bluuebunny/crossref_metadata_2025 huggingface dataset:
Waterwise House and Garden
Authors: Windust Allan
Published: March 2019

This practical guide shows how we can contribute to conserving water, our most precious resource, in our home and garden.
Waterwise House and Garden takes a planned approach to saving water in the home using different household reticulation options including the use of rainwater tanks and recycling greywater. It shows how to eliminate unnecessary watering in the garden by working with nature to create a garden that is both enjoyable and sensitive to the environment.
It explains the science behind survival strategies of plants in dry conditions, shows how soil and water interact, and demonstrates how to improve the soil in your garden. Included is an extensive list of native and exotic plants that are tolerant to dry conditions in both tropical and temperate climates.
The result is an accessible and informative resource guaranteed to help you reduce the environmental impact of everyday living, and dramatically reduce your household water bill in the process.
Shortlisted in TAFE Vocational Education category in the 2003 Awards for Excellence in Educational Publishing.
Olive Propagation Manual
Authors: Fabbri Andrea , Bartolini Giorgio , Lambardi Maurizio , Kailis Stan
Published: March 2019

This practical manual is an authoritative guide to olive propagation, providing extended information on seed germination, rooting of cuttings, grafting and micropropagation. The authors describe each topic in detail and discuss the relative advantages and disadvantages of each procedure.
The Olive Propagation Manual has been developed to take into account the future demand for olive oil, which is expected to increase to three million tonnes annually over the next 10 years. Such volumes will require active farming programs and olive trees for new orchards and the replacement of olive trees in existing orchards. As the olive industry moves from traditional manual methods to mechanised operations, planting stock will need to be developed to meet future challenges. Varietal selection will need to be directed to clones that are early bearing, disease resistant, able to be mechanically harvested, and produce quality fruit and oil. Each of these issues are addressed throughout this book.
The Olive Propagation Manual explores historical perspectives, traditional methods and state-of-the-art olive propagation including theoretical explanations and all practical aspects.
Practical Straw Bale Building
Authors: Hollis Murray
Published: March 2019

Building with straw bales is being embraced by amateurs and professionals for its versatility, comfort, environmental friendliness and high insulation. New methods should expand its growing worldwide popularity.
In Practical Straw Bale Building, Murray Hollis uses simple, easy to understand language to describe the established techniques of straw bale construction and ways in which they can be improved. He also presents a new straw bale construction system that has substantial benefits over current methods. This system incorporates a new tensioning system that replaces the use of fence strainers for tensioning the hold-down/compression wires and eliminates uneven tensioning on opposite sides of the wall. It also allows for fabricating wall modules on-site as horizontal modules that are then swung into the vertical wall position after fabrication. Aspects of structures other than walls are addressed only to the extent that they are relevant to the use of straw bales, e.g. issues such as types of floors, roof structures and methods of heating or cooling.
The innovative methods in this book will help to progress straw bale building technology and move it into the mainstream of the building industry.
Building Your Straw Bale Home
Authors: Hodge Brian
Published: March 2019

This practical guide is written especially for the owner-builder and provides step-by-step instructions supported by diagrams and photographs.
It covers the construction process from site preparation through to foundations, concrete slabs, strip footings and stumps. Special techniques for straw bale construction and the integration of these techniques with those of conventional house building are also covered, including floors, timber wall-frames, ceilings and roof framing. Advice is offered on plumbing and electrical work in a straw bale house.
Written with first-hand knowledge of the challenges that face the owner-builder, the author explores local council issues and requirements, the potential pitfalls of building and what to look for when ordering second-hand material, aided by a useful glossary of terms. The book concludes by covering the various safety issues that arise during construction, including fire prevention, equipment usage and the working environment.
Ecotourism
Authors: Beeton S
Published: March 2019

Tourism, with its niche element of ecotourism, is one of Australia’s fastest growing industries, overtaking the traditional export items of coal, wheat and wool in export earnings.
This book covers everything a person needs to think about before venturing into the ecotourism market. It explains what ecotourism is and who the ecotourists are. It describes how to work with the local community and the local environment, highlighting some of the constraints and pitfalls. It explains what is needed to make a successful venture work - and how to make it pay.
Risk variants disrupting enhancers of T
H
1 and T
REG
cells in type 1 diabetes
Authors: Gao Peng , Uzun Yasin , He Bing , Salamati Sarah E. , Coffey Julie K. M. , Tsalikian Eva , Tan Kai
Published: March 2019

