bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear solitary waves (oscillitons) in dusty magnetized pair plasmas
Authors: Cramer N. F. , Verheest Frank
Published: December 2018

Nonlinear theory is presented for solitary waves propagating parallel to the magnetic field in a cold plasma with charged dust grains or heavy ions. The particular case of an imbalanced electron-positron plasma with a portion of the charge residing on the dust particles is investigated. The charge imbalance plays a similar role to unequal ion and electron masses, in that an “oscilliton” type solution is found, using an approximate analytic solution, as well as numerical solutions of approximate equations and the full non-relativistic equations. Circularly polarized oscillitons occur for the electron-positron plasma for a Mach number above a critical value which is <1, in contrast to the pure pair plasma which has a linearly polarized non-oscillatory nonlinear wave solution for Mach number >1.
Integral Cross Sections for Electron–Magnesium Scattering Over a Broad Energy Range (0–5000 eV)
Authors: McEachran R. P. , Blanco F. , García G. , Stokes P. W. , White R. D. , Brunger M. J.
Published: December 2018

We report the results from the application of our optical potential and relativistic optical potential (ROP) methods to electron–magnesium scattering. The energy range of this study was 0–5000 eV, with the results for the integral elastic cross sections, summed discrete electronic-state excitation integral cross sections, momentum transfer cross sections, and total ionisation cross sections being reported. Where possible, we compare the present results to the available experimental data and to the earlier results from close coupling and R-matrix type computations. Typically, a quite fair level of accord is found between our ROP calculations and the earlier theoretical and experimental cross sections. Additionally, from the assembled database, we provide for the modeling community some recommended cross section sets for use in their simulations, in which magnesium is a constituent. Electron transport coefficients are subsequently calculated for reduced electric fields ranging from 0.1 to 1000 Td using a multi-term solution of Boltzmann’s equation. Substantial differences in the transport coefficients between the ROP calculations and the recommended cross sections are observed over the range of fields considered, clearly illustrating the importance of the veracity of the database in the simulations.
Ramet versus sporocarp production in the aquatic fern Salvinia auriculata (Salviniaceae): the role of shading
Authors: Medeiros Jessica Cristina Carvalho , Silva Josiane Carvalho Fonseca , Resende Tamiris da Silveira Campos , Teodoro Grazielle Sales , Pereira Fabrício José , Coelho Flávia de Freitas
Published: December 2018

Aquatic plants exposed to environmental changes exhibit plastic responses, resulting in functional adjustments to reduce stress effects. Lack of light can limit plant development and can affect biomass allocation and reproduction, stressing plants and sometimes halting their growth. Shading techniques have been used to control the excessive growth of weed plants, such as the aquatic fern Salvinia auriculata Aublet that can form dense mats on the water surface, causing problems in water use. We used shading nets in a greenhouse experiment to evaluate the effect of shade on the biomass of S. auriculata, and to determine if the fern changes its allocation of biomass to sexual (sporocarps) or asexual (buds) reproduction under different shade levels (full-sun control, 35% shade, and 70% shade). Under shade conditions, ramet biomass decreased and no sporocarps were produced, although the number of buds increased. Production of structures for sexual reproduction incurs a high energy cost, so S. auriculata invested in bud production (clonal reproduction). The differing energy requirements resulted in a significant trade-off between bud and sporocarp production. In conclusion, our study indicated that shading is not an efficient control technique for S. auriculata since it did not affect the clonal reproduction, a strategy that accelerates colonisation and facilitates rapid spread.
Continuous-range tunable multilayer frequency-selective surfaces using origami and inkjet printing
Authors: Nauroze Syed Abdullah , Novelino Larissa S. , Tentzeris Manos M. , Paulino Glaucio H.
Published: December 2018

Significance

Conventional reconfigurable electrical and radio frequency (RF) structures commonly used in applications involving real-time reconfigurability in response to fast varying operational scenarios require specialized substrates or complex electrical circuits. Origami-based RF reconfigurable components and modules offer a solution featuring unique properties. First, they enable reconfigurability over continuous-state ranges (as opposed to discrete states). Second, they do not require specialized mechanical support for multilayer frequency-selective surface structures. Moreover, deployable origami-based RF structures can achieve large surface reconfigurability ratios from folded to unfolded states. Finally, these structures allow for independent control of multiple figures of merit: bandwidth, frequency of operation, and angle of incidence.
Multilayer network switching rate predicts brain performance
Authors: Pedersen Mangor , Zalesky Andrew , Omidvarnia Amir , Jackson Graeme D.
Published: December 2018

