bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of differential DNA methylation on transgene expression in cotton (Gossypium hirsutum L.) events generated by targeted sequence insertion
Authors: Verkest Aurine , Bourout Stephane , Debaveye Jurgen , Reynaert Kristine , Saey Bernadette , den Brande Ilse Van , D'Halluin Kathleen
Published: December 2018

Targeted Genome Optimization (TGO) using site‐specific nucleases to introduce a DNA double‐strand break (DSB) at a specific target locus has broadened the options available to breeders for generation and combination of multiple traits. The use of targeted DNA cleavage in combination with homologous recombination (HR)‐mediated repair, enabled the precise targeted insertion of additional trait genes (2mepsps, hppd, axmi115) at a pre‐existing transgenic locus in cotton. Here we describe the expression and epigenome analyses of cotton Targeted Sequence Insertion (TSI) events over generations. In a subset of events, we observed variability in the level of transgene (hppd, axmi115) expression between independent but genetically identical TSI events. Transgene expression could also be differential within single events and variable over generations. This expression variability and silencing occurred independently of the transgene sequence and could be attributed to DNA methylation that was further linked to different DNA methylation mechanisms. The trigger(s) of transgene DNA methylation remains elusive but we hypothesize that targeted DSB induction and repair could be a potential trigger for DNA methylation.
Gilt by Associations: Appointments to Federal Advisory Committees in U.S. National Security Politics
Authors: Levinson Chad
Published: December 2018

Federal Advisory Committees (FACs) offer opportunities for private citizens to gain access to the national security apparatus of the U.S. government. What explains the appointment of interest group affiliates to national security FACs? This article analyzes patterns of interest‐group membership in FACs, using an original data set based on official General Services Administration data. Organizational affiliations are identified across thousands of appointments. The analysis shows that interest‐group appointments to critical national security FACs increase with opposition‐party power in Congress. This suggests that interest‐group access improves when the administration needs help with a political strategy to overcome legislative opposition.
A New Methodology for Before–After Safety Assessment Using Survival Analysis and Longitudinal Data
Authors: Xie Kun , Ozbay Kaan , Yang Hong , Yang Di
Published: December 2018

The widely used empirical Bayes (EB) and full Bayes (FB) methods for before–after safety assessment are sometimes limited because of the extensive data needs from additional reference sites. To address this issue, this study proposes a novel before–after safety evaluation methodology based on survival analysis and longitudinal data as an alternative to the EB/FB method. A Bayesian survival analysis (SARE) model with a random effect term to address the unobserved heterogeneity across sites is developed. The proposed survival analysis method is validated through a simulation study before its application. Subsequently, the SARE model is developed in a case study to evaluate the safety effectiveness of a recent red‐light‐running photo enforcement program in New Jersey. As demonstrated in the simulation and the case study, the survival analysis can provide valid estimates using only data from treated sites, and thus its results will not be affected by the selection of defective or insufficient reference sites. In addition, the proposed approach can take into account the censored data generated due to the transition from the before period to the after period, which has not been previously explored in the literature. Using individual crashes as units of analysis, survival analysis can incorporate longitudinal covariates such as the traffic volume and weather variation, and thus can explicitly account for the potential temporal heterogeneity.
“With AIDS I am happier than I have ever been before”
Authors: Wardlow Holly
Published: December 2018

In her 2016 article Sherry Ortner discusses what she calls the rise of ‘dark anthropology’: that is, ethnographic work that analyses situations of domination, dispossession, and violence. She, like Joel Robbins (), posits as a counterpoint the emergence of ‘anthropologies of the good,’ which emphasise care and ethics. In this paper I put these two anthropological projects into generative tension through an analysis of HIV‐positive women's lives in Papua New Guinea. In the first part of the paper I demonstrate the ways in which resource extraction has created vulnerabilities to HIV—in part through the coerced marriages of women to powerful landowners. In the second, I discuss ways in which the antiretroviral era has made possible unexpected forms of kindness towards HIV‐positive women. I end the paper with a discussion of what HIV‐positive women mean when they claim that they are happier now than in their pre‐diagnosis lives.
Use of network analysis multidrug‐resistant tuberculosis contact investigation in Kanchanaburi, Thailand
Authors: Boonthanapat N. , Soontornmon K. , Pungrassami P. , Sukhasitwanichkul J. , Mahasirimongkol S. , Jiraphongsa C. , Monkongdee P. , Angchokchatchawal K. , Wiratsudakul A.
Published: December 2018

Objective

To characterise MDR‐TB outbreak and incorporate social network analysis with contact investigation to detect case–contact linkages and clusters.

Methods

MDR‐TB cases registered in the district hospital between October 2012 and September 2015 were interviewed and their contacts were investigated. A relationship‐based weighted network was constructed.

Results

Among 43 interviewed MDR‐TB cases, 20 (47%) were male, five (12%) were asymptomatic (and discovered incidentally) and 22 (51%) had underlying diseases. From the documented 115 contacts, 61 (53%) were household contacts and 49 (43%) were close (non‐household) contacts; 70 (61%) were screened for TB using various tests. In this network, we prioritised 37 contacts connected with more than one MDR‐TB patient. The largest cluster was identified in the pharmacy unit of the hospital.