Genome-wide association studies (GWASs) have revealed 59 genomic loci associated with type 1 diabetes (T1D). Functional interpretation of the SNPs located in the noncoding region of these loci remains challenging. We perform epigenomic profiling of two enhancer marks, H3K4me1 and H3K27ac, using primary T
H
1 and T
REG
cells isolated from healthy and T1D subjects. We uncover a large number of deregulated enhancers and altered transcriptional circuitries in both cell types of T1D patients. We identify four SNPs (rs10772119, rs10772120, rs3176792, rs883868) in linkage disequilibrium (LD) with T1D-associated GWAS lead SNPs that alter enhancer activity and expression of immune genes. Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively. Loss of binding by YY1 also results in the loss of long-range enhancer–promoter interaction. These findings provide insights into how noncoding variants affect the transcriptomes of two T-cell subtypes that play critical roles in T1D pathogenesis.
Microbial ecosystem dynamics drive fluctuating nitrogen loss in marine anoxic zones
Authors: Penn Justin L. , Weber Thomas , Chang Bonnie X. , Deutsch Curtis
Published: March 2019

The dynamics of nitrogen (N) loss in the ocean’s oxygen-deficient zones (ODZs) are thought to be driven by climate impacts on ocean circulation and biological productivity. Here we analyze a data-constrained model of the microbial ecosystem in an ODZ and find that species interactions drive fluctuations in local- and regional-scale rates of N loss, even in the absence of climate variability. By consuming O
2
to nanomolar levels, aerobic nitrifying microbes cede their competitive advantage for scarce forms of N to anaerobic denitrifying bacteria. Because anaerobes cannot sustain their own low-O
2
niche, the physical O
2
supply restores competitive advantage to aerobic populations, resetting the cycle. The resulting ecosystem oscillations induce a unique geochemical signature within the ODZ—short-lived spikes of ammonium that are found in measured profiles. The microbial ecosystem dynamics also give rise to variable ratios of anammox to heterotrophic denitrification, providing a mechanism for the unexplained variability of these pathways observed in the ocean.
A natural anti-periodontitis agent, epimedokoreanin B, inhibits virulence activities of gingipains from Porphyromonas gingivalis
Authors: Kariu Toru , Ikeda Tsuyoshi , Nakashima Keisuke , Potempa Jan , Imamura Takahisa
Published: March 2019

Gingipains are potent virulence cysteine proteases secreted by Porphyromonas gingivalis, a major pathogen of periodontitis. We previously reported that epimedokoreanin B inhibits the activities of gingipains. In this report, we show that epimedokoreanin B inhibits the virulence of gingipains-containing P. gingivalis culture supernatants, indicating the potential use of this prenylated flavonoid as a new agent to combat against periodontal pathogens.
Ingestion of difructose anhydride III partially suppresses the deconjugation and 7α-dehydroxylation of bile acids in rats fed with a cholic acid-supplemented diet
Authors: Lee Dong Geun , Hori Shota , Kohmoto Ohji , Kitta Shinri , Yoshida Ryo , Tanaka Yasutake , Shimizu Hidehisa , Takahashi Keisuke , Nagura Taizo , Uchino Hirokatsu , Fukiya Satoru , Yokota Atsushi , Ishizuka Satoshi
Published: March 2019

Difructose anhydride III (DFAIII) is a prebiotic involved in the reduction of secondary bile acids (BAs). We investigated whether DFAIII modulates BA metabolism, including enterohepatic circulation, in the rats fed with a diet supplemented with cholic acid (CA), one of the 12α-hydroxylated BAs. After acclimation, the rats were fed with a control diet or a diet supplemented with DFAIII. After 2 weeks, each group was further divided into two groups and was fed diet with or without CA supplementation at 0.5 g/kg diet. BA levels were analyzed in aortic and portal plasma, liver, intestinal content, and feces. As a result, DFAIII ingestion reduced the fecal deoxycholic acid level via the partial suppression of deconjugation and 7α-dehydroxylation of BAs following CA supplementation. These results suggest that DFAIII suppresses production of deoxycholic acid in conditions of high concentrations of 12α-hydroxylated BAs in enterohepatic circulation, such as obesity or excess energy intake.