Large-scale brain dynamics are characterized by repeating spatiotemporal connectivity patterns that reflect a range of putative different brain states that underlie the dynamic repertoire of brain functions. The role of transition between brain networks is poorly understood, and whether switching between these states is important for behavior has been little studied. Our aim was to model switching between functional brain networks using multilayer network methods and test for associations between model parameters and behavioral measures. We calculated time-resolved fMRI connectivity in 1,003 healthy human adults from the Human Connectome Project. The time-resolved fMRI connectivity data were used to generate a spatiotemporal multilayer modularity model enabling us to quantify network switching, which we define as the rate at which each brain region transits between different networks. We found (i) an inverse relationship between network switching and connectivity dynamics, where the latter was defined in terms of time-resolved fMRI connections with variance in time that significantly exceeded phase-randomized surrogate data; (ii) brain connectivity was lower during intervals of network switching; (iii) brain areas with frequent network switching had greater temporal complexity; (iv) brain areas with high network switching were located in association cortices; and (v) using cross-validated elastic net regression, network switching predicted intersubject variation in working memory performance, planning/reasoning, and amount of sleep. Our findings shed light on the importance of brain dynamics predicting task performance and amount of sleep. The ability to switch between network configurations thus appears to be a fundamental feature of optimal brain function.
Liver-related Events in Human Immunodeficiency Virus–infected Persons With Occult Cirrhosis
Authors: Benmassaoud Amine , Nitulescu Roy , Pembroke Thomas , Halme Alex S , Ghali Peter , Deschenes Marc , Wong Philip , Klein Marina B , Sebastiani Giada
Published: December 2018

Background

Human immunodeficiency virus (HIV)–infected patients are at increased risk of liver-related mortality. The effect of occult cirrhosis (OcC), defined as preclinical compensated cirrhosis without any clinical findings, on liver-related events is unknown.

Methods

HIV-infected patients from 2 Canadian cohorts underwent transient elastography (TE) examination and were classified as (1) OcC (TE ≥13 kPa with no sign of cirrhosis, including absence of thrombocytopenia and signs of advanced liver disease on ultrasound or gastroscopy); (2) overt cirrhosis (OvC) (TE ≥13 kPa with signs of cirrhosis); or (3) noncirrhotic patients (TE <13 kPa). Incidence and risk factors of liver-related events were investigated through Kaplan-Meier and Cox regression analyses, respectively. We estimated monitoring rates according to screening guidelines for hepatocellular carcinoma (HCC) by OcC and OvC status.

Results

A total of 1092 HIV-infected patients (51% coinfected with hepatitis C virus) were included. Prevalence of OcC and OvC at baseline was 2.7% and 10.7%, respectively. During a median follow-up of 1.8 (interquartile range, 1.5–2.8) years, the incidence of liver-related events in noncirrhosis, OcC, and OvC was 3.4 (95% confidence interval [CI], 1.2–7.3), 34.0 (95% CI, 6.0–104.0), and 37.0 (95% CI, 17.0–69.1) per 1000 person-years, respectively. Baseline OcC (adjusted hazard ratio [aHR], 7.1 [95% CI, 1.3–38.0]) and OvC (aHR, 8.5 [95% CI, 2.8–26.0]) were independently associated with liver-related events. Monitoring rates for HCC were lower in patients with OcC (24%) compared to those with OvC (40%).

Conclusions

HIV-infected patients with OcC have a high incidence of liver-related events. Greater surveillance and earlier recognition with appropriate screening strategies are necessary for improved outcomes.
The Interconnected Development of Personal Controls and Antisocial Behavior
Authors: Le Blanc Marc
Published: December 2018

This chapter describes a multidisciplinary, multilayered, and developmental theoretical journey inspired by Travis Hirschi’s book, Causes of Delinquency (1969). It first discusses the conceptual roots and meta-control theory that emerged from this journey. The chapter then presents a definitive statement of a systemic theory of the development of antisocial behavior—particularly the argument that the mechanisms and courses of the development of offending apply to all forms of antisocial behaviors. Next, the chapter specifies the content of an integrative personal control theory and the development of self-control and social control. It also reviews the mechanism of the developmental interaction between the self and social control systems based on the chaos-order perspective. Finally, this chapter discusses the importance of its personal control theory for criminology and sequels to this theoretical and empirical journey.
The Age-Graded Theory of Informal Social Control
Authors: Laub John H. , Rowan Zachary R. , Sampson Robert J.
Published: December 2018

This chapter turns to the age-graded theory of informal social control. This theory posits that crime is more likely to occur when an individual's bond to conventional society is weakened. This chapter briefly considers Sampson and Laub’s Crime in the Making before providing a summary of the revised version of the theory in Shared Beginnings, Divergent Lives. It then provides an updated theoretical and empirical assessment of the core principles of the theory, namely a review of current research on turning points and human agency. The chapter next details current challenges to the importance of turning points in adulthood and reviews contemporary barriers to mechanisms of desistance. The chapter concludes with some commentary and final thoughts on the theory.
The Impact of Changes in Family Situations on Persistence and Desistance from Crime
Authors: Theobald Delphine , Farrington David P. , Piquero Alex R.
Published: December 2018

This chapter emphasizes the significance of the family environment in the onset, persistence, and desistance from offending. Consequently, family effects have been empirically examined in the criminological literature for several decades, with the most recent attention devoted to the effects of marriage on patterns of desistance. This chapter reviews the literature on the effects of getting married but also considers the relatively limited evidence on the effects of cohabitation. Next, the chapter considers the evidence on the effects of parenthood and reviews the effect of separation/divorce on offending. Much of the empirical work in this area has studied effects on men, but the relatively limited literature on the effects on women is also reviewed.
Conclusions and Implications for Developmental and Life-Course Criminology
Authors: Farrington David P. , Kazemian Lila , Piquero Alex R.
Published: December 2018

