bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms
Authors: Xu Min , Chai Xiaoqi , Muthakana Hariank , Liang Xiaodan , Yang Ge , Zeev-Ben-Mordehai Tzviya , Xing Eric P
Published: April 2017

Motivation

Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data.

Results

To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data.

Availability and Implementation

Source code freely available at http://www.cs.cmu.edu/∼mxu1/software.

Supplementary information

Supplementary data are available at Bioinformatics online.
LabRS: A Rosetta stone for retrospective standardization of clinical laboratory test results
Authors: Hauser Ronald George , Quine Douglas B , Ryder Alex
Published: April 2017

Objective

Clinical laboratories in the United States do not have an explicit result standard to report the 7 billion laboratory tests results they produce each year. The absence of standardized test results creates inefficiencies and ambiguities for secondary data users. We developed and tested a tool to standardize the results of laboratory tests in a large, multicenter clinical data warehouse.

Methods

Laboratory records, each of which consisted of a laboratory result and a test identifier, from 27 diverse facilities were captured from 2000 through 2015. Each record underwent a standardization process to convert the original result into a format amenable to secondary data analysis. The standardization process included the correction of typos, normalization of categorical results, separation of inequalities from numbers, and conversion of numbers represented by words (eg, “million”) to numerals. Quality control included expert review.

Results

We obtained 1.266 × 109 laboratory records and standardized 1.252 × 109 records (98.9%). Of the unique unstandardized records (78.887 × 103), most appeared <5 times (96%, eg, typos), did not have a test identifier (47%), or belonged to an esoteric test with <100 results (2%). Overall, these 3 reasons accounted for nearly all unstandardized results (98%).

Conclusion

Current results suggest that the tool is both scalable and generalizable among diverse clinical laboratories. Based on observed trends, the tool will require ongoing maintenance to stay current with new tests and result formats. Future work to develop and implement an explicit standard for test results would reduce the need to retrospectively standardize test results.
Mental disorders, network models, and dynamical systems
Authors: Borsboom Denny
Published: April 2017

Network approaches have been proposed as an alternative way of thinking about relations between symptoms of mental disorders. Unlike traditional psychometric approaches, network models view these associations as the result of direct interactions between symptoms. Disorders are defined as alternative stable states of a network due to increased connectivity between symptoms. This increased connectivity creates a pattern of reinforcement, so the system can get stuck in a state of prolonged activation. Mental health is defined as the stable state of a weakly connected network. Although symptomatology may be temporarily increased in a healthy network (e.g., due to adverse life events), as the influence of a shock wanes the network will spontaneously return to its healthy state. Strongly connected networks, however, may transition into disordered states upon similar external shocks, and may not naturally recover. Thus, the proposed definitions yield plausible conceptualizations of resilience and vulnerability.
Introduction to “The ontology and epistemology of symptoms: The case of auditory verbal hallucinations in schizophrenia”
Authors: Kendler Kenneth S.
Published: April 2017

This chapter presents an introduction to the ontology and epistemology of psychiatric symptoms, as further discussed in the following chapter. It considers the practical implications for diagnosis of psychiatric symptoms.
Beyond the Treatment Box: Perspectives on the Federal Response to Opioid Use, Pregnancy, and Neonatal Abstinence Syndrome
Authors: Terplan Mishka
Published: April 2017

There has been much activity within Federal agencies in response to the opioid epidemic particularly in regards to pregnant women and their infants. Substance Abuse and Mental Health Services Administration's recently released document, Advancing the Care of Pregnant and Parenting Women With Opioid Use Disorder and Their Infants: A Foundation for Clinical Guidance, provides an important and timely guidance. Uptake of the guide should improve quality of care and hopefully help lessen the discrimination experienced by pregnant women with opioid use disorder. However, most pregnant women with addiction do not have access to treatment. This unmet need is large and vexing and only tangentially addressed in the Guide. Future Federal efforts should focus beyond the “treatment box.”
A New Local Flap Nipple Reconstruction Technique Using Dermal Bridge and Preoperatively Designed Tattoo
Authors: Komiya Takako , Iwahira Yoshiko
Published: April 2017

Background:

Nipple–areolar reconstruction is the final step in breast reconstruction. Reconstruction using local flaps and tattooing is useful in cases of bilateral reconstruction, a small nipple–areolar complex (NAC) as the donor site, and avoiding disturbance of the normal side and other body parts. However, this method can cause projection loss and color fading of the nipple. Moreover, the breast mound is reconstructed with an implant.

Methods:

We performed nipple–areolar reconstruction of 90 nipples using clover-designed flaps oriented at 120 degrees and tattooing after breast silicone implantation in 64 women. The tattoo was designed before flap operation and stained darker. Following donor site closure, a dermal flap was made as a bridge for nipple support. The nipple space was separated by the dermal flap from the breast mound and was filled with subcutaneous tissue. The size of the reconstructed nipple projection was measured postoperatively and 1 year later. The projection maintenance rate was calculated.