Abbreviation: BA: bile acid; BSH: bile salt hydrolase; CA: cholic acid; DCA: deoxycholic acid; DFAIII: difructose anhydride III; MCA: muricholic acid; MS: mass spectrometry; NCDs: non-communicable diseases; LC: liquid chromatography; SCFA: short-chain fatty acid; TCA: taurocholic acid; TCDCA: taurochenodeoxycholic acid; TDCA: taurodeoxycholic acid; TUDCA: tauroursodeoxychlic acid; TαMCA: tauro-α-muricholic acid; TβMCA: tauro-β-muricholic acid; TωMCA: tauro-ω-muricholic acid
Enhancement of mechanical and functional properties of welded NiTi by controlling nickel vapourisation
Authors: Shamsolhodaei A. , Zhou Y. N. , Michael A.
Published: March 2019

This work investigates the effect of nickel vapourisation on mechanical properties and superelasticity of a NiTi wire by selecting the highest and lowest power within a laser processing window. The dominant phase at room temperature changes from austenite to a mixture of austenite and martensite under low power and high power condition, respectively due to higher nickel loss in the high power sample. Furthermore, the high power sample has more deviation from base material texture (111)B2 that causes deterioration in mechanical properties compared with the low power sample with has 81% of base material strength. Better superelasticity of the low power sample (0.38% residual strain) was explained by the existence of the martensite phase and coarser grain structure in the high power sample.
Extramitochondrial cardiolipin suggests a novel function of mitochondria in spermatogenesis
Authors: Ren Mindong , Xu Yang , Erdjument-Bromage Hediye , Donelian Alec , Phoon Colin K.L. , Terada Naohiro , Strathdee Douglas , Neubert Thomas A. , Schlame Michael
Published: March 2019

Mitochondria contain cardiolipin (CL), an organelle-specific phospholipid that carries four fatty acids with a strong preference for unsaturated chains. Unsaturation is essential for the stability and for the function of mitochondrial CL. Surprisingly, we found tetrapalmitoyl-CL (TPCL), a fully saturated species, in the testes of humans and mice. TPCL was absent from other mouse tissues but was the most abundant CL species in testicular germ cells. Most intriguingly, TPCL was not localized in mitochondria but was in other cellular membranes even though mitochondrial CL was the substrate from which TPCL was synthesized. During spermiogenesis, TPCL became associated with the acrosome, a sperm-specific organelle, along with a subset of authentic mitochondrial proteins, including Ant4, Suox, and Spata18. Our data suggest that mitochondria-derived membranes are assembled into the acrosome, challenging the concept that this organelle is strictly derived from the Golgi apparatus and revealing a novel function of mitochondria.
Research Methodology in Educational Leadership and Management
Authors: Briggs Ann , Coleman Marianne
Published: March 2019

Research in educational leadership and management spans settings from early childhood to tertiary education and life-long learning. From its mid-20th-century beginnings as a tool for organizing educational systems, the wide range of methodologies in present use reflects the shifting focus of the field. The current mix of quantitative and qualitative approaches indicates differing epistemological stances and a range of purposes from instrumental responses to government policy initiatives, through investigation of issues of social justice, to personal enquiry into leadership influence on environments for learning. Research in the field encompasses the values and dilemmas underpinning educational leadership roles, the enactment of middle leadership, teacher leadership and student leadership, and includes leaders conducting research to improve their own practice.

Multiple aspects of decision-making are involved in educational leadership research. The philosophical assumptions of researchers inform their positivist or interpretivist stance and the associated choices of quantitative or qualitative methodology. The external drivers of the investigation, together with its purpose and scope, influence the choice of research approach —for example, data-mining, survey, case study, action research—and technique—interview, questionnaire, documentary analysis, narrative, and life-history. These approaches and techniques in turn invite a range of analytical methods, from statistical modeling, systematic qualitative data analysis and discourse analysis to auto-ethnographic critical reflection and reflective narrative. The interpretation of the analysis hinges on the purpose of the research: to understand, inform, improve, or bring about change.

Twenty-first-century challenges for the field include expanding theory beyond a largely Western-centric focus; responding to the development of new theories of leadership, including the voice of non-leaders in perspectives on leadership; ensuring that research informs policy rather than vice versa; and addressing the sheer volume and nature of data available through emerging technologies.
Barley in Archaeology and Early History
Authors: Riehl Simone
Published: March 2019

In 2018 barley accounts for only 5% of the cereal production worldwide, and regionally for up to 40% of cereal production. The cereal represents the oldest crop species and is one of the best adapted crop plants to a broad diversity of climates and environments.