This concluding chapter summarizes current knowledge about developmental and life-course criminology based on the previous chapters, reviews some areas in need of further research, and makes some recommendations about how future research can address these gaps in current knowledge. It shows how a great deal is known about risk factors for offending in general (especially for the prevalence of offending), but less is known about risk factors for specific criminal career features, such as the age of onset, the frequency of offending per year, and so on. The chapter discusses the limitations and challenges to current research and provides some recommendations for research that can expand on the topics already covered in this volume. Finally, this chapter suggests some methods for further research. It also provides some examples of studies undertaken along these lines.
Specialization and Versatility in Offending
Authors: Mazerolle Paul , McPhedran Samara
Published: December 2018

This chapter is an overview of the specialization/versatility debate. It presents the key elements of this debate, from the theoretical to the methodological, with the aim of capturing the contested, evolving, and dynamic nature of this important topic. This chapter first discusses the theoretical underpinnings of the specialization/versatility debate. Next, the practical implications of this debate for policy and program development are considered. The chapter then gives an overview of key empirical findings. Challenges and confounds within existing research are afterward discussed. From here, the chapter presents different ways in which specialization/versatility is operationalized. Finally, this chapter examines a range of data and measurement issues.
Trajectories of Criminal Behavior Across the Life Course
Authors: Morizot Julien
Published: December 2018

This chapter provides an overview of developmental-typological theories of criminal behavior best known by criminologists. These theories aim to explain heterogeneity in intra-individual change in criminal behavior across the life course by postulating developmental trajectories differing in terms of onset, variety and frequency of offending, criminal career duration, and period of desistance. The chapter outlines the most popular statistical methods for modeling developmental trajectories. It also summarizes the empirical findings from available developmental trajectory research. Overall, available longitudinal studies tend to support only some postulates of developmental-typological theories. This chapter thus proposes a number of directions for future research and provides some concluding insights.
Women, Peace, and Security
Authors: Davies Sara E. , True Jacqui
Published: December 2018

The Women, Peace, and Security agenda (WPS) stands at a juncture with significant potential to prevent conflicts, protect human rights, and promote recovery from conflict but inadequate progress and institutional resistance to meeting the commitments enshrined in UNSCR 1325. The chapter builds on feminist constructivist theories of normative change to put forward a pragmatist understanding of “women, peace, and security” as a “work in progress,” wherein advocates and scholars work together with activist states to advance principles of equal and lasting peace. We argue that WPS theory and practice in conflict, post-conflict, and peaceful situations is a dynamic, normative agenda, and iterative reform process committed to realizing a critical gender perspective on peace and security. Drawing on scholars, practitioners, and advocates’ experiences from the Global North and South working on the WPS thematic agenda and on women’s diverse practical experiences of promoting peace and inclusion, we defend a gender-sensitive and gender-inclusive perspective on peace and security.
Epigenetic Foundations of Emotion Dysregulation
Authors: Brown Mindy , Conradt Elisabeth , Crowell Sheila E.
Published: December 2018

Emotion dysregulation is a pervasive clinical problem that likely emerges from complex Gene × Environment interactions across development. Epigenetic processes provide a molecular basis by which genotype interacts with the environment across the lifespan to produce phenotype. Epigenetics is defined by molecular processes occurring on and around the genome that regulate gene activity without changing DNA sequence. This chapter describes how epigenetic mechanisms are assessed and provides a brief review of current research on epigenetics, emotion dysregulation, and associated disorders. It then highlights four biological pathways of interest, the serotonin, dopamine, and norepinephrine systems and the limbic-hypothalamic pituitary adrenal (L-HPA) axis, and argues that, to advance understanding of the pathophysiology of emotion dysregulation, biological pathways rather than single genes must be measured. The chapter describes challenges for the field of epigenetics and how novel methods could be leveraged to overcome those challenges.
Neuron Types, Intrinsic Circuits, and Plasticity in the Inferior Colliculus
Authors: Ito Tetsufumi , Ono Munenori , Oliver Douglas L.
Published: December 2018

The inferior colliculus is a critical auditory center in the midbrain which virtually acts as a hub of all ascending and descending auditory information flows. Wide variety of neuronal responses to sound is found in the IC, and this variety emerges not only from the wide range of extrinsic afferent inputs, but also from the complex features of the local circuits in the IC, for example, the mosaic pattern of extrinsic fiber termination, the various neuronal types each of which compose different patterns of local connection, and the unique forms of synaptic plasticity de novo. This chapter reviews the recent progress in understanding these features, and identifies the key issues for future research.
Government and Fiscal Policy in American Economic History
Authors: Wallis John Joseph
Published: December 2018