Results:

The heights of the nipple projection were 11.3 ± 1.8 mm (95% confidence interval [CI]: 10.9–11.7) just after the operation and 6.09 ± 2.4 mm (95% CI: 5.6–6.6) 1 year later. The actual range of nipple projection between these 2 heights was 5.2 ± 2.4 mm (95% CI: 4.7–5.7). The maintenance rate of the reconstructed nipple projection after 12 months was 54.1 ± 20.9 (95% CI: 49.7–58.5). The nipple color was maintained for over a year.

Conclusions:

Our nipple–areolar reconstruction technique could maintain the projection and color of the reconstructed nipple for a long period. Good outcomes were obtained in this implant-based breast reconstruction.
PREDICTIVE VALUE OF OPTICAL COHERENCE TOMOGRAPHIC FEATURES IN THE BEVACIZUMAB AND RANIBIZUMAB IN PATIENTS WITH DIABETIC MACULAR EDEMA (BRDME) STUDY
Authors: Fickweiler Ward , Schauwvlieghe Ann-Sofie M. E. , Schlingemann Reinier O. , Maria Hooymans Johanna M. , Los Leonoor I. , Verbraak Frank D. ,   the BRDME Research Group
Published: April 2017

Purpose:

To establish the predictive value of specific optical coherence tomography retinal features on visual outcomes and retinal thickness during anti–vascular endothelial growth factor treatment in patients with diabetic macular edema.

Methods:

Post hoc analysis of compound data of a prospective, 6-month, multicenter, randomized controlled trial of 119 patients with diabetic macular edema receiving either intravitreal bevacizumab or ranibizumab were analyzed to assess the associations between baseline retinal morphologic parameters and change in best-corrected visual acuity and central subfield thickness. Based on the study protocol of the core study, best-corrected visual acuity and central subfield thickness were obtained before each mandatory monthly injection during 6 months.

Results:

The presence of serous retinal detachment at baseline was associated with significant improvement in best-corrected visual acuity letter score at Month 3 and Month 6 (P < 0.001 and P = 0.01, respectively). In addition, the presence of disorganization of retinal inner layers was associated with lower best-corrected visual acuity letter score at Month 3 and Month 6 (P < 0.05 and P = 0.01, respectively).

Conclusion:

This study found that serous retinal detachment and disorganization of retinal inner layers were associated with different treatment responses to anti–vascular endothelial growth factor therapy in patients with diabetic macular edema.
Pink Plaques on the Face
Authors: So Jessica Kim , Nelson Fern , Jacob Sharon E.
Published: April 2017

Teledermatology is a term to describe the provision of dermatologic medical services through telecommunication technology. In this modality, there is transfer of patient medical information electronically (including history and visual data) obtained in one location to a provider who is in another location (Roman & Jacob, 2015). The construct of the TeleDermViewPoint column is such that cases are presented in a standardized teledermatology reader format reflective of an actual teledermatology report. This is a case of pink plaques on the face.
Post-colonoscopy colorectal cancers in Sweden: room for quality improvement
Authors: Forsberg Anna , Hammar Ulf , Ekbom Anders , Hultcrantz Rolf
Published: April 2017

Objective

Post-colonoscopy colorectal cancer (PCCRC), a cancer occurring within a short interval of a colonoscopy, might be partly explained as missed or incompletely resected lesions. Associated risk factors are age, sex, comorbidity, cancer location, and colonoscopy volume. There is a gap in the knowledge of prevalence of PCCRC and the impact of different risk factors in Sweden.

Methods

This is a retrospective population-based observational cohort study of the colonoscopies performed on adults during the years 2001–2010 that were identified from Swedish health registers. The rate of PCCRC (diagnosed 6–36 months after the first colonoscopy) was defined as the number of PCCRCs divided by the number of colorectal cancers (CRC) in the interval of 0–36 months. Univariate and multivariate Poisson regression analyses examined associations with PCCRC.

Results

There were 289 729 colonoscopies performed on 249 079 individuals included in the study. There were 16 319 individuals with a colorectal cancer diagnosis 0–36 months after a colonoscopy. Of these, 1286 (7.9%) were PCCRCs. In the multivariate analysis, young age (18–30 years) and former polyp diagnosis had the highest risks [relative risk (RR)=3.3; 95% confidence interval: 2.1–5.2 and RR=3.1; 95% confidence interval: 2.7–3.6]. The impact of other risk factors, such as female sex, comorbidity, right sided colorectal cancer location, and time period, was consistent with the finding in other studies.