Originating from the wild progenitor species Hordeum vulgare ssp. spontaneum, biogeographically located in the Fertile Crescent of the Near East, the domesticated form developed as a founder crop in aceramic Neolithic societies 11,000 years ago, was cultivated in monocultures in Bronze Age Mesopotamia, entered the New World after 1492 ce, reached a state of global distribution in the 1950s and had reached approximately 200 accepted botanical varieties by the year 2000.

Its stress tolerance in response to increased aridity and salinity on one hand and adaptability to cool climates on the other, partially explains its broad range of applications for subsistence and economy across different cultures, such as for baking, cooking, beer brewing and as an animal feed.

Although the use of fermented starch for producing alcoholic beverages and foods is globally documented in archaeological contexts dating from at least the beginning of the Holocene era, it becomes concrete only in societies with a written culture, such as Bronze Age Mesopotamia and Egypt, where beer played a considerable role in everyday diet and its production represented an important sector of productivity.

In 2004 approximately 85% of barley production was destined for feeding animals. However, as a component of the human diet, studies on the health benefits of the micronutrients in barley have found that it has a positive effect on blood cholesterol and glucose levels, and in turn impacts cardiovascular health and diabetes control. The increasing number of barley-breeding programs worldwide focus on improving the processing characteristics, nutritional value, and stress tolerance of barley within the context of global climate change.
Kinpute: using identity by descent to improve genotype imputation
Authors: Abney Mark , ElSherbiny Aisha
Published: March 2019

Motivation

Genotype imputation, though generally accurate, often results in many genotypes being poorly imputed, particularly in studies where the individuals are not well represented by standard reference panels. When individuals in the study share regions of the genome identical by descent (IBD), it is possible to use this information in combination with a study-specific reference panel (SSRP) to improve the imputation results. Kinpute uses IBD information—due to recent, familial relatedness or distant, unknown ancestors—in conjunction with the output from linkage disequilibrium (LD) based imputation methods to compute more accurate genotype probabilities. Kinpute uses a novel method for IBD imputation, which works even in the absence of a pedigree, and results in substantially improved imputation quality.

Results

Given initial estimates of average IBD between subjects in the study sample, Kinpute uses a novel algorithm to select an optimal set of individuals to sequence and use as an SSRP. Kinpute is designed to use as input both this SSRP and the genotype probabilities output from other LD-based imputation software, and uses a new method to combine the LD imputed genotype probabilities with IBD configurations to substantially improve imputation. We tested Kinpute on a human population isolate where 98 individuals have been sequenced. In half of this sample, whose sequence data was masked, we used Impute2 to perform LD-based imputation and Kinpute was used to obtain higher accuracy genotype probabilities. Measures of imputation accuracy improved significantly, particularly for those genotypes that Impute2 imputed with low certainty.

Availability and implementation

Kinpute is an open-source and freely available C++ software package that can be downloaded from.

Supplementary information

Supplementary data are available at Bioinformatics online.
FusionLearn: a biomarker selection algorithm on cross-platform data
Authors: Gao Xin , Zhong Yuan
Published: March 2019

Motivation

In high dimensional genetic data analysis, the objective is to select important biomarkers which are involved in some biological processes, such as disease progression, immune response, etc. The experimental data are often collected from different platforms including microarray experiments and proteomic experiments. The conventional single-platform approach lacks the capability to learn from multiple platforms, and the resulted lists of biomarkers vary across different platforms. There is a great need to develop an algorithm which can aggregate information across platforms and provide a consolidated list of biomarkers across different platforms.

Results

In this paper, we introduce an R package FusionLearn, which implements a fusion learning algorithm to analyze cross-platform data. The consolidated list of biomarkers is selected by the technique of group penalization. We first apply the algorithm on a collection of breast cancer microarray experiments from the NCBI (National Centre for Biotechnology Information) microarray database and the resulted list of selected genes have higher classification accuracy rate across different datasets than the lists generated from each single dataset. Secondly, we use the software to analyze a combined microarray and proteomic dataset for the study of the growth phase versus the stationary phase in Streptomyces coelicolor. The selected biomarkers demonstrate consistent differential behavior across different platforms.

