gene expression in this bacterium go well beyond the induction of a relatively small number of molecular chaperones and proteases in order to ensure cellular survival at non-physiological temperatures.
q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data
Authors: Bokulich Nicholas A. , Zhang Yilong , Dillon Matthew , Rideout Jai Ram , Bolyen Evan , Li Huilin , Albert Paul S. , Caporaso J. Gregory
Published: November 2017

Studies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sectional and pre/post study designs. To support the needs of microbiome researchers performing longitudinal studies, we developed q2-longitudinal, a software plugin for the QIIME 2 microbiome analysis platform (https://qiime2.org). The q2-longitudinal plugin incorporates multiple methods for analysis of longitudinal and paired-sample data, including paired differences and distances, linear mixed effects models, microbial interdependence test, first differencing, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open source software released under a BSD-3-Clause license and is freely available, including for commercial use.
The temporal evolution of conceptual object representations revealed through models of behavior, semantics and deep neural networks
Authors: Bankson B. B. , Hebart M.N. , Groen I.I.A. , Baker C.I.
Published: November 2017

Visual object representations are commonly thought to emerge rapidly, yet it has remained unclear to what extent early brain responses reflect purely low-level visual features of these objects and how strongly those features contribute to later categorical or conceptual representations. Here, we aimed to estimate a lower temporal bound for the emergence of conceptual representations by defining two criteria that characterize such representations: 1) conceptual object representations should generalize across different exemplars of the same object, and 2) these representations should reflect high-level behavioral judgments. To test these criteria, we compared magnetoencephalography (MEG) recordings between two groups of participants (n = 16 per group) exposed to different exemplar images of the same object concepts. Further, we disentangled low-level from high-level MEG responses by estimating the unique and shared contribution of models of behavioral judgments, semantics, and different layers of deep neural networks of visual object processing. We find that 1) both generalization across exemplars as well as generalization of object-related signals across time increase after 150 ms, peaking around 230 ms; 2) behavioral judgments explain the most unique variance in the response after 150 ms. Collectively, these results suggest a lower bound for the emergence of conceptual object representations around 150 ms following stimulus onset.
Quantitative relationships for radiation induced chromosome instability: data analysis
Authors: Eidelman Y.A. , Slanina S.V. , Pyatenko V.S. , Khvostunov I.K. , Andreev S.G.
Published: November 2017

The experimental observations demonstrate that different cell lines reveal various shape of dynamic curves for radiation-induced chromosomal instability (RICI). We analyzed our own and published data on RICI for three cell lines, CHO-K1, V79 and TK6, on the basis of the mechanistic RICI model. We demonstrate that all three dynamic curves can be successfully described by the proposed model with partially cell line specific parameters.
Snapshot and crystallographic observations of kinetic and thermodynamic products for NO2S2 macrocyclic complexes
Authors: Park In-Hyeok , Kang Yunji , Lee Eunji , Ju Huiyeong , Kim Seulgi , Seo Sujin , Jung Jong Hwa , Lee Shim Sung
Published: November 2017

Direct observation and structural characterization of a kinetic product and a thermodynamic product for complexes with an NO2S2 macrocycle (L) are reported. L reacts with copper(I) iodide to give a mononuclear complex [Cu(L)]2(Cu2I4)·2CH2Cl2 (1), featuring three separate units. When cadmium(II) iodide was reacted with L, an anion-coordinated complex [Cd(L)I]2(Cd2I6)·4CH3CN (2) with a needle-type crystal shape was formed as the kinetic product. Interestingly, when the needle-type kinetic product was left undisturbed in the mother solution it gradually transformed to the pseudo-dimer complex [Cd2(L)2I2](Cd2I6) (3) with a brick-type crystal shape as the thermodynamic product. The dissolution–recrystallization process resulted in the elimination of the lattice solvent molecules (acetonitrile) in 2 and the contraction of two neighboring macrocyclic complex units [Cd(L)I]+, forming the pseudo-dimer 3
via an intermolecular Cd...I interaction between two monomers. For the entire process from kinetic to thermodynamic products, it was possible to obtain sequential photographic snapshots, single-crystal X-ray structures and powder X-ray diffraction patterns. For the copper(I) and cadmium(II) complexes, competitive NMR results agree with the solid-state data that show copper(I) has a higher affinity for L than does cadmium(II).
Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2
Authors: Fugel Malte , Jayatilaka Dylan , Hupf Emanuel , Overgaard Jacob , Hathwar Venkatesha R. , Macchi Piero , Turner Michael J. , Howard Judith A. K. , Dolomanov Oleg V. , Puschmann Horst , Iversen Bo B. , Bürgi Hans-Beat , Grabowsky Simon
Published: November 2017

Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element–hydrogen distances, r(X—H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X—H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydrocarbon rubrene (orthorhombic 5,6,11,12-tetraphenyltetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element–hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.
Fatigue based design and life estimation of viscoelastic rotors
Authors: Roy Haraprasad , Khare Abhinav , Chandraker Saurabh , Dutt J.K.
Published: November 2017

Purpose

High-speed rotor subjected to cyclic stress during operation may cause fatigue failure. Thus, the design of a rotor-shaft should involve the fatigue analysis for predicting safe life.