Conclusion

The prevalence of PCCRC in Sweden seems to be relatively high, indicating that there is room for improvement in colonoscopy quality. The high RR of PCCRC in the youngest age group, even though there were only a few cases, has not been described in other studies.
Neck Rhabdoid Tumors: Clinical Features and Consideration of Autologous Stem Cell Transplant
Authors: Wolfe Adam D. , Capitini Christian M. , Salamat Shahriar M. , DeSantes Kenneth , Bradley Kristin A. , Kennedy Tabassum , Dehner Louis P. , Patel Neha J.
Published: April 2017

Extrarenal malignant rhabdoid tumors (MRT) have a poor prognosis despite aggressive therapy. Adding high-dose chemotherapy with autologous stem cell rescue (HDC-ASCR) as consolidative therapy for MRT is controversial. We describe 2 patients, age 13 years and 19 months, with unresectable neck MRT. After chemotherapy and radiotherapy, both underwent HDC-ASCR and remain in remission over 4 years later. We reviewed all published cases of neck MRT, and found poorer outcomes and more variable age of presentation and time to progression than MRT at other sites. Neck MRT may represent a higher-risk subset of MRT, and addition of HDC-ASCR merits consideration.
Association Between Vitamin D Status and Schizophrenia
Authors: Salavert José , Grados Dolors , Ramiro Nuria , Carrión Maria Isabel , Fadeuilhe Christian , Palma Felipe , López Laura , Erra Alba , Ramírez Nicolás
Published: April 2017

Vitamin D deficiency has been linked with schizophrenia. We aimed to determine whether patients with a first episode of psychosis (FEP) had lower vitamin D levels compared with controls considering their final diagnosis. We conducted a cross-sectional study determining 25-hydroxyvitamin D blood levels. 25-Hydroxyvitamin D levels were considered optimum at 20 ng/mL or greater. A group of 45 adult patients with FEP and a group of 22 healthy controls matched for age were recruited. The patient group was subdivided in two final diagnosis groups (schizophrenia versus other psychoses) after a 6-month follow-up. Average vitamin D values were deficient for FEP patients, especially those 22 with a final diagnosis of schizophrenia. These results relating vitamin D and schizophrenia generate interest to further examine this association.
Cerclage Use: A Review of 3 National Guidelines
Authors: Sperling Jeffrey D. , Dahlke Joshua D. , Gonzalez Juan M.
Published: April 2017

Importance

Preterm birth is a major contributor to perinatal morbidity and mortality. The most common intervention performed to improve perinatal outcomes for a woman experiencing cervical dilation in the second trimester without signs or symptoms of preterm labor is the cerclage.

Objective

We sought to review and compare available national guidelines on cerclage use.

Evidence Acquisition

We performed a descriptive review of 3 national guidelines on cerclage: The American Congress of Obstetricians and Gynecologists Practice Bulletin on “Cerclage for the Management of Cervical Insufficiency,” Green-top Guideline from the Royal College of Obstetricians and Gynaecologists entitled “Cervical Cerclage,” and the Society of Obstetricians and Gynaecologists of Canada Clinical Practice Bulletin entitled “Cervical Insufficiency and Cervical Cerclage.” Guidelines were compared, and the following aspects of cerclage use for prevention of preterm delivery were summarized: indications and contraindications, risk factors for cervical insufficiency, perioperative considerations, and timing of removal. Recommendations and strength of evidence were reviewed based on each guideline's method of reporting. The references were compared with regard to the total number of randomized control trials, Cochrane Reviews, and systematic reviews/meta-analyses cited.

Results

The variations highlighted in the guidelines reflect the heterogeneity of the literature contributing to guidelines and the challenges of diagnosing and managing cervical insufficiency.

Conclusions

A cohesive international guideline may improve safety and quality and optimize patient outcomes.

Target Audience

Obstetricians and gynecologists, family physicians.

Learning Objectives

After completing this activity, the learner should be better able to outline variations in indications and contraindications for cervical cerclage use by international guideline, identify variation in perioperative considerations for cervical cerclage use by international guideline, and recognize variation in timing of removal by international guideline.
A Randomized Controlled Trial of Corticosteroids in Pediatric Septic Shock: A Pilot Feasibility Study*
Authors: Menon Kusum , McNally Dayre , O’Hearn Katharine , Acharya Anand , Wong Hector R. , Lawson Margaret , Ramsay Tim , McIntyre Lauralyn , Gilfoyle Elaine , Tucci Marisa , Wensley David , Gottesman Ronald , Morrison Gavin , Choong Karen
Published: April 2017

Objective:

To determine the feasibility of conducting a randomized controlled trial of corticosteroids in pediatric septic shock.

Design:

Randomized, double-blind, placebo controlled trial.

Setting:

Seven tertiary level PICUs in Canada.

Patients:

Children newborn to 17 years old inclusive with suspected septic shock.

Intervention:

Administration of IV hydrocortisone versus placebo until hemodynamic stability is achieved or for a maximum of 7 days.