Conclusion

This investigation yielded a significant number of MDR‐TB contacts, and social network analysis facilitated the prioritisation for screening. Social network analysis is useful and feasible in this program setting and complements MDR‐TB contact investigation.
Evaluating the Accuracy of RANS Wind Flow Modeling Over Forested Terrain—Part 1: Canopy Model Validation
Authors: Morales Garza Viridiana G. , Sumner Jonathon , Nathan Jörn , Masson Christian
Published: December 2018

This study uses the Reynolds-averaged Navier–Stokes (RANS) equations to validate a canopy model by computing a fully developed wind flow within and above a horizontally homogeneous dense forest as in the work of Dalpé and Masson. The model is paired with a modified k–ε turbulence closure. A set of boundary conditions (BCs) that rely on the law of the wall for a sustainable atmospheric boundary layer (ABL) is used. All simulations are conducted in the open source software OpenFOAM v.2.4.0 (OpenCFD Ltd (ESI Group)). Two practical aspects are considered in the validation process. First, an accurate leaf area index (LAI) integration to exactly fit the wind shear is evaluated. Since the physical foliage parameters may not be accessible for all type of forests, a generic leaf area density α distribution is tested. The results of this test show that a generic distribution is sufficient for preliminary analyses to improve accuracy of wind flow predictions over forested terrain. Second, the approach of Dalpé and Masson is limited to cyclic BCs which are not practical for real sites. For cases without cyclic BCs, imposing a proper slope on the inlet velocity profile is of high importance. This condition can be achieved through adjustment of the roughness length at the inlet.
Methodology for Preliminary Design of Buildings Using Multi-Objective Optimization Based on Performance Simulation
Authors: Zemero Bruno Ramos , Tostes Maria Emília de Lima , Bezerra Ubiratan Holanda , Batista Vitor dos Santos , Carvalho Carminda Célia M. M.
Published: December 2018

Buildings' energy consumption has a great energetic and environmental impact worldwide. The architectural design has great potential to solve this problem because the building envelope exerts influence on the overall system performance, but this is a task that involves many objectives and constraints. In the last two decades, optimization studies applied to energy efficiency of buildings have helped specialists to choose the best design options. However, there is still a lack of optimization approaches applied to the design stage, which is the most influential stage for building energy efficiency over its entire life cycle. Therefore, this article presents a multi-objective optimization model to assist designers in the schematic building design, by means of the Pareto archived evolutionary strategies (PAES) algorithm with the EnergyPlus simulator coupled to evaluate the solutions. The search process is executed by a binary array where the array components evolve over the generations, together with the other building components. The methodology aims to find optimal solutions (OSs) with the lowest constructive cost associated with greater energy efficiency. In the case study, it was possible to simulate the process of using the optimization model and analyze the results in relation to: a standard building; energy consumption classification levels; passive design guidelines; usability and accuracy, proving that the tool serves as support in building design. The OSs reached an average of 50% energy savings over typical consumption, 50% reduction in CO2 operating emissions, and investment return less than 3 years in the four different weathers.
Offshore Wind Turbine Nonlinear Wave Loads and Their Statistics
Authors: Sclavounos Paul D. , Zhang Yu , Ma Yu , Larson David F.
Published: December 2018

The development of an analytical model for the prediction of the stochastic nonlinear wave loads on the support structure of bottom mounted and floating offshore wind turbines is presented. Explicit expressions are derived for the time-domain nonlinear exciting forces in a sea state with significant wave height comparable to the diameter of the support structure based on the fluid impulse theory (FIT). The method is validated against experimental measurements with good agreement. The higher order moments of the nonlinear load are evaluated from simulated force records and the derivation of analytical expressions for the nonlinear load statistics for their efficient use in design is addressed. The identification of the inertia and drag coefficients of a generalized nonlinear wave load model trained against experiments using support vector machine learning algorithms is discussed.
Dynamic Collapse Mechanism of Global Hull Girder of Container Ships Subjected to Hogging Moment
Authors: Yamada Yasuhira
Published: December 2018

The purpose of the present study is to investigate dynamic ultimate strength of global hull girder of container ships using large-scale nonlinear finite element analysis (FEA). A series of time domain nonlinear finite element (FE)-simulation is carried out using large-scale FE models of a 8000 twenty-foot equivalent unit (TEU) container ship where a hogging moment is applied to the midship section. Five types of finite element models (three full models, a half hold model, a one transverse model) are used. These models adopt elastoplastic material model, which includes strain rate effect. The hogging moment, which is modeled by sinusoidal impulse, is applied to these models, and collapse mechanism as well as dynamic hull girder ultimate strength is investigated by varying the load time duration. Moreover, effects of load time duration, mass inertia, strain rate, and analysis models are investigated in detail. It is found from the present study that ultimate strength as well as collapse mode is significantly dependent on load time duration of hogging moment.
On evaporation via an inclined rotating circular lift-off shadow or stencil mask
Authors: Arscott Steve
Published: December 2018