Availability and implementation

R package: https://cran.r-project.org/package=FusionLearn.
parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems
Authors: Shegay Maksim V , Suplatov Dmitry A , Popova Nina N , Švedas Vytas K , Voevodin Vladimir V
Published: March 2019

Motivation

Accurate structural alignment of proteins is crucial at studying structure-function relationship in evolutionarily distant homologues. Various software tools were proposed to align multiple protein 3D-structures utilizing one CPU and thus are of limited productivity at large-scale analysis of protein families/superfamilies.

Results

The parMATT is a hybrid MPI/pthreads/OpenMP parallel re-implementation of the MATT algorithm to align multiple protein 3D-structures by allowing translations and twists. The parMATT can be faster than MATT on a single multi-core CPU, and provides a much greater speedup when executed on distributed-memory systems, i.e. computing clusters and supercomputers hosting memory-independent computing nodes. The most computationally demanding steps of the MATT algorithm—the initial construction of pairwise alignments between all input structures and further iterative progression of the multiple alignment—were parallelized using MPI and pthreads, and the concluding refinement step was optimized by introducing the OpenMP support. The parMATT can significantly accelerate the time-consuming process of building a multiple structural alignment from a large set of 3D-records of homologous proteins.

Availability and implementation

The source code is available at https://biokinet.belozersky.msu.ru/parMATT.

Supplementary information

Supplementary data are available at Bioinformatics online.
Parallel repulsive logic regression with biological adjacency
Authors: Yoneoka Daisuke , Im Cindy , Yasui Yutaka
Published: March 2019

Logic regression, an extension of generalized linear models with Boolean combinations of binary variables as predictors, is a useful tool in exploring interactions among single-nucleotide polymorphisms (SNPs) in genome-wide association studies. However, since the search space defined by all possible combinations of SNPs, their complements, and logical operators in Boolean expressions can be exceedingly large in such studies, objective function optimization is slow and likely to be trapped in many local solutions, resulting in model over-fitting. We introduce a new search algorithm, parallel repulsive logic regression (PRLR), to efficiently estimate parameters of a logic regression to find a best model within the large space of SNP interactions by incorporating: (i) relevant biological adjacency matrix between SNPs to define similarity of estimation paths or trees, which are derived from physical SNP positions on chromosomes and/or memberships in biological gene pathways; and (ii) two repulsive forces to counter the similarity between and within estimation paths considered in parallel, which are introduced as penalty terms in the objective function. We compare our method’s performance for identifying biologically-meaningful SNP interactions through simulations and with real genetic-epidemiological data. PRLR’s detection-accuracy measures outperform existing approaches, especially in terms of positive predictive value and sensitivity for detecting SNP–SNP interactions.
The presence of residents during orthopedic operation exerts no negative influence on outcome
Authors: Giordano Lorenzo , Oliviero Antonio , Peretti Giuseppe M , Maffulli Nicola
Published: March 2019

Background

Operative procedural training is a key component of orthopedic surgery residency. It is unclear how and whether residents participation in orthopedic surgical procedures impacts on post-operative outcomes.

Sources of data

A systematic search was performed to identify articles in which the presence of a resident in the operating room was certified, and was compared with interventions without the presence of residents.

Areas of agreement

There is a likely beneficial role of residents in the operating room, and there is only a weak association between the presence of a resident and a worse outcome for orthopedic surgical patients

Areas of controversy

Most of the studies were undertaken in USA, and this represents a limit from the point of view of comparison with other academic and clinical realities.

Growing point

The data provide support for continued and perhaps increased involvement of resident in orthopedic surgery.

Areas of research

To clarify the role of residents on clinically relevant outcomes in orthopedic patients, appropriately powered randomized control trials should be planned.
Severe Illnesses Associated With Outbreaks of Respiratory Syncytial Virus and Influenza in Adults
Authors: Zhou James A , Schweinle Jo Ellen , Lichenstein Richard , Walker Robert E , King James C
Published: March 2019

Background

Recent reports have described the contribution of adult respiratory syncytial virus (RSV) infections to the use of advanced healthcare resources and death.