Measurements and Main Results:

One hundred seventy-four patients were potentially eligible of whom 101 patients met eligibility criteria. Fifty-seven patients were randomized, and 49 patients (23 and 26 patients in the hydrocortisone and placebo groups, respectively) were included in the final analysis. The mean time from screening to randomization was 2.4 ± 2.1 hours and from screening to first dose of study drug was 3.8 ± 2.6 hours. Forty-two percent of potentially eligible patients (73/174) received corticosteroids prior to randomization: 38.5% (67/174) were already on corticosteroids for shock at the time of screening, and in 3.4% (6/174), the treating physician wished to administer corticosteroids. Six of 49 randomized patients (12.2%) received open-label steroids, three in each of the hydrocortisone and placebo groups. Time on vasopressors, days on mechanical ventilation, PICU and hospital length of stay, and the rate of adverse events were not statistically different between the two groups.

Conclusions:

This study suggests that a large randomized controlled trial on early use of corticosteroids in pediatric septic shock is potentially feasible. However, the frequent use of empiric corticosteroids in otherwise eligible patients remains a significant challenge. Knowledge translation activities, targeted recruitment, and alternative study designs are possible strategies to mitigate this challenge.
A Hyper-Crosslinked Carbohydrate Polymer Scaffold Facilitates Lineage Commitment and Maintains a Reserve Pool of Proliferating Cardiovascular Progenitors
Authors: Baio Jonathan M. , Walden Ryan C. , Fuentes Tania I. , Lee Charles C. , Hasaniya Nahidh W. , Bailey Leonard L. , Kearns-Jonker Mary K.
Published: April 2017

Background

Cardiovascular progenitor cells (CPCs) have been cultured on various scaffolds to resolve the challenge of cell retention after transplantation and to improve functional outcome after cell-based cardiac therapy. Previous studies have reported successful culture of fully differentiated cardiomyocytes on scaffolds of various types, and ongoing efforts are focused on optimizing the mix of cardiomyocytes and endothelial cells as well as on the identification of a source of progenitors capable of reversing cardiovascular damage. A scaffold culture that fosters cell differentiation into cardiomyocytes and endothelial cells while maintaining a progenitor reserve would benefit allogeneic cell transplantation.

Methods

Isl-1 + c-Kit + CPCs were isolated as clonal populations from human and sheep heart tissue. After hyper-crosslinked carbohydrate polymer scaffold culture, cells were assessed for differentiation, intracellular signaling, cell cycling, and growth factor/chemokine expression using real time polymerase chain reaction, flow cytometry, immunohistochemistry, and calcium staining.

Results

Insulin-like growth factor 1, hepatocyte growth factor, and stromal cell derived factor 1α paracrine factors were induced, protein kinase B signaling was activated, extracellular signal-regulated kinase phosphorylation was reduced and differentiation into both cardiomyocytes and endothelial cells was induced by scaffold-based cell culture. Interestingly, movement of CPCs out of the G1 phase of the cell cycle and increased expression of pluripotency genes PLOU5F1 (Oct4) and T (Brachyury) within a portion of the cultured population occurred, which suggests the maintenance of a progenitor population. Two-color immunostaining and 3-color fluorescence-activated cell sorting analysis confirmed the presence of both Isl-1 expressing undifferentiated cells and differentiated cells identified by troponin T and von Willebrand factor expression. Ki-67 labeling verified the presence of proliferating cells that remained in situ alongside the differentiated functional derivatives.

Conclusions

Cloned Isl-1 + c-kit + CPCs maintained on a hyper-cross linked polymer scaffold retain dual potential for proliferation and differentiation, providing a scaffold-based stem cell source for transplantation of committed and proliferating cardiovascular progenitors for functional testing in preclinical models of cell-based repair.
Guillain–Barré Syndrome and Swallowing Dysfunction
Authors: Mengi Tuğçe , Seçil Yaprak , İncesu Tülay Kurt , Arici Şehnaz , Akkiraz Zehra Özde , Gürgör Nevin , Gedizlioğlu Muhteşem , Ertekin Cumhur
Published: April 2017

Purpose:

Patients with Guillain–Barré syndrome (GBS), especially severe cases that require treatment in intensive care units, often experience swallowing difficulties. However, the oropharyngeal function of patients with GBS not treated in intensive care units is not typically evaluated using neurophysiological techniques.

Methods:

Electrophysiological techniques were used to determine dysphagia limit and sequential water swallowing values in an electromyography laboratory.

Results:

This study assessed 18 patients with GBS who were not treated in the intensive care unit between 4 and 45 days after their hospital admission; 18 healthy volunteers were used as a control group. Of the 18 patients with GBS, 7 exhibited the clinical involvement of either a single cranial nerve or a combination of cranial nerves while 11 did not show any lower cranial nerve involvement. Clinical dysphagia was observed in seven patients and six of these cases involved a lower cranial nerve while five patients without cranial nerve involvement had silent dysphagia according to the dysphagia limit test. In addition, the duration of sequential swallowing was significantly prolonged in all patients with GBS compared with the control subjects.