A mathematical model is developed to calculate the topography of a mesa obtained by evaporation of matter via inclined rotating lift-off shadow masking. Two types of masking are considered: a circular mask and a cylindrical mask—the latter involves sidewall deposition. The model is able to predict various topographic profiles obtained via the evaporative deposition of matter, e.g., metals, when using a physical mask, e.g., a photoresist or an electron beam-sensitive resist patterned onto a flat wafer. The model predicts a range of profiles, e.g., sharp cones, round-tipped cones, spikes, irregular bumps, flat-topped features, “bagel-shaped” features, flat rings, and cylinders (fixed to the wafer and releasable)—depending on the aspect ratio of the circular opening, the deposition thickness, and the evaporation tilt angle. The ideas are extended to model an idealized resist-based lift-off mask involving overhang and undercut features. The model is simple to implement and should be of use for predicting the shape of deposited matter when using lift-off and stencil procedures—even at sub-micrometer dimensions. Despite its simplicity, the model goes some way in helping to understand the sensitivity of the various parameters on the final topography of the deposited matter. For example, the tilt angle—even when small—has an influence on the curvature radius of cone tips. In this way, the prediction—and even optimization—of the shape of the deposited material is possible prior to embarking on time-consuming, and perhaps costly, experimentation.
Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation
Authors: Rhie Suhn K. , Schreiner Shannon , Witt Heather , Armoskus Chris , Lay Fides D. , Camarena Adrian , Spitsyna Valeria N. , Guo Yu , Berman Benjamin P. , Evgrafov Oleg V. , Knowles James A. , Farnham Peggy J.
Published: December 2018

Profiling olfactory neuronal cells from many individuals reveals variations in epigenetic signatures.
Atmospheric
14
C/
12
C changes during the last glacial period from Hulu Cave
Authors: Cheng Hai , Edwards R. Lawrence , Southon John , Matsumoto Katsumi , Feinberg Joshua M. , Sinha Ashish , Zhou Weijian , Li Hanying , Li Xianglei , Xu Yao , Chen Shitao , Tan Ming , Wang Quan , Wang Yongjin , Ning Youfeng
Published: December 2018

The whole story

An accurate, precise record of the carbon-14 (
14
C) content of the atmosphere is important for developing chronologies in climate change, archaeology, and many other disciplines. Cheng
et al.
provide a record that covers the full range of the
14
C dating method (∼54,000 years), using paired measurements of
14
C/
12
C and thorium-230 (
230
Th) ages from two stalagmites from Hulu Cave, China. The advantage of matching absolute
230
Th ages and
14
C/
12
C allowed the authors to fashion a seamless record from a single source with low uncertainties, particularly in the older sections.

Science
, this issue p.
1293
Multiproxy evidence highlights a complex evolutionary legacy of maize in South America
Authors: Kistler Logan , Maezumi S. Yoshi , Gregorio de Souza Jonas , Przelomska Natalia A. S. , Malaquias Costa Flaviane , Smith Oliver , Loiselle Hope , Ramos-Madrigal Jazmín , Wales Nathan , Ribeiro Eduardo Rivail , Morrison Ryan R. , Grimaldo Claudia , Prous Andre P. , Arriaza Bernardo , Gilbert M. Thomas P. , de Oliveira Freitas Fabio , Allaby Robin G.
Published: December 2018

The complexity of maize domestication

Maize originated in what is now central Mexico about 9000 years ago and spread throughout the Americas before European contact. Kistler
et al.
applied genomic analysis to ancient and extant South American maize lineages to investigate the genetic changes that accompanied domestication (see the Perspective by Zeder). The origin of modern maize cultivars likely involved a “semidomesticated” lineage that moved out of Mexico. Later improvements then occurred among multiple South American populations, including those in southwestern Amazonia.

Science
, this issue p.
1309
; see also p.
1246
The Sommerfeld ground-wave limit for a molecule adsorbed at a surface
Authors: Chen Li , Lau Jascha A. , Schwarzer Dirk , Meyer Jörg , Verma Varun B. , Wodtke Alec M.
Published: December 2018

Climbing vibrational levels

Vibrational excitation of molecules adsorbed on a surface is usually limited because the vibrational energy is rapidly transferred into phonons, the vibrational modes of the substrate. Chen
et al.
found that this is not the case for CO molecules adsorbed on a surface of NaCl. The CO molecules efficiently transferred vibrational energy within groups of molecules from one high excitation state to another until they reached the dissociation limit. This process was possible because of the close proximity of the molecules and the limited transfer of energy to just one phonon mode in the salt surface.