Methods

Data regarding patients aged ≥18 years admitted to any of Maryland’s 50 acute-care hospitals were evaluated over 12 consecutive years (2001–2013). We examined RSV and influenza (flu) surveillance data from the US National Respiratory and Enteric Virus Surveillance System and the Centers for Disease Control and Prevention and used this information to define RSV and flu outbreak periods in the Maryland area. Outbreak periods consisted of consecutive individual weeks during which at least 10% of RSV and/or flu diagnostic tests were positive. We examined relationships of RSV and flu outbreaks to occurrence of 4 advanced medical outcomes (hospitalization, intensive care unit admission, intubated mechanical ventilation, and death) due to medically attended acute respiratory illness (MAARI).

Results

Occurrences of all 4 MAARI-related hospital advanced medical outcomes were consistently greater for all adult ages during RSV, flu, and combined RSV–flu outbreak periods compared to nonoutbreak periods and tended to be greatest in adults aged ≥65 years during combined RSV–flu outbreak periods. Rate ratios for all 4 MAARI-related advanced medical outcomes ranged from 1.04 to 1.38 during the RSV, flu, or combined RSV–flu outbreaks compared to the nonoutbreak periods, with all 95% lower confidence limits >1.

Conclusions

Both RSV and flu outbreaks were associated with surges in MAARI-related advanced medical outcomes (hospitalization, intensive care unit admission, intubated mechanical ventilation, and death) for adults of all ages.
Molecular Approach to Diagnosis of Cardiovascular Implantable Electronic Device Infection
Authors: Esquer Garrigos Zerelda , Sohail M Rizwan , Greenwood-Quaintance Kerryl E , Cunningham Scott A , Vijayvargiya Prakhar , Fida Madiha , Friedman Paul A , Mandrekar Jayawant , DeSimone Daniel C , Baddour Larry M , Patel Robin
Published: March 2019

Background

Sonicate fluid (SF), a solution derived from vortexing and sonication of explanted cardiovascular implantable electronic devices (CIEDs), is a higher-yield specimen compared with swabs or tissues for culture-based detection of microorganisms associated with CIED infection. Despite this, SF culture fails to identify a causative organism in ~50% of cases. We aimed to evaluate the diagnostic performance of 16S ribosomal RNA gene (rRNA) polymerase chain reaction (PCR)/sequencing of SF and compare it with that of SF culture.

Methods

We identified 322 SF specimens from extracted CIEDs and reviewed clinical data for each patient. Subjects were classified as having or not having CIED infection. Cases were subcategorized as culture negative if no significant growth was reported from SF cultures and as culture positive if an organism was detected above predefined thresholds. 16S rRNA PCR/sequencing was performed, with the organisms identified reported according to Clinical and Laboratory Standards Institute guidelines for sequence data interpretation.

Results

A total of 278 SF samples corresponded to infected cases, of which 160 were culture positive and 118 culture negative. The remaining 44 were from noninfected cases, of which 2 were culture positive. Compared with SF culture, the sensitivity of 16S rRNA PCR/sequencing was higher (64% vs 57.5%, P = .003). 16S rRNA PCR/sequencing detected a potential pathogen in 28 of 118 culture-negative cases, identifying staphylococci in the majority (18/28).

Conclusions

16S rRNA PCR/sequencing has higher sensitivity to detect bacteria in SF from extracted CIEDs than does SF culture.
YeasTSS: an integrative web database of yeast transcription start sites
Authors: McMillan Jonathan , Lu Zhaolian , Rodriguez Judith S , Ahn Tae-Hyuk , Lin Zhenguo
Published: March 2019

The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5′ boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters (CPs). In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for 12 important yeast species, inferred their CPs and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, CPs and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.
A clampless anastomosis technique using the aortic cannula mounted by a prosthetic graft for a severely calcified aorta in a patient with subclavian steal syndrome
Authors: Sumi Kohei , Yoshida Shigehiko , Okamura Yoshitaka , Kunimoto Hideki
Published: March 2019

Patients with severely calcified aorta are at high risk of embolic stroke during surgery and it is not feasible to clamp the aorta, necessitating alternative surgical strategies. We present a clampless anastomosis technique using the aortic cannula mounted by a prosthetic graft for a severely calcified aorta in a patient with subclavian–vertebral artery steal syndrome.
Mycobacterium tuberculosisinfection of host cells in space and time
Authors: Bussi Claudio , Gutierrez Maximiliano G
Published: March 2019