Conclusions:

The present findings demonstrated that neurophysiological techniques are useful and easily applicable for patients with GBS and that there were no complications. Furthermore, cranial nerve involvement in patients with GBS likely increased the incidence of oropharyngeal dysphagia, and subclinical dysphagia may be present in this population as well. Therefore, neurophysiological techniques can be initially used and then repeated during follow-up visits for all types of patients with GBS.
Increased food availability raises eviction rate in a cooperative breeding mammal
Authors: Dubuc C. , English S. , Thavarajah N. , Dantzer B. , Sharp S. P. , Spence-Jones H. C. , Gaynor D. , Clutton-Brock T. H.
Published: April 2017

In group-living mammals, the eviction of subordinate females from breeding groups by dominants may serve to reduce feeding competition or to reduce breeding competition. Here, we combined both correlational and experimental approaches to investigate whether increases in food intake by dominant females reduces their tendency to evict subordinate females in wild meerkats (
Suricata suricatta
). We used 20 years of long-term data to examine the association between foraging success and eviction rate, and provisioned dominant females during the second half of their pregnancy, when they most commonly evict subordinates. We show that rather than reducing the tendency for dominants to evict subordinates, foraging success of dominant females is positively associated with the probability that pregnant dominant females will evict subordinate females and that experimental feeding increased their rates of eviction. Our results suggest that it is unlikely that the eviction of subordinate females serves to reduce feeding competition and that its principal function may be to reduce reproductive competition. The increase in eviction rates following experimental feeding also suggests that rather than feeding competition, energetic constraints may normally constrain eviction rates.
Sperm as moderators of environmentally induced paternal effects in a livebearing fish
Authors: Evans Jonathan P. , Lymbery Rowan A. , Wiid Kyle S. , Rahman Md. Moshiur , Gasparini Clelia
Published: April 2017

Until recently, paternal effects—the influence of fathers on their offspring due to environmental factors rather than genes—were largely discarded or assumed to be confined to species exhibiting paternal care. It is now recognized that paternal effects can be transmitted through the ejaculate, but unambiguous evidence for them is scarce, because it is difficult to isolate effects operating via changes to the ejaculate from maternal effects driven by female mate assessment. Here, we use artificial insemination to disentangle mate assessment from fertilization in guppies, and show that paternal effects can be transmitted to offspring exclusively via ejaculates. We show that males fed reduced diets produce poor-quality sperm and that offspring sired by such males (via artificial insemination) exhibit reduced body size at birth. These findings may have important implications for the many mating systems in which environmentally induced changes in ejaculate quality have been reported.
Dynamic cellular finite-element method for modelling large-scale cell migration and proliferation under the control of mechanical and biochemical cues: a study of re-epithelialization
Authors: Zhao Jieling , Cao Youfang , DiPietro Luisa A. , Liang Jie
Published: April 2017

Computational modelling of cells can reveal insight into the mechanisms of the important processes of tissue development. However, current cell models have limitations and are challenged to model detailed changes in cellular shapes and physical mechanics when thousands of migrating and interacting cells need to be modelled. Here we describe a novel dynamic cellular finite-element model (DyCelFEM), which accounts for changes in cellular shapes and mechanics. It also models the full range of cell motion, from movements of individual cells to collective cell migrations. The transmission of mechanical forces regulated by intercellular adhesions and their ruptures are also accounted for. Intra-cellular protein signalling networks controlling cell behaviours are embedded in individual cells. We employ DyCelFEM to examine specific effects of biochemical and mechanical cues in regulating cell migration and proliferation, and in controlling tissue patterning using a simplified re-epithelialization model of wound tissue. Our results suggest that biochemical cues are better at guiding cell migration with improved directionality and persistence, while mechanical cues are better at coordinating collective cell migration. Overall, DyCelFEM can be used to study developmental processes when a large population of migrating cells under mechanical and biochemical controls experience complex changes in cell shapes and mechanics.
On the biomechanical analysis of the calories expended in a straight boxing jab
Authors: Zohdi T. I.
Published: April 2017

Boxing and related sports activities have become a standard workout regime at many fitness studios worldwide. Oftentimes, people are interested in the calories expended during these workouts. This note focuses on determining the calories in a boxer's jab, using kinematic vector-loop relations and basic work–energy principles. Numerical simulations are undertaken to illustrate the basic model. Multi-limb extensions of the model are also discussed.
Synthetic associative learning in engineered multicellular consortia
Authors: Macia Javier , Vidiella Blai , Solé Ricard V.
Published: April 2017