Science
, this issue p.
158
Galactose Impacts the Size and Intracellular Composition of the Asaccharolytic Oral Pathobiont Porphyromonas gingivalis
Authors: Moye Zachary D. , Gormley Courtney M. , Davey Mary E.
Published: December 2018

Environmental perturbations are central to the ability of pathobionts, such as
Porphyromonas gingivalis
, to promote the development of diseased sites. In the case of periodontal disease, increased local pH, a shift to anaerobic surroundings, and the accumulation of Gram-negative anaerobes at the expense of Gram-positive cocci are known ecological fluctuations prominently associated with progression toward disease. Importantly, in contrast, the alterations to subgingival food webs in disease sites remain poorly characterized. We hypothesized that given the dramatic shift in community structure during disease, it is possible that free carbohydrates, which would typically be readily metabolized by Gram-positive cocci after cleavage from glycoproteins, may increase in concentration locally and thereby affect the physiological state of the subgingival microbiota. In this study, we explored the impact of free monosaccharides on
P. gingivalis
to gain deeper insight into the effect of dysbiotic conditions on the growth and physiology of this periodontal pathogen.
Molecular Identification of Enteroviruses from Cattle and Goat Feces and Environment in Thailand
Authors: Income Nicharee , Kosoltanapiwat Nathamon , Taksinoros Sarawut , Leaungwutiwong Pornsawan , Maneekan Pannamas , Chavez Irwin Fernandez
Published: December 2018

Possible new EV-E and EV-G genotypes were identified for EVs detected in this study. The EV-E viruses were also successfully isolated from MDBK cells. The goat EV sequence analysis suggested the presence of an ovine/caprine-specific EV group that is different from EV-G of porcine origin. The significance of our research is that it identifies and characterizes possible novel EVs, thereby indicating that enteroviruses in animals are continually evolving. The facts that enteroviruses can persist in the environment, contaminate it for long periods, and be transmitted between animals raise serious concerns regarding this group of viruses as emerging livestock pathogens.
Brettanomyces bruxellensis SSU1Haplotypes Confer Different Levels of Sulfite Tolerance When Expressed in aSaccharomyces cerevisiae SSU1Null Mutant
Authors: Varela C. , Bartel C. , Roach M. , Borneman A. , Curtin C.
Published: December 2018

Brettanomyces bruxellensisis one of the most important wine spoilage microorganisms, with the use of sulfite being the major method to control spoilage. However, this species displays a wide intraspecies distribution in sulfite tolerance, with some strains capable of tolerating high concentrations of SO2, with relatively high concentrations of this antimicrobial needed for their control. Although SO2tolerance has been studied in several organisms and particularly inS. cerevisiae, little is known about the mechanisms that confer SO2tolerance inB. bruxellensis. Here, we confirmed the functionality of the sulfite efflux pump encoded byBbSSU1and determined the efficiencies of four differentBbSSU1haplotypes. Gene expression analysis showed greater expression of the haplotype conferring greater SO2tolerance. Our results suggest that a combination ofBbSSU1haplotype efficiency, copy number, and haplotype expression levels likely contributes to the diverse SO2tolerances observed for differentB. bruxellensisstrains.
Two Photolyases Repair Distinct DNA Lesions and Reactivate UVB-Inactivated Conidia of an Insect Mycopathogen under Visible Light
Authors: Wang Ding-Yi , Fu Bo , Tong Sen-Miao , Ying Sheng-Hua , Feng Ming-Guang
Published: December 2018

Protecting fungal cells from damage from solar UVB irradiation is critical for development and application of fungal insecticides but is mechanistically not understood in
Beauveria bassiana
, a classic insect pathogen. We unveil that two intranuclear photolyases, Phr1 and Phr2, play essential roles in repairing UVB-induced dsDNA lesions through respective decomposition of cytotoxic cyclobutane pyrimidine dimers and (6-4)-pyrimidine-pyrimidine photoproducts, hence reactivating UVB-inactivated cells effectively under visible light. Our findings shed light on the high potential of both photolyase genes for use in improving UVB resistance and application strategy of fungal insecticides.
Whole-Genome Sequence of a Reemerging Listeria monocytogenes Serovar 1/2a Strain in Central Italy
Authors: Orsini Massimiliano , Torresi Marina , Patavino Claudio , Centorame Patrizia , Rinaldi Antonio , Acciari Vicdalia Aniela , Centorotola Gabriella , Marcacci Maurilia , Ancora Massimo , Di Domenico Marco , Blasi Giuliana , Duranti Anna , Perticara Samuel , Di Pasquale Adriano , Cammà Cesare , Pomilio Francesco , Migliorati Giacomo
Published: December 2018

We report the whole-genome sequence of a
Listeria monocytogenes
strain isolated from a child in central Italy. Interestingly, the sequence showed a difference of only 13 single-nucleotide polymorphisms (SNPs) from a strain responsible for a severe listeriosis outbreak that occurred between January 2015 and March 2016 in the same region.
Understanding the principle biophysics concepts of pulmonary surfactant in health and disease
Authors: Autilio Chiara , Pérez-Gil Jesús
Published: December 2018