Tuberculosis (TB) caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb) remains one of the deadliest infectious diseases with over a billion deaths in the past 200 years (Paulson 2013). TB causes more deaths worldwide than any other single infectious agent, with 10.4 million new cases and close to 1.7 million deaths in 2017. The obstacles that make TB hard to treat and eradicate are intrinsically linked to the intracellular lifestyle of Mtb. Mtb needs to replicate within human cells to disseminate to other individuals and cause disease. However, we still do not completely understand how Mtb manages to survive within eukaryotic cells and why some cells are able to eradicate this lethal pathogen. Here, we summarise the current knowledge of the complex host cell-pathogen interactions in TB and review the cellular mechanisms operating at the interface between Mtb and the human host cell, highlighting the technical and methodological challenges to investigating the cell biology of human host cell-Mtb interactions.
Classroom active breaks: a feasibility study in Southern Italy
Authors: Calella Patrizia , Mancusi Caterina , Pecoraro Pierluigi , Sensi Serena , Sorrentino Carmelina , Imoletti Maria , Franzese Adriana , Gallè Francesca , Liguori Giorgio , Valerio Giuliana
Published: March 2019

Though classroom time has been identified as a contributing factor to sedentary behavior, school has been recognized as the main educational setting providing physical activity (PA) opportunities. The purpose of this study was to develop and evaluate the feasibility of a classroom-based intervention which integrates PA during the school time, and assess its potential effect on reducing inactivity in primary school children. The intervention was performed in a sample of 47 children attending a primary school in the south of Italy and it was structured in two sessions of classroom active breaks (CABs) in three school days a week, shared with and supervised by the teachers. CABs showed an overall potential positive effect on the reduction of inactivity of ∼12 min and an equivalent increase in PA levels, of which 5 min were of moderate/vigorous intensity. Girls showed lower time spent in light and moderate PA and higher amount of inactivity than boys and responded better to the intervention. The satisfaction of children and teachers was high. CABs program is a safe tool to reduce inactivity and increase moderate/vigorous PA. Designing structured exercise breaks adapted in a flexible way to meet the needs of the school curriculum program may increase the feasibility of such PA program in the schools.
The association of urine metals and metal mixtures with cardiovascular incidence in an adult population from Spain: the Hortega Follow-Up Study
Authors: Domingo-Relloso Arce , Grau-Perez Maria , Briongos-Figuero Laisa , Gomez-Ariza Jose L , Garcia-Barrera Tamara , Dueñas-Laita Antonio , Bobb Jennifer F , Chaves F Javier , Kioumourtzoglou Marianthi-Anna , Navas-Acien Ana , Redon-Mas Josep , Martin-Escudero Juan C , Tellez-Plaza Maria
Published: March 2019

Background

The association of low-level exposure to metals and metal mixtures with cardiovascular incidence in the general population has rarely been studied. We flexibly evaluated the association of urinary metals and metal mixtures concentrations with cardiovascular diseases in a representative sample of a general population from Spain.

Methods

Urine antimony (Sb), barium (Ba), cadmium (Cd), chromium (Cr), cobalt (Co), copper (Cu), molybdenum (Mo), vanadium (V) and zinc (Zn) were measured in 1171 adults without clinical cardiovascular diseases, who participated in the Hortega Study. Cox proportional hazard models were used for evaluating the association between single metals and cardiovascular incidence. We used a Probit extension of Bayesian Kernel Machine Regression (BKMR-P) to handle metal mixtures in a survival setting.

Results

In single-metal models, the hazard ratios [confidence intervals (CIs)] of cardiovascular incidence, comparing the 80th to the 20th percentiles of metal distributions, were 1.35 (1.06, 1.72) for Cu, 1.43 (1.07, 1.90) for Zn, 1.51 (1.13, 2.03) for Sb, 1.46 (1.13, 1.88) for Cd, 1.64 (1.05, 2.58) for Cr and 1.31 (1.01, 1.71) for V. BKMR-P analysis was confirmatory of these findings, supporting that Cu, Zn, Sb, Cd, Cr and V are related to cardiovascular incidence in the presence of the other metals. Cd and Sb showed the highest posterior inclusion probabilities.

Conclusions

Urine Cu, Zn, Sb, Cd, Cr and V were independently associated with increased cardiovascular risk at levels relevant for the general population of Spain. Urine metals in the mixture were also jointly associated with cardiovascular incidence, with Cd and Sb being the most important components of the mixture.
The relationship between sleep duration, cognition and dementia: a Mendelian randomization study
Authors: Henry Albert , Katsoulis Michail , Masi Stefano , Fatemifar Ghazaleh , Denaxas Spiros , Acosta Dionisio , Garfield Victoria , Dale Caroline E
Published: March 2019

Background

Short and long sleep duration have been linked with poorer cognitive outcomes, but it remains unclear whether these associations are causal.