Over the last 225 years, government finances in the United States have gone through three distinct stages. In the first stage, 1790–1850, state governments actively pursued policies to promote economic development and financed them from revenues from state investments. In the second, 1850–1930, local governments became the most important level of government, as measured by revenues and expenditures, and revenues shifted toward the property tax. In the third period, 1930 to the present, the national government became the most active and largest level of government, financed through income and payroll taxes, and developed an extensive network of grants to state and local governments. The chapter tracks the changes in sources of revenues and purpose of expenditures, with specific attention paid to military spending over the entire period.
Development of Lying and Cognitive Abilities
Authors: Talwar Victoria
Published: December 2018

The emergence and development of children’s lie-telling is closely associated with their developing cognitive abilities. Telling a lie involves complicated cognitive functions including theory-of-mind understanding and executive functioning abilities. Recent research has found that lie-telling emerges in the preschool years and children’s abilities to maintain their lies improves with age. The current chapter reviews existing literature on the development of children’s lie-telling behavior and its relation to various aspects of children’s cognitive development. It covers the work of Lewis, Stanger, and Sullivan (1989), including the well-known guessing-game experiment, where the child is left alone with temptation and the instruction not to peek. Much of Talwar, Lee, et al.’s research into three-to-seven-year-old children’s lie-telling behavior is covered; and the interaction between these studies and Theory of Mind is emphasized; this is illuminated in the account of research using child subjects with Autism Spectrum Disorder.
The History of Neuropsychology at the Boston VA
Authors: Hebben Nancy , O'Connor Margaret
Published: December 2018

The Veterans Administration’s response to WWII altered the fields of psychology and neurology and made it possible for the Boston VA Hospital to evolve into an environment where neuropsychology, aphasiology, and behavioral neurology could jointly flourish. Starting with Harold Goodglass, Edith Kaplan, and Norman Geschwind in the 1950s, a multi-disciplinary group of clinicians and scientists helped usher in a transition from holistic “black box” empiricist models of the brain to models that were more localizationist and modular. Under the influence of this pioneering trio of astute observers, experimentalists, and thinkers, the Boston VA became the epicenter of basic research in human cognitive and behavioral neuroscience in the world. While signaling a revolution in psychology that unified neurobiology and behavioral principles, the work done at the Boston VA established a direct link from this neuroscience of the mind to patient care, especially as it affected the veterans of the United States.
History of Neuropsychology in France
Authors: Derouesné Christian , Poirier Jacques
Published: December 2018

Neuropsychology in France has a long tradition, beginning with Paul Broca, Jean-Martin Charcot, and their followers who established an anatomo-clinical approach, operating primarily within the field of neurology. Henri Hécaen at Sainte Anne and François Lhermitte at the Salpêtrière in the 1950s–1960s introduced the methodology of experimental and cognitive international neuropsychology into French neuropsychology. Subsequently, most research in neuropsychology has been conducted by psychologists in collaboration with national research organizations. The development and practice of clinical neuropsychology grew in the 1980s in response to needs for the diagnosis and care of patients with Alzheimer’s disease and related disorders. In the end, advances in the science and psychology of the field of neuropsychology have resulted in its institutionalization within France, but its establishment as an independent profession and discipline remains incomplete.
History of CT Scan Studies in Aphasia—1970s to 1990s
Authors: Naeser Margaret A. , Palumbo Carole L. , Martin Paula I.
Published: December 2018

This chapter summarizes early computed tomography (CT) scan studies in stroke patients with aphasia from the 1970s through the 1990s. Studies took place at the Boston University Aphasia Research Center located at the Boston Veterans Affairs Medical Center. Earliest studies associated classical aphasia syndromes with lesions located in cortical language areas on CT scans. In the 1980s, studies reported that chronic aphasia could be associated with subcortical lesion only; emphasis was on lesion in white matter pathways. In the 1990s, studies showed that lesion sites on CT scans performed after 2 months poststroke could be predictive for recovery of auditory language comprehension, and meaningful nonfluent speech at 1 year poststroke. Lesion site patterns were identified for different outcome levels following specific language therapy programs. Some rare aphasia cases are included: left-handers with separate hemispheric dominance locations for speech versus comprehension in the same person; and a unilateral, word deafness case.
Infliximab trough levels are decreasing over time in patients with inflammatory bowel disease on maintenance treatment with infliximab
Authors: Orfanoudaki Eleni , Gazouli Maria , Foteinogiannopoulou Kalliopi , Theodoraki Eirini , Legaki Evangelia , Romanos Ioannis , Mouzas Ioannis , Koutroubakis Ioannis E.
Published: December 2018

Background

Infliximab trough levels (IFX-TLs) and antibodies to infliximab (ATIs) have been suggested as useful markers for the optimization of treatment in inflammatory bowel disease (IBD). We aimed to estimate the patterns over time of IFX-TLs and ATIs in IBD patients on maintenance treatment with IFX.

Methods

Two different measurements of IFX-TLs and ATIs were performed (ELISA; Eagle BioSciences) at a 10-month interval using serum samples of consecutive patients on maintenance treatment with IFX. Certain biomarkers [hemoglobin, erythrocyte sedimentation rate, C-reactive protein (CRP), platelets, albumin] measured at the same time as well as clinical disease activity and quality of life were assessed.