Pulmonary surfactant (PS) is a lipid-protein complex essential to stabilise the delicate structure of mammalian alveoli along with successive compression-expansion respiratory cycles. To do so, surfactant reduces dramatically surface tension at the air-liquid interface, an activity that depends critically on a proper lipid composition and the presence of some specific surfactant proteins. Lack or dysfunction of this system is associated with severe respiratory pathologies, which are in some cases treated by supplementation with exogenous surfactant materials. The biophysical function and performance of PS, in health and disease, are directly influenced by its composition, structure and mechanical properties. This review summarises the main biophysics concepts behind the mechanisms that define surfactant function in a healthy lung and in pathological situations. It also revises some of the most useful biophysical techniques that provide information about surfactant-related processes. Finally, translational biophysics will be invoked to illustrate how biophysical studies may contribute to understand the role of surfactant in health and disease and to design better surfactant-based therapeutic approaches.
Relationship between hospital or surgeon volume and outcomes in joint arthroplasty: protocol for a suite of systematic reviews and dose–response meta-analyses
Authors: Wu Xiang-Dong , Liu Meng-Meng , Sun Ya-Ying , Zhao Zhi-Hu , Zhou Quan , Kwong Joey S W , Xu Wei , Tian Mian , He Yao , Huang Wei
Published: December 2018

Introduction

Joint arthroplasty is a particularly complex orthopaedic surgical procedure performed on joints, including the hip, knee, shoulder, ankle, elbow, wrist and even digit joints. Increasing evidence from volume–outcomes research supports the finding that patients undergoing joint arthroplasty in high-volume hospitals or by high-volume surgeons achieve better outcomes, and minimum case load requirements have been established in some areas. However, the relationships between hospital/surgeon volume and outcomes in patients undergoing arthroplasty are not fully understood. Furthermore, whether elective arthroplasty should be restricted to high-volume hospitals or surgeons remains in dispute, and little is known regarding where the thresholds should be set for different types of joint arthroplasties.

Methods and analyses

This is a protocol for a suite of systematic reviews and dose–response meta-analyses, which will be amended and updated in conjunction with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols. Electronic databases, including PubMed and Embase, will be searched for observational studies examining the relationship between the hospital or surgeon volume and clinical outcomes in adult patients undergoing primary or revision of joint arthroplasty. We will use records management software for study selection and a predefined standardised file for data extraction and management. Quality will be assessed using the Newcastle-Ottawa Scale, and the meta-analysis, subgroup analysis and sensitivity analysis will be performed using Stata statistical software. Once the volume–outcome relationships are established, we will examine the potential non-linear relationships between hospital/surgeon volume and outcomes and detect whether thresholds or turning points exist.

Ethics and dissemination

Ethical approval is not required, because these studies are based on aggregated published data. The results of this suite of systematic reviews and meta-analyses will be submitted to peer-reviewed journals for publication.

PROSPERO registration number

CRD42017056639.
Efficacy and safety of the pulsed electromagnetic field in osteoarthritis: a meta-analysis
Authors: Wu Ziying , Ding Xiang , Lei Guanghua , Zeng Chao , Wei Jie , Li Jiatian , Li Hui , Yang Tuo , Cui Yang , Xiong Yilin , Wang Yilun , Xie Dongxing
Published: December 2018

Objective

To investigate the efficacy and safety of the pulsed electromagnetic field (PEMF) therapy in treating osteoarthritis (OA).

Design

Meta-analysis.

Data sources

PubMed, Embase, the Cochrane Library and Web of Science were searched through 13 October 2017.

Eligibility criteria for selecting studies

Randomised controlled trials compared the efficacy of PEMF therapy with sham control in patients with OA.

Data extraction and synthesis

Pain, function, adverse effects and characteristics of participants were extracted. RevMan V.5.2 was used to perform statistical analyses.

Results

Twelve trials were included, among which ten trials involved knee OA, two involved cervical OA and one involved hand OA. The PEMF group showed more significant pain alleviation than the sham group in knee OA (standardised mean differences (SMD)=−0.54, 95% CI −1.04 to –0.04, p=0.03) and hand OA (SMD=−2.85, 95% CI −3.65 to –2.04, p<0.00001), but not in cervical OA. Similarly, comparing with the sham–control treatment, significant function improvement was observed in the PEMF group in both knee and hand OA patients (SMD=−0.34, 95% CI −0.53 to –0.14, p=0.0006, and SMD=−1.49, 95% CI −2.12 to –0.86, p<0.00001, respectively), but not in patients with cervical OA. Sensitivity analyses suggested that the exposure duration <=30 min per session exhibited better effects compared with the exposure duration >30 min per session. Three trials reported adverse events, and the combined results showed that there was no significant difference between PEMF and the sham group.

Conclusions

PEMF could alleviate pain and improve physical function for patients with knee and hand OA, but not for patients with cervical OA. Meanwhile, a short PEMF treatment duration (within 30 min) may achieve more favourable efficacy. However, given the limited number of study available in hand and cervical OA, the implication of this conclusion should be cautious for hand and cervical OA.
Is the decline in neonatal mortality in northern Ghana, 1996–2012, associated with the decline in the age of BCG vaccination? An ecological study
Authors: Welaga Paul , Debpuur Cornelius , Aaby Peter , Hodgson Abraham , Azongo Daniel K , Benn Christine S , Oduro Abraham Rexford
Published: December 2018

Objective

To examine the association between early Bacille Calmette-Guerin (BCG) vaccination and neonatal mortality in northern Ghana.