Associative learning (AL) is one of the key mechanisms displayed by living organisms in order to adapt to their changing environments. It was recognized early as a general trait of complex multicellular organisms but is also found in ‘simpler’ ones. It has also been explored within synthetic biology using molecular circuits that are directly inspired in neural network models of conditioning. These designs involve complex wiring diagrams to be implemented within one single cell, and the presence of diverse molecular wires become a challenge that might be very difficult to overcome. Here we present three alternative circuit designs based on two-cell microbial consortia able to properly display AL responses to two classes of stimuli and displaying long- and short-term memory (i.e. the association can be lost with time). These designs might be a helpful approach for engineering the human gut microbiome or even synthetic organoids, defining a new class of decision-making biological circuits capable of memory and adaptation to changing conditions. The potential implications and extensions are outlined.
Tuning cancer fate: the unremitting role of host immunity
Authors: Calì B. , Molon B. , Viola A.
Published: April 2017

Host immunity plays a central and complex role in dictating tumour progression. Solid tumours are commonly infiltrated by a large number of immune cells that dynamically interact with the surrounding microenvironment. At first, innate and adaptive immune cells successfully cooperate to eradicate microcolonies of transformed cells. Concomitantly, surviving tumour clones start to proliferate and harness immune responses by specifically hijacking anti-tumour effector mechanisms and fostering the accumulation of immunosuppressive immune cell subsets at the tumour site. This pliable interplay between immune and malignant cells is a relentless process that has been concisely organized in three different phases: elimination, equilibrium and escape. In this review, we aim to depict the distinct immune cell subsets and immune-mediated responses characterizing the tumour landscape throughout the three interconnected phases. Importantly, the identification of key immune players and molecules involved in the dynamic crosstalk between tumour and immune system has been crucial for the introduction of reliable prognostic factors and effective therapeutic protocols against cancers.
Robust
H
∞
state-feedback control for linear systems
Authors: Chen Hao , Zhang Zhenzhen , Wang Huazhang
Published: April 2017

This paper investigates the problem of robust
H
∞
control for linear systems. First, the state-feedback closed-loop control algorithm is designed. Second, by employing the geometric progression theory, a modified augmented Lyapunov–Krasovskii functional (LKF) with the geometric integral interval is established. Then, parameter uncertainties and the derivative of the delay are flexibly described by introducing the convex combination skill. This technique can eliminate the unnecessary enlargement of the LKF derivative estimation, which gives less conservatism. In addition, the designed controller can ensure that the linear systems are globally asymptotically stable with a guaranteed
H
∞
performance in the presence of a disturbance input and parameter uncertainties. A liquid monopropellant rocket motor with a pressure feeding system is evaluated in a simulation example. It shows that this proposed state-feedback control approach achieves the expected results for linear systems in the sense of the prescribed
H
∞
performance.
Design of rigid-foldable doubly curved origami tessellations based on trapezoidal crease patterns
Authors: Song Keyao , Zhou Xiang , Zang Shixi , Wang Hai , You Zhong
Published: April 2017

This paper presents a mathematical framework for the design of rigid-foldable doubly curved origami tessellations based on trapezoidal crease patterns that can simultaneously fit two target surfaces with rotational symmetry about a common axis. The geometric parameters of the crease pattern and the folding angles of the target folded state are determined through a set of combined geometric and constraint equations. An algorithm to simulate the folding motion of the designed crease pattern is provided. Furthermore, the conditions and procedures to design folded ring structures that are both developable and flat-foldable and stacked folded structures consisting of two layers that can fold independently or compatibly are discussed. The proposed framework has potential applications in designing engineering doubly curved structures such as deployable domes and folded cores for doubly curved sandwich structures on the aircraft.
Modernization, wealth and the emergence of strong alpha oscillations in the human EEG
Authors: Parameshwaran Dhanya , Thiagarajan Tara C.
Published: April 2017

Oscillations in the alpha range (8-15 Hz) have been found to appear prominently in the EEG signal when people are awake with their eyes closed, and since their discovery have been considered a fundamental cerebral rhythm. While the mechanism of this oscillation continues to be debated, it has been shown to bear positive relation to memory capacity, attention and a host of other cognitive outcomes. Here we show that this feature is largely undetected in the EEG of adults without post-primary education and access to modern technologies. Furthermore, we show that the spatial extent and energy of the oscillation have wide variation, with energy ranging over a thousand fold across the breath of humanity with no centralizing mean. This represents a divergence in a fundamental functional characteristic of an organ demonstrating both that modernization has had a profound influence on brain dynamics and that a meaningful ‘average’ human brain does not exist in a dynamical sense.
The feature-weighted receptive field: an interpretable encoding model for complex feature spaces
Authors: St-Yves Ghislain , Naselaris Thomas
Published: April 2017

We introduce the feature-weighted receptive field (fwRF), an encoding model designed to balance expressiveness, interpretability and scalability. The fwRF is organized around the notion of a feature map—a transformation of visual stimuli into visual features that preserves the topology of visual space (but not necessarily the native resolution of the stimulus). The key assumption of the fwRF model is that activity in each voxel encodes variation in a spatially localized region across multiple feature maps. This region is fixed for all feature maps; however, the contribution of each feature map to voxel activity is weighted. Thus, the model has two separable sets of parameters: “where” parameters that characterize the location and extent of pooling over visual features, and “what” parameters that characterize tuning to visual features. The “where” parameters are analogous to classical receptive fields, while “what” parameters are analogous to classical tuning functions. By treating these as separable parameters, the fwRF model complexity is independent of the resolution of the underlying feature maps. This makes it possible to estimate models with thousands of high-resolution feature maps from relatively small amounts of data. Once a fwRF model has been estimated from data, spatial pooling and feature tuning can be read-off directly with no (or very little) additional post-processing or in-silico experimentation.