Results

Among a total of 86 IBD patients under maintenance treatment with IFX, 64 [49 Crohn’s disease, 15 ulcerative colitis (UC), 42 men, mean age 44.2±15.2 years, 41 in combination therapy with immunomodulator, six in intensified dose], with two available measurements of IFX-TLs and ATIs (A and B), were included in the study. The median levels of IF-TLs were 5.07 (interquartiles range: 1.60–12.73) μg/ml in measurement A and 4.68 (1.19–7.83) μg/ml in measurement B (P<0.0001). Patients whose dose was intensified after the first measurement showed an increase in their median IFX-TLs from 1.47 to 8.5 μg/ml, whereas patients with stable IFX dose showed a significant reduction in the median IFX-TLs from 5.65 to 3.8 μg/ml (P<0.0001). In the logistic regression analysis, the decrease in IFX-TL was correlated significantly and independently with the increase in CRP [odds ratio 5.2 (1.4–19.0), P=0.01].

Conclusion

IBD patients on maintenance treatment with IFX show decreasing patterns of IFX-TLs over time associated with increasing patterns of CRP levels.
Activation of Supraspinatus and Infraspinatus Partitions and Periscapular Musculature During Rehabilitative Elastic Resistance Exercises
Authors: Joseph Ranjit , Alenabi Talia , Lulic Tea , Dickerson Clark R.
Published: December 2018

Objective

The purpose of this study was to quantify the activation of partitions within supraspinatus and infraspinatus and some periscapular muscles during four resistance exercises with elastic bands.

Design

Twenty-seven right-handed healthy volunteers (age, 22.5 ± 2.7 yrs) were recruited. Intramuscular electromyography from supraspinatus (anteriorandposterior)and infraspinatus (superiorandmiddle) and surface electromyography data from the upper, middle, and lower trapezius and serratus anterior were recorded during four elastic resistance exercises (Y, T, W, L). Kinematics were recorded synchronously. Electromyography values were presented as percentage of maximal voluntary isometric contraction and compared across exercises using analysis of variance. Muscle activation ratios were also calculated.

Results

The mean activations of all rotator cuff partitions were more than 40% maximal voluntary isometric contraction, except middle infraspinatus during the T exercise (29.3% maximal voluntary isometric contraction). Serratus anterior activity was significantly higher during the Y exercise (P< 0.008). Lower trapezius was activated more than 80% maximal voluntary isometric contraction in all four exercises with higher contributions compared with the upper trapezius.

Conclusions

The investigated exercises induced moderate to high activation in supraspinatus and infraspinatus partitions and very high activation in lower trapezius. YTWL exercises are appropriate for strengthening of some rotator cuff and periscapular muscles and for late stages of shoulder rehabilitation.
Third Molar Eruption and Hardware Fungal Infection Following Treatment of Mandibular Angle Fracture
Authors: Olenczak Jonathon Bryce , Shaffrey Ellen , Shaeffer Catherine A. , Black Jonathan S.
Published: December 2018

Appropriate management of lower 3rd molars is crucial to successful treatment of mandibular angle fractures. A unique case of a patient who presented for initial management of a left mandibular angle fracture with an unerupted lower 3rd molar was discussed in this study. After treatment with open reduction and internal fixation of the fracture, the lower 3rd molar erupted and the patient subsequently developed fungal osteomyelitis and hardware failure. This was successfully treated with hardware removal, maxillomandibular fixation, and combined use of an intravenous antibiotic and oral antifungal.
The conservation status of Costa Rican velvet worms (Onychophora)
Authors: Morera-Brenes Bernal , Monge-Najera Julian , Carrera-Mora Paola
Published: December 2018

Charismatic species, like the panda, play an important role in conservation, and velvet worms arguably are charismatic worms. Thanks to their extraordinary hunting mechanism, they have inspired from a female metal band in Japan, to origami worms in Russia and video game monsters in the USA. Objective: To assess their conservation status in Costa Rica. Methods: we located all collection records of the 29 known species from the Onychophora Database in the map of the Costa Rican Conservation Network. Results: We found that seven species are protected inside forest reserves, five in Protected Zones, four in Wildlife Refuges, two in National Parks and one, Principapillatus hitoyensis, in a strictly pristine Biological Reserve. The largest species in the world, Peripatus solorzanoi, occurs both inside a Forest Reserve and in protected private land. Protection inside Costa Rican nature areas is enforced year round by personnel that includes armed guards, and is supported by educational programs in surrounding communities. Twelve species have not been found in protected areas, but in Costa Rica, all biological species, named and unnamed, are protected by law and cannot be legally collected, or exported, without technically issued permits. Conclusion: Like in the only other country with similar information (New Zealand), the conservation of onychophorans seems to be of least concern for at least two thirds of the known species. Epiperipatus isthmicola, recently rediscovered after a century of absence in collections, can be considered Threatened because nearly all of its natural habitat has now been covered by a city.
Ultra-Efficient Short Read Sequencing of T Cell Receptor Repertoires
Authors: Montagne Janelle M. , Zheng Xuwen Alice , Pinal-Fernandez Iago , Milisenda Jose C. , Christopher-Stine Lisa , Lloyd Thomas E. , Mammen Andrew L. , Larman H. Benjamin
Published: December 2018