Methods

This ecological study used vaccination and mortality data from the Navrongo Health and Demographic Surveillance System. First, we assessed and compared changes in neonatal mortality rates (NMRs) and median BCG vaccination age from 1996 to 2012. Second, we compared the changes in NMR and median BCG vaccination age from 2002 to 2012 by delivery place when data on delivery place were available.

Results

Neonatal mortality rates declined from 46 to 12 per 1000 live births between 1996 and 2012 (trend test: p<0.001). Within the same period, median BCG vaccination age declined from 46 to 4 days (trend test: p<0.001). Among home deliveries, BCG vaccination age declined from 39 days in 2002 to 7 days in 2012 (trend test: p<0.001) and neonatal mortality declined by 24/1000 (trend test: p<0.001). Among health facility deliveries, BCG vaccination age was stable around 3 days from 2002 to 2012 (trend test: p=0.49) and neonatal mortality declined by 9/1000 (trend test: p=0.04). In a small study of children whose vaccination cards were inspected within the first 28 days of life, the HR for BCG-vaccinated compared with BCG-unvaccinated children was 0.55 (95% CI 0.12 to 2.40).

Conclusion

The data support the hypothesis that early BCG vaccination may be associated with a decrease in neonatal mortality. However, as suggested by WHO, randomised control trials are required to address the question of whether there is indeed a causal association between early BCG vaccination and neonatal mortality.
Definition of whole person care in general practice in the English language literature: a systematic review
Authors: Thomas Hayley , Mitchell Geoffrey , Rich Justin , Best Megan
Published: December 2018

Objectives

The importance of ‘whole person’ or ‘holistic’ care is widely recognised, particularly with an increasing prevalence of chronic multimorbidity internationally. This approach to care is a defining feature of general practice. However, its precise meaning remains ambiguous. We aimed to determine how the term ‘whole person’ care is understood by general practitioners (GPs), and whether it is synonymous with ‘[w]holistic’ and ‘biopsychosocial’ care.

Design

Systematic literature review.

Methods

MEDLINE, PubMed, EMBASE, CINAHL, PsycINFO, Web of Science, Proquest Dissertations and Theses, Science.gov (Health and Medicine database), Google Scholar and included studies’ reference lists were searched with an unlimited date range. Systematic or literature reviews, original research, theoretical articles or books/book chapters; specific to general practice; relevant to the research question; and published in English were included. Included literature was critically appraised, and data were extracted and analysed using thematic synthesis.

Results

Fifty publications were included from 4297 non-duplicate records retrieved. Six themes were identified: a multidimensional, integrated approach; the importance of the therapeutic relationship; acknowledging doctors’ humanity; recognising patients’ individual personhood; viewing health as more than absence of disease; and employing a range of treatment modalities. Whole person, biopsychosocial and holistic terminology were often used interchangeably, but were not synonymous.

Conclusions

Whole person, holistic and biopsychosocial terminology are primarily characterised by a multidimensional approach to care and incorporate additional elements described above. Whole person care probably represents the closest representation of the basis for general practice. Health systems aiming to provide whole person care need to address the challenge of integrating the care of other health professionals, and maintaining the patient–doctor relationship central to the themes identified. Further research is required to clarify the representativeness of the findings, and the relative importance GPs’ assign to each theme.

PROSPERO registration number

CRD42017058824.
Poor school attendance and exclusion: a systematic review protocol on educational risk factors for self-harm and suicidal behaviours
Authors: Epstein Sophie , Roberts Emmert , Sedgwick Rosemary , Finning Katie , Ford Tamsin , Dutta Rina , Downs Johnny
Published: December 2018

Introduction

Schools have an important role in recognising and preventing self-harm and suicidal behaviour in their students, however little is known about which educational factors are associated with heightened risk. We will systematically review the existing evidence on two key educational performance indicators that are routinely collected by school administrative systems: school attendance and exclusion. We will investigate their association with self-harm and suicidal behaviour in school-age children and adolescents. Knowledge of this association could help inform suicide prevention strategies at clinical, school and population levels.

Methods and analysis

We will conduct a systematic search of Medline, EMBASE, PsycINFO, British Education Index and Education Resources Information Centre (ERIC) from 1 January 1990, and conduct a manual search for additional references. We aim to identify studies that explore the association between poor school attendance or exclusion and self-harm or suicidal behaviours in school-age children and adolescents. Two independent reviewers will screen titles, abstracts and full-text documents and independently extract relevant data for analysis. Study quality will be assessed using a modified Newcastle-Ottawa Scale. A descriptive analysis will be performed, and where appropriate, results will be combined in meta-analyses.

Ethics and dissemination

This is a systematic review of published literature, and therefore ethical approval will not be sought. We will publish reports in health and education journals, present our work at conferences focused on school mental health and communicate our findings to practitioners and managers in public health, education and child mental health.