We describe an optimization algorithm for estimating fwRF models from data acquired during standard visual neuroimaging experiments. We then demonstrate the model’s application to two distinct sets of features: Gabor wavelets and features supplied by a deep convolutional neural network. We show that when Gabor feature maps are used, the fwRF model recovers receptive fields and spatial frequency tuning functions consistent with known organizational principles of the visual cortex. We also show that a fwRF model can be used to regress entire deep convolutional networks against brain activity. The ability to use whole networks in a single encoding model yields state-of-the-art prediction accuracy. Our results suggest a wide variety of uses for the feature-weighted receptive field model, from retinotopic mapping with natural scenes, to regressing the activities of whole deep neural networks onto measured brain activity.
Temporal changes in the nasal microbiota and host antimicrobial responses to intranasal mupirocin decolonisation: Observations in healthy staphylococcal carriers
Authors: Liu Su-Hsun , Tang Yi-Ching , Lin Yi-Hsiung , Chen Kuan-Fu , Chen Chih-Jung , Huang Yhu-Chering , Chen Leslie Y.
Published: April 2017

Background

How intranasal mupirocin decolonisation affects the human nasal microbiota remains unknown. To characterize the temporal dynamics of the nasal microbial community in healthy staphylococcal carriers in response to intranasal mupirocin decolonisation, we serially sampled the anterior nares of four healthy carriers to determine the nasal microbial profile via sequencing of bacterial 16S ribosomal DNA.

Results

Before decolonisation, the nasal microbiota differed by the initial, culture-based staphylococcal carriage status, withFirmicutes(54.1%) andProteobacteria(75.8%) dominating the microbial community in the carriers and the noncarrier, separately. The nasal microbiota lost its diversity immediately after decolonisation (Shannon diversity: 1.33, 95% confidence interval [CI]: 1.06-1.54) as compared to before decolonisation (1.78, 95%CI: 0.58-1.93). The initial staphylococcal carriage status, expression levels of human neutrophil peptide 1, and sampling times were major contributors to the between-community dissimilarities (Pfor marginal permutation test: .014) though of borderline significance when considering data correlation (Pfor blocked permutation test: .047) in both nonmetric multidimensional scaling and constrained correspondence analysis. Results of univariable and multivariable differential abundance analysis further showed that, in addition to Staphylococci, multiple genera of Actinobacteria and Proteobacteria were differentially enriched or depleted by mupirocin use.

Conclusions

Mupirocin could affect both Gram-positive and Gram-negative commensals along with altered host antimicrobial responses. How the nasal microbiome recovered after short-term antibiotic perturbation depended on the initial staphylococcal carriage status. The potential risks associated with loss of colonisation resistance need to be considered in high-risk populations receiving targeted decolonisation.
Spatial gene drives and pushed genetic waves
Authors: Tanaka Hidenori , Stone Howard A. , Nelson David R.
Published: April 2017

Gene drives have the potential to rapidly replace a harmful wild-type allele with a gene drive allele engineered to have desired functionalities. However, an accidental or premature release of a gene drive construct to the natural environment could damage an ecosystem irreversibly. Thus, it is important to understand the spatiotemporal consequences of the super-Mendelian population genetics prior to potential applications. Here, we employ a reaction-diffusion model for sexually reproducing diploid organisms to study how a locally introduced gene drive allele spreads to replace the wild-type allele, even though it posses a selective disadvantages> 0. Using methods developed by N. Barton and collaborators, we show that socially responsible gene drives require 0.5 <s< 0.697, a rather narrow range. In this “pushed wave” regime, the spatial spreading of gene drives will be initiated only when the initial frequency distribution is above a threshold profile called “critical propagule”, which acts as a safeguard against accidental release. We also study how the spatial spread of the pushed wave can be stopped by making gene drives uniquely vulnerable (“sensitizing drive”) in a way that is harmless for a wild-type allele. Finally, we show that appropriately sensitized drives in two dimensions can be stopped even by imperfect barriers perforated by a series of gaps.
Logistics optimisation in road construction project
Authors: Choudhari Sanjay , Tindwani Amit
Published: April 2017

Purpose

This study aims to assist the project manager in minimising the material logistics cost of road project by planning the optimal movement of aggregate across three stages of supply chain: sourcing, processing and distribution.