T cell receptor (TCR) repertoire sequencing is increasingly employed to characterize adaptive immune responses. However, current TCR sequencing methodologies are complex and expensive, limiting the scale of feasible studies. Here we present Framework Region 3 AmplifiKation sequencing (FR3AK-seq), a simplified multiplex PCR-based approach for the ultra-efficient analysis of TCR complementarity determining region 3 (CDR3) repertoires. By using minimal primer sets targeting a conserved region adjacent to CDR3, undistorted amplicons are analyzed via short read, single-end sequencing. We find that FR3AK-seq is sensitive and quantitative, performing comparably to two industry standards. FR3AK-seq was utilized to quickly and inexpensively characterize the T cell infiltrates of muscle biopsies obtained from 145 patients with idiopathic inflammatory myopathies and controls. A cluster of related TCRs was identified in samples from patients with sporadic inclusion body myositis, suggesting the presence of a shared antigen-driven response. The ease and minimal cost of FR3AK-seq removes critical barriers to routine, large-scale TCR CDR3 repertoire analyses.
Kinetic And Structural Parameters Governing Fic-Mediated Adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78
Authors: Mattoo Seema , Sanyal Anwesha , Zbornik Erica A , Watson Ben G , Christoffer Charles , Ma Jia , Kihara Daisuke
Published: December 2018

Fic (filamentation induced by cAMP) proteins regulate diverse cell signaling events by post-translationally modifying their protein targets, predominantly by the addition of an AMP (adenosine monophosphate). This modification is called Fic-mediated Adenylylation or AMPylation. We previously reported that the human Fic protein, HYPE/FicD, is a novel regulator of the unfolded protein response (UPR) that maintains homeostasis in the endoplasmic reticulum (ER) in response to stress from misfolded proteins. Specifically, HYPE regulates UPR by adenylylating the ER chaperone, BiP/GRP78, which serves as a sentinel for UPR activation. Maintaining ER homeostasis is critical for determining cell fate, thus highlighting the importance of the HYPE-BiP interaction. Here, we study the kinetic and structural parameters that determine the HYPE-BiP interaction. By measuring the binding and kinetic efficiencies of HYPE in its activated (Adenylylation-competent) and wild type (de-AMPylation-competent) forms for BiP in its wild type and ATP-bound conformations, we determine that HYPE displays a nearly identical preference for the wild type and ATP-bound forms of BiP in vitro and preferentially de-AMPylates the wild type form of adenylylated BiP. We also show that AMPylation at BiP Thr366 versus Thr518 sites differentially affect its ATPase activity, and that HYPE does not adenylylate UPR accessory proteins like J-protein ERdJ6. Using molecular docking models, we explain how HYPE is able to adenylylate Thr366 and Thr518 sites in vitro. While a physiological role for AMPylation at both the Thr366 and Thr518 sites has been reported, our molecular docking model supports Thr518 as the structurally preferred modification site. This is the first such analysis of the HYPE-BiP interaction and offers critical insights into substrate specificity and target recognition.
Noninvasive lung cancer detection via pulmonary protease profiling
Authors: Kirkpatrick Jesse , Warren Andrew D. , Tammela Tuomas , Westcott Peter M. K. , Voog Justin C. , Jacks Tyler , Bhatia Sangeeta N.
Published: December 2018

Lung cancer is the leading cause of cancer-related death and patients most commonly present with incurable metastatic disease. National guidelines recommend screening for high-risk patients with low-dose computed tomography (LDCT), but this approach has limitations including high false positive rates. Activity-based nanosensors (ABNs) detect dysregulated proteases in vivo and release a reporter to provide a urinary readout of disease activity. Here, we demonstrate the translational potential of ABNs by coupling ABN multiplexing with intrapulmonary delivery to detect early-stage lung cancer in an immunocompetent, genetically engineered mouse model (GEMM). The design of the multiplexed panel of sensors was informed by comparative transcriptomic analysis of human and mouse lung adenocarcinoma data sets and in vitro cleavage assays with recombinant candidate proteases. When employed in a Kras and Trp53 mutant lung adenocarcinoma mouse model, this approach confirmed the role of metalloproteases in lung cancer and enabled accurate early detection of disease, with 92% sensitivity and 100% specificity.
Automated Seizure Detection Tailored Towards Portable Patient Care Using A Novel, Computationally Efficient Method of Analysis
Authors: Huang Zachary , Ying Yiming
Published: December 2018