PROSPERO registration number

CRD42018088608.
Understanding cauda equina syndrome: protocol for a UK multicentre prospective observational cohort study
Authors: Woodfield Julie , Hoeritzauer Ingrid , Jamjoom Aimun A B , Pronin Savva , Srikandarajah Nisaharan , Poon Michael , Roy Holly , Demetriades Andreas K , Sell Philip , Eames Niall , Statham Patrick F X
Published: December 2018

Introduction

Cauda equina syndrome (CES) is a potentially devastating condition caused by compression of the cauda equina nerve roots. This can result in bowel, bladder and sexual dysfunction plus lower limb weakness, numbness and pain. CES occurs infrequently, but has serious potential morbidity and medicolegal consequences. This study aims to identify and describe the presentation and management of patients with CES in the UK.

Methods and analysis

Understanding Cauda Equina Syndrome (UCES) is a prospective and collaborative multicentre cohort study of adult patients with confirmed CES managed at specialist spinal centres in the UK. Participants will be identified using neurosurgical and orthopaedic trainee networks to screen referrals to spinal centres. Details of presentation, investigations, management and service usage will be recorded. Both patient-reported and clinician-reported outcome measures will be assessed for 1 year after surgery. This will establish the incidence of CES, current investigation and management practices, and adherence to national standards of care. Outcomes will be stratified by clinical presentation and patient management. Accurate and up to date information about the presentation, management and outcome of patients with CES will inform standards of service design and delivery for this important but infrequent condition.

Ethics and dissemination

UCES received a favourable ethical opinion from the South East Scotland Research Ethics Committee 02 (Reference: 18/SS/0047; IRAS ID: 233515). All spinal centres managing patients with CES in the UK will be encouraged to participate in UCES. Study results will be published in medical journals and shared with local participating sites.

Trial registration number

ISRCTN16828522; Pre-results.
A Machine Learning Approach to Reveal the NeuroPhenotypes of Autisms
Authors: Górriz Juan M. , Ramírez Javier , Segovia F. , Martínez Francisco J. , Lai Meng-Chuan , Lombardo Michael V. , Baron-Cohen Simon ,   MRC AIMS Consortium, Suckling John
Published: December 2018

Although much research has been undertaken, the spatial patterns, developmental course, and sexual dimorphism of brain structure associated with autism remains enigmatic. One of the difficulties in investigating differences between the sexes in autism is the small sample sizes of available imaging datasets with mixed sex. Thus, the majority of the investigations have involved male samples, with females somewhat overlooked. This paper deploys machine learning on partial least squares feature extraction to reveal differences in regional brain structure between individuals with autism and typically developing participants. A four-class classification problem (sex and condition) is specified, with theoretical restrictions based on the evaluation of a novel upper bound in the resubstitution estimate. These conditions were imposed on the classifier complexity and feature space dimension to assure generalizable results from the training set to test samples. Accuracies above [Formula: see text] on gray and white matter tissues estimated from voxel-based morphometry (VBM) features are obtained in a sample of equal-sized high-functioning male and female adults with and without autism ([Formula: see text], [Formula: see text]/group). The proposed learning machine revealed how autism is modulated by biological sex using a low-dimensional feature space extracted from VBM. In addition, a spatial overlap analysis on reference maps partially corroborated predictions of the “extreme male brain” theory of autism, in sexual dimorphic areas.
Exact scattering and bound states solutions for novel hyperbolic potentials with inverse square singularity
Authors: Alhaidari A. D.
Published: December 2018

We use the Tridiagonal Representation Approach (TRA) to obtain exact scattering and bound states solutions of the Schrödinger equation for short-range inverse-square singular hyperbolic potentials. The solutions are series of square integrable functions written in terms of the Jacobi polynomial with the Wilson polynomial as expansion coefficients. The series is finite for the discrete bound states and infinite but bounded for the continuum scattering states.
New Approach to Quartz Coarse Particles Flotation Using Nanobubbles, with Emphasis on the Bubble Size Distribution
Authors: Nazari Sabereh , Shafaei Sied Ziaedin , Gharabaghi Mahdi , Ahmadi Rahman , Shahbazi Behzad , Tehranchi Arash
Published: December 2018

This study investigates the influence of bubble size distribution and operational parameters on the flotation behavior of quartz coarse particles. The parameters evaluated during this study include the different bubble size distribution, air flow rate and impeller speed. Experiments were conducted at three different bubble sizes: 110, 171 and 293[Formula: see text]nm as db(32). Then, the results were compared with common air bubbles of the conventional flotation process. The bubble size distribution was measured using a laser particle size analyzer (LPSA). Results showed that the recovery of [Formula: see text]m particles increased in presence of nano bubbles (NBs) up to 25% compared to the conventional flotation. The maximum recovery of 95.59% was obtained using NBs size of 171[Formula: see text]nm at the impeller speed of 900[Formula: see text]rpm and air flow rate of 30[Formula: see text]l/h. It was also indicated that NBs caused an increasing in flotation recovery for all the samples in any size ranges in comparison with the conventional method.
Fast Learning Requires Good Memory
Authors: Raz Ran
Published: December 2018

We prove that any algorithm for learning parities requires either a memory of quadratic size or an exponential number of samples. This proves a recent conjecture of  Steinhardt et al. (2016) and shows that for some learning problems, a large storage space is crucial.