Design/methodology/approach

The paper conceptualises the raw material consumption in a road project as a logistics network distribution problem. A linear programming (LP) formulation is constructed with appropriate decision variables by integrating the three stages of material movement. The series of LP scenarios are solved using an LP solver to decide the optimal movement of the aggregate to be consumed in different layers of road segments.

Findings

The results obtained from the model show that planning material logistics of an entire road project using optimisation provides substantial saving in logistics costs than using common sense. Further, the magnitude of cost saving improves as the complexity of the model increases in term of enormous feasible options.

Practical implications

The model shown in this paper may serve as a basis for planning the logistics of raw materials consumed in the road projects. The small improvement in material flows by optimising supply chain shows sensible cost benefit to the project manager and hence control and monitor the overall cost and activities of the project. The output of the model is also expected to help the project team as an input in the decision-making processes such as appropriate material sourcing contract, capacity assessment of material processing facility and transportation planning.

Originality/value

While the optimisation models are widely used and popular among the many industrial applications, this research shows distinct application of such a model in managing the logistics of the road construction project.
Risk assessment in public-private partnership infrastructure projects
Authors: Osei-Kyei Robert , Chan Albert P.C.
Published: April 2017

Purpose

The purpose of this paper is to empirically compare the risk factors in public-private partnership (PPP) projects in developing and developed countries, represented by Ghana and Hong Kong, respectively.

Design/methodology/approach

A structured questionnaire survey was conducted with PPP practitioners in Ghana and Hong Kong. In total, 103 valid responses were received for analysis. Kendall’s coefficient of concordance and mean ranking were used for data analysis.

Findings

The results show that respondents from Ghana ranked country risk factors higher, whereas their Hong Kong counterparts ranked project-specific risks higher. The top five significant risks in Ghana are corruption, inflation rate fluctuation, exchange rate fluctuation, delay in project completion and interest rate fluctuation. In Hong Kong, the top five significant risk factors are delay in land acquisition, operational cost overruns, construction cost overruns, delay in project completion and political interference.

Originality/value

The results of the study inform international investors of the appropriate risk mitigation measures and preventive actions to use when engaging in PPP arrangements in any part of the world. Further, governments who are yet to use the PPP concept would be informed of the prevailing risk factors in other neighbouring countries (i.e. developing or developed countries).
A future for facility management
Authors: Atkin Brian , Bildsten Louise
Published: April 2017

Purpose

This paper aims to discuss the current debates in facility management to understand where the research community is working and where the facility management sector and discipline might be heading.

Design/methodology/approach

A review of research outputs has been undertaken to identify research themes. The discussion is based on developments that are already shaping how one should view facility management and outlines a possible future based on a number of strategically important questions and their likely answers.

Findings

There is a broad landscape of research themes; yet, a significant portion of the most-cited journal papers were published more than 10-15 years ago. Current debates are focused mostly on operational improvement; few are directed at more strategic objectives. Those in the informal media are concerned with more speculative themes, particularly the internet of things (IoT) and artificial intelligence (AI), which are indicative of disruptive technology. These themes are debated mostly by practitioners.

Originality/value

Many views are expressed in this editorial – some are controversial whilst others should be regarded as matters of fact. The underlying aim is to stimulate debate and action among readers about what appears to be a dilemma for the facility management sector and discipline. Does it continue along the same trajectory or should it be bold and strike out in new directions and meet the challenges presented by disruptive innovations, notably the IoT and AI? Hard choices await and not all decisions will lead to preferred outcomes.
A cyclical learning model to promote children’s online and on-site museum learning
Authors: Hsu Tien-Yu , Liang Hsin-Yi
Published: April 2017

Purpose

This paper aims to propose an online and on-site cyclical learning model (OOCLM). It considers how combining digital applications can promote a museum’s virtuous learning cycle between online and on-site spaces for children.

Design/methodology/approach

A practical cyclical learning service has been successfully implemented in a science museum in Taiwan. This provides a thematic game-based learning environment, allowing all the children to create their unique museum experiences before, during and after their visit. A questionnaire was developed to examine the children’s perceptions of the OOCLM to ascertain whether they were satisfied with the pre-visit, on-site visit and post-visit services offered.

Findings

The learning model considered the contextual factors that influence digital applications in museums. The digital and physical resources are well integrated, and the museum’s online and on-site services are linked to effectively promote children’s cyclical learning.

Practical implications

The results show that most of the children highly appreciated the learning model. The model presents an interactive learning environment for children’s cyclical learning and repeat visits.

Originality/value

The OOCLM considers the related contextual influences of digital applications in museum learning; it effectively bridges the museum’s online and on-site services to promote the museum’s virtuous learning cycle and long-term museum learning resource management. This study provides a benchmark example to develop sustainable cyclical learning services for target visitor groups and to motivate their long-term interaction with the museum.