Epilepsy is a devastating neurological disorder that affects approximately 1-3% population worldwide. Wearables have recently gained more popularity as having a promising future in epilepsy management including seizure alert and close-loop therapy for severe forms of seizures. Due to the random and low frequency of seizures, seizure evaluation requires continuous, long-term EEG monitoring, which produces a large volume of data. The future treatment systems will rely on algorithms that can detect seizures with high precision and low computational cost. Previous implemented algorithms have used various computationally expensive methods of data transformation and feature extraction. In the present study, we developed a new computationally efficient seizure detection algorithm based on analysis of the broad, global shape EEG data of tonic-clonic seizures from a mouse model of temporal lobe epilepsy (TLE). To perform this algorithm, EEG data was normalized and processed through a rolling mean function, producing smoothed, simplified EEG clips that represent the global shape of the clip. These signals were then directly inputted for SVM training and testing. This novel method of seizure analysis only requires a small fraction of EEG data points, yet achieved an accuracy rate of approximately 98.51%. Our study provides a proof of principle that this simpler method could have an advantage in low-power platform such as wearables. Recently, the FDA approved a seizure detection app called embrace2 by Empatica. However, their algorithm detects seizures indirectly by monitoring heart rate and muscle contractions. Our novel algorithm detects seizures directly through analysis of brain activity. Thus, our algorithm may be better suited for future wearables in epilepsy management.
Different impacts of naturally occurring variants of the globally disseminated carbapenemase-encoding plasmid pKpQIL on the biology of host strains
Authors: Saw Howard T. H. , Webber Mark A. , Woodford Neil , Piddock Laura J. V.
Published: December 2018

Synopsis

Klebsiella-associated plasmid pKpQIL and its variant have been isolated globally. Our study aimed to determine whether a naturally occurring variant has altered host range and impacts on the fitness of different bacterial host strains. The plasmids pKpQIL-UK and pKpQIL-D2 were transferred from the original clinical isolate host strains of Klebsiella pneumoniae into Escherichia coli, Salmonella Typhimurium, Enterobacter cloacae and Serratia marcescens strains by filter-mating and conjugation frequencies determined and compared. The fitness of the resulting transconjugants was assessed by determining growth kinetics, ability to form a biofilm and persistence of the plasmids in each host was also measured. Transfer of either plasmid into Salmonella and S. marcescens was similar. However, pKpQIL-UK transferred into E. coli at a higher rate than did pKpQIL-D2; the reverse was found for E. cloacae. Both plasmids were rapidly lost from the E. coli population. Plasmid pKpQIL-UK, but not -D2, was able to persist in Salmonella. Although pKpQIL-UK imposed a greater fitness cost (inferred from an increased generation time) than -D2 on E. cloacae, it was able to persist as well as pKpQIL-D2 in this host. The pKpQIL-D2 plasmid did not confer any fitness benefit on any of the hosts under the conditions tested. Variants of the globally important pKpQIL plasmid have arisen in patients due to recombination. The impacts of the pKpQIL-UK plasmid and the -D2 variant in various Enterobacteriaceae are host-dependent. Continuing evolution of pKpQIL may alter its host range in the future.
Cloud-based improved Monte Carlo localization algorithm with robust orientation estimation for mobile robots
Authors: Li I-hsum , Wang Wei-Yen , Li Chung-Ying , Kao Jia-Zwei , Hsu Chen-Chien
Published: December 2018

Purpose

This paper aims to demonstrate a cloud-based version of the improved Monte Carlo localization algorithm with robust orientation estimation (IMCLROE). The purpose of this system is to increase the accuracy and efficiency of indoor robot localization.

Design/methodology/approach

The cloud-based IMCLROE is constructed with a cloud–client architecture that distributes computation between servers and a client robot. The system operates in two phases: in the offline phase, two maps are built under the MapReduce framework. This framework allows parallel and even distribution of map information to a cloud database in pre-described formats. In the online phase, an Apache HBase is adopted to calculate a pose in-memory and promptly send the result to the client robot. To demonstrate the efficiency of the cloud-based IMCLROE, a two-step experiment is conducted: first, a mobile robot implemented with a non-cloud IMCLROE and a UDOO single-board computer is tested for its efficiency on pose-estimation accuracy. Then, a cloud-based IMCLROE is implemented on a cloud–client architecture to demonstrate its efficiency on both pose-estimation accuracy and computation ability.

Findings

For indoor localization, the cloud-based IMCLROE is much more effective in acquiring pose-estimation accuracy and relieving computation burden than the non-cloud system.

Originality/value

The cloud-based IMCLROE achieves efficiency of indoor localization by using three innovative strategies: firstly, with the help of orientation estimation and weight calculation (OEWC), the system can sort out the best orientation. Secondly, the system reduces computation burden with map pre-caching. Thirdly, the cloud–client architecture distributes computation between the servers and client robot. Finally, the similar energy region (SER) technique provides a high-possibility region to the system, allowing the client robot to locate itself in a short time.
A parametric study on the droplet detachment process from the ceiling under the effect of gravity
Authors: Manik Jai , Dalal Amaresh , Natarajan Ganesh
Published: December 2018

Purpose

The purpose of this paper is to numerically investigate the effect of various parameters such as density ratio, surface wettabilities and Weber number on the droplet dripping and detachment process.

Design/methodology/approach

By using algebraic volume of fluid method, the governing equations are solved using a collocated finite volume approach in two-dimensions.

Findings

The results indicate that, for small densities of droplet, it adheres to the surface except when the surface is hydrophobic, while an increase in Weber number or presence of an additional droplet in the vicinity led to detachment.