Design/methodology/approach

A damped rotor shaft with a centrally mounted disc, which is simulated as steam turbine rotor, is considered for fatigue analysis. The shaft is subjected to thermal load and axial torque. It is supported by two orthotropic flexible bearings at its two extreme ends. The bearings are modelled with two-element Voigt model along each orthogonal direction to consider the elastic damped behaviour. Finite element modelling is done through Rayleigh beam theory, where each element is also considered as a Voigt model. The mathematical model involves effect of external axial torque, softening and compressive action of the shaft due to thermal load by the high temperature steam.

Findings

This paper attempts to find dynamic stresses in a viscoelastic rotor-shaft subject to combined bending and torsional loading and is exposed to thermal environment during operation. The dynamic stress is then used to determine fatigue and also the life of rotors.

Research limitations/implications

Internal damping plays an important role in deciding dynamic behaviour of rotor shaft systems. Because of this, the rotor shaft becomes unstable after a certain spin speed. Thus, the design of the rotor based on fatigue analysis is limited to the stable zone.

Practical implications

For this purpose, equations of whirl motion of a viscoelastic rotor-shaft are first obtained after discretizing the continuum with finite beam elements and then the time domain solution of rotor displacement is used to find the bending stress and shear stress at various locations of the rotor. Location for the maximum stress decides the failure point. Safe rotor dimensions have been predicted by comparing dynamic stresses with the Soderberg diagram.

Originality/value

Design of rotor for safe life operation and prediction of stability could serve a good reference for designers.
In-flight icing risk prediction and management in consideration of wing stall
Authors: Pei Binbin , Xu Haojun , Xue Yuan , Chen Wei , Shen Anwei
Published: November 2017

Purpose

The purpose of this work is to develop an in-flight icing risk assessment methodology by quantification of changing flight dynamic characteristics under icing conditions.

Design/methodology/approach

This paper develops an approach for the quantitative assessment of flight risk under icing conditions. Using the six degree-of-freedom simulation model, the icing effects model is used to obtain the extreme values of the key parameters relevant to fight safety, allowing calculation of accident probability based on extreme value theory. The risk portion of the flight risk index is designed to account for different levels of flight risk and to provide criteria to allow pilots’ decision-making. Numerical examples are carried out by a series of simulated elevator overshoots of various levels and different distributions of ice accretion to compare the risk index under different icing conditions.

Findings

Case results show that the proposed methodology is able to analyze conditions of different severity and distribution of icing and assess quantitatively how these different parameters affect flight safety.

Practical implications

The quantification of flight risk in icing conditions demonstrated here can be applied to provide an objective and intuitive instrument to facilitate decisions by the aircrew or air traffic controller, especially prior to the aircraft entering into areas with adverse meteorological conditions.

Originality/value

Existing flight risk assessments under icing conditions are typically guided by aerodynamic changes, ice accumulation process or the subjective feeling of the pilot. Here, it is proposed to use the probability of flight risk event to measure different icing intensity levels in a quantitative way. This quantitative metric combines the alteration of aerodynamic characteristics, flight dynamic characteristics and limitation of critical parameters, providing a new and comprehensive viewpoint to measure in-flight icing risk. This may be a promising and more reasonable way to assess the risk.
Modeling and control for ultra-low altitude cargo airdrop
Authors: Han Yanhua
Published: November 2017

Purpose

The purpose of this paper is to model the aircraft-cargo’s coupling dynamics during ultra-low altitude heavy cargo airdrop and to design the aircraft’s robust flight control law counteracting its aerodynamic coefficients perturbation induced by ground effect and the disturbance from the sliding cargo inside.

Design/methodology/approach

Aircraft-cargo system coupling dynamics model in vertical plane is derived using the Kane method. Trimmed point is calculated when the cargo fixed in the cabin and then the approximate linearized motion equation of the aircraft upon it is derived. The robust stability and robust H∞ optimal disturbance restraint flight control law are designed countering the aircraft’s aerodynamic coefficients perturbation and the disturbance moment, respectively.

Findings

Numerical simulation shows the effectiveness of the proposed control law with elevator deflection as a unique control input.

Practical implications

The model derived and control law designed in the paper can be applied to heavy cargo airdrop integrated design and relevant parameters choice.

Originality/value

The dynamics model derived is closed, namely, the model can be called in numerical simulation free of assuming the values of parachute’s extraction force or cargo’s relative sliding acceleration or velocity as seen in many literatures. The modeling is simplified using Kane method rather than Newton’s laws. The robust control law proposed is effective in guaranteeing the aircraft’s flight stability and disturbance restraint performance in the presence of aerodynamic coefficients perturbation.