More formally, in the problem of parity learning, an unknown string
x
∈ {0,1}

n

was chosen uniformly at random. A learner tries to learn
x
from a stream of samples (
a
1
,
b
1
), (
a
2
,
b
2
) …, where each 
a

t

is uniformly distributed over {0,1}

n

and
b

t

is the inner product of
a

t

and
x
, modulo 2. We show that any algorithm for parity learning that uses less than
n
2
/25 bits of memory requires an exponential number of samples.

Previously, there was no non-trivial lower bound on the number of samples needed for any learning problem, even if the allowed memory size is
O
(
n
) (where
n
is the space needed to store one sample).

We also give an application of our result in the field of bounded-storage cryptography. We show an encryption scheme that requires a private key of length
n
, as well as time complexity of
n
per encryption/decryption of each bit, and is provably and unconditionally secure as long as the attacker uses less than
n
2
/25 memory bits and the scheme is used at most an exponential number of times. Previous works on bounded-storage cryptography assumed that the memory size used by the attacker is at most linear in the time needed for encryption/decryption.
Data Lifecycle Challenges in Production Machine Learning
Authors: Polyzotis Neoklis , Roy Sudip , Whang Steven Euijong , Zinkevich Martin
Published: December 2018

Machine learning has become an essential tool for gleaning knowledge from data and tackling a diverse set of computationally hard tasks. However, the accuracy of a machine learned model is deeply tied to the data that it is trained on. Designing and building robust processes and tools that make it easier to analyze, validate, and transform data that is fed into large-scale machine learning systems poses data management challenges. Drawn from our experience in developing data-centric infrastructure for a production machine learning platform at Google, we summarize some of the interesting research challenges that we encountered, and survey some of the relevant literature from the data management and machine learning communities. Specifically, we explore challenges in three main areas of focus - data understanding, data validation and cleaning, and data preparation. In each of these areas, we try to explore how different constraints are imposed on the solutions depending on where in the lifecycle of a model the problems are encountered and who encounters them.
Frustrated Quantum Rare-Earth Pyrochlores
Authors: Rau Jeffrey G. , Gingras Michel J.P.
Published: December 2018

In this review, we provide an introduction to the physics of a series of frustrated quantum rare-earth pyrochlores. We first give a background on the microscopic single- and two-ion physics of these materials, discussing the origins and properties of their exchange interactions and their minimal low-energy effective models before outlining what is known about their classical and quantum phases. We then make use of this understanding to discuss four important material examples, Er2Ti2O7, Yb2Ti2O7, Tb2Ti2O7, and Pr2Zr2O7, covering in some detail what is known experimentally and theoretically for each and then summarizing some key questions that remain open. Finally, we offer an outlook on some alternative material platforms for realizing similar physics and discuss what we see as prospects for future investigations on these quantum rare-earth pyrochlores.
Floquet Engineering of Quantum Materials
Authors: Oka Takashi , Kitamura Sota
Published: December 2018

Floquet engineering, the control of quantum systems using periodic driving, is an old concept in condensed matter physics dating back to ideas such as the inverse Faraday effect. However, there is a renewed interest in this concept owing to ( a) the rapid developments in laser and ultrafast spectroscopy techniques, ( b) discovery and understanding of various “quantum materials” hosting interesting exotic quantum properties, and ( c) communication with different areas of physics such as artificial matter and nonequilibrium quantum statistical physics. Here, starting from a nontechnical introduction with emphasis on the Floquet picture and effective Hamiltonians, we review the recent applications of Floquet engineering in ultrafast, nonlinear phenomena in the solid state. In particular, Floquet topological states and their application to ultrafast spintronics and strongly correlated electron systems are overviewed.
Effect of flipped teaching on student performance and perceptions in an Introductory Physiology course
Authors: Gopalan Chaya
Published: December 2018

Flipped teaching (FT) has caught educators’ attention due to its success in engaging students through pre- and in-class activities. To learn if FT improved student performance, scores from the quizzes and exams of a fully flipped classroom with retrieval exercises were compared with those of five semesters of traditional lecture-based [unflipped (UF)] teaching in an undergraduate sophomore-level physiology course. Student attitude surveys were also evaluated. Student performance on both the quizzes and exams was significantly higher in the FT class in general compared with that of the UF teaching. Interestingly, however, when the individual exam scores were compared between the two styles, the scores for students in the FT were significantly higher for exams 2 and 3, yet lower for exam 1. The shift in performance from exam 1 to exams 2 and 3 is likely explained by the need for time to adjust to the new teaching style. Students reported an overall positive perception of FT in their course evaluations at the end of the semester. In conclusion, FT improved student performance compared with that of lecture-based traditional teaching practice, but required some time to adjust in the beginning of the semester.