Originality/value

The paper explores various characteristics of a droplet when two competing forces, namely, gravity and surface tension, act simultaneously. The detachment is observed for a given initial droplet size, as it becomes denser in an uniform gravitational field. The effect of droplet affinity for two droplets is also presented using the simulations.
Darcy–Forchheimer flow of nanofluid due to a curved stretching surface
Authors: Saif Rai Sajjad , Hayat T. , Ellahi R. , Muhammad Taseer , Alsaedi A.
Published: December 2018

Purpose

The purpose of present communication is to analyze Darcy–Forchheimer flow of viscous nanofluid by curved stretchable surface. Flow in porous medium is characterized by Darcy–Forchheimer relation. Brownian diffusion and thermophoresis are considered. Convective heat and mass boundary conditions are also used at the curved stretchable surface.

Design/methodology/approach

The resulting nonlinear system is solved through shooting technique.

Findings

Skin friction coefficient is enhanced for larger porosity parameter and inertia coefficient while reverse trend is noticed for curvature parameter. Local Nusselt number is enhanced for higher Prandtl number and thermal Biot number, whereas the opposite trend is seen via curvature parameter, porosity parameter, inertia coefficient, thermophoresis parameter and Brownian motion parameter. Local Sherwood number is enhanced for Schmidt number, Brownian motion parameter and concentration Biot number, while reverse trend is noticed for curvature parameter, porosity parameter, inertia coefficient and thermophoresis parameter.

Originality/value

To the best of author’s knowledge, no such consideration has been given in the literature yet.
Scaffolding and supporting use of information for ambitious learning practices
Authors: Glazewski Krista D. , Hmelo-Silver Cindy E.
Published: December 2018

Purpose

This paper aims to lay out the goals and challenges in using information for ambitious learning practices.

Design/methodology/approach

Through a review of the literature, the authors integrate across learning, information sciences and instructional design to identify challenges and possibilities for information searching and sense-making in ambitious learning practices (ALPs).

Findings

Learners face a number of challenges in using information in ALPs such as a problem-based learning. These include searching and sourcing, selecting information and sense-making. Although ALPs can be effective, providing appropriate scaffolding, supports and resources is essential.

Originality/value

To make complex ALPs available to a wide range of learners requires considering the information literacy demands and how these can be supported. This requires deep understanding and integration across different research literature areas to move toward solutions.
How do an alliance firm’s strategic orientations drive its knowledge acquisition? Evidence from Sino-foreign alliance partnership
Authors: Yang Qian , Liu Yi , Li Yuan
Published: December 2018

Purpose

This paper aims to investigate how a Chinese firm’s strategic orientation impact its knowledge acquisition from its foreign alliance partners through governance mechanisms used in the Sino-foreign alliance partnership.

Design/methodology/approach

This research first proposes an integrated model which links a firm’s strategic orientations (entrepreneurial and market orientations), governance mechanism (contract and trust controls), and its knowledge acquisition together. Then, this research collected data from 198 Chinese firms involved in Sino-foreign alliances to test the conceptual model.

Findings

For entrepreneurial-oriented alliance firms, a moderate level of contract and a high level of trust are the most efficient uses of control mechanisms for Chinese firms’ knowledge acquisition. In comparison, for market-oriented alliance firms, both contract and trust control mechanisms should be used at the moderate level to achieve maximum knowledge acquisition from their foreign partners.

Originality/value

By introducing a new antecedent for the choice of control mechanisms in the context of Sino-foreign alliance relationships, this study empirically finds a non-linear relationship between contract control and knowledge acquisition and confirms the significant role of trust in facilitating knowledge acquisition between alliance partners from the perspective of alliance firms in emerging markets.
How game difficulty and ad framing influence memory of in-game advertisements
Authors: Dardis Frank , Schmierbach Mike , Sherrick Brett , Luckman Britani
Published: December 2018

Purpose

In-game advertising continues to increase in importance for both industry and academia. However, game difficulty – an important, real-world factor – has received little attention as a specific game-related factor that might impact the effectiveness of in-game advertisements. This study aims to investigate the influence of game difficulty on players’ affective response and subsequent memory of in-game ads, which were presented as either gain- or loss-framed messages.

Design/methodology/approach

Three experiments were conducted. Study 1 and Study 3 implemented a 2 (difficulty: easy/difficult) × 2 (ad framing: gain/loss) design. Study 2 implemented a 2 (background music: calm/stressful) × 2 (ad framing: gain/loss) design. All experiments took place in a research laboratory in which participants consented to the study, completed a pre-test questionnaire, played a video game, completed a post-test questionnaire and were debriefed.

Findings

More difficult game play led to greater negative affective response. A different game-based attribute – background music – did not influence affective response. A significant interaction in Study 1 revealed that brand recognition increased as players in a more negative affective state were exposed to the loss-framed message. The results were explained to occur via the congruency effects that game difficulty exerts on players’ affective and cognitive states.

Originality/value

The studies are the first to incorporate both videogame difficulty and ad framing into one study, which two real-world factors that can influence advertising’s effectiveness. Theoretical and practical implications are discussed.