Methods

We conducted the first Mendelian randomization (MR) study with 77 single-nucleotide polymorphisms (SNPs) for sleep duration using individual-participant data from the UK Biobank cohort (N = 395 803) and summary statistics from the International Genomics of Alzheimer’s Project (N cases/controls = 17 008/37 154) to investigate the potential impact of sleep duration on cognitive outcomes.

Results

Linear MR suggested that each additional hour/day of sleep was associated with 1% [95% confidence interval (CI) = 0–2%; P = 0.008] slower reaction time and 3% more errors in visual-memory test (95% CI = 0–6%; P = 0.05). There was little evidence to support associations of increased sleep duration with decline in visual memory [odds ratio (OR) per additional hour/day of sleep = 1.10 (95% CI = 0.76–1.57); P = 0.62], decline in reaction time [OR = 1.28 (95% CI = 0.49–3.35); P = 0.61], all-cause dementia [OR = 1.19 (95% CI = 0.65–2.19); P = 0.57] or Alzheimer’s disease risk [OR = 0.89 (95% CI = 0.67–1.18); P = 0.41]. Non-linear MR suggested that both short and long sleep duration were associated with poorer visual memory (P for non-linearity = 3.44e–9) and reaction time (P for non-linearity = 6.66e–16).

Conclusions

Linear increase in sleep duration has a small negative effect on reaction time and visual memory, but the true association might be non-linear, with evidence of associations for both short and long sleep duration. These findings suggest that sleep duration may represent a potential causal pathway for cognition.
Predictive Value of Tenofovir Diphosphate in Dried Blood Spots for Future Viremia in Persons Living With HIV
Authors: Morrow Mary , MaWhinney Samantha , Coyle Ryan P , Coleman Stacey S , Gardner Edward M , Zheng Jia-Hua , Ellison Lucas , Bushman Lane R , Kiser Jennifer J , Anderson Peter L , Castillo-Mancilla Jose R
Published: March 2019

Background

Tenofovir diphosphate (TFV-DP) in dried blood spots (DBS) is associated with viral suppression in persons living with HIV (PLWH) taking tenofovir disoproxil fumarate (TDF). However, its value as a predictor of future viremia remained unknown.

Methods

Blood for plasma viral load (VL) and TFV-DP in DBS were collected (up to 3 visits within 48 weeks) in PLWH on TDF. TFV-DP cut points were selected using logistic prediction models maximizing the area under the receiver operation characteristic curve, and estimated adjusted odds ratio (aOR) of future viremia (≥20 copies/mL) were compared to the highest TFV-DP category.

Results

Among all 451 participants in the analysis, aOR of future viremia for participants with TFV-DP <800 and 800 to <1650 fmol/punch were 4.7 (95% CI, 2.6–8.7; P < .0001) and 2.1 (95% CI, 1.3–3.3; P = .002) versus ≥1650 fmol/punch, respectively. These remained significant for participants who were virologically suppressed at the time of the study visit (4.2; 95% CI, 1.5–12.0; P = .007 and 2.2; 95% CI, 1.2–4.0; P = .01).

Conclusions

TFV-DP in DBS predicts future viremia in PLWH on TDF, even in those who are virologically suppressed. This highlights the utility of this biomarker to inform about adherence beyond VL.

Clinical Trials Registration. NCT02012621.
On- and off-label utilization of dalbavancin and oritavancin for Gram-positive infections
Authors: Morrisette Taylor , Miller Matthew A , Montague Brian T , Barber Gerard R , McQueen R Brett , Krsak Martin
Published: March 2019

Background

Long-acting lipoglycopeptides (laLGPs) are FDA approved only for acute bacterial skin and skin structure infections (ABSSSIs). However, these antibiotics show promise for off-label use, reductions in hospital length of stay (LOS) and healthcare cost savings.

Objectives

To assess the effectiveness, safety, impact on LOS and estimated cost savings from laLGP treatment for Gram-positive infections.

Methods

Retrospective cohort of adult patients who received at least one dose of laLGPs at the University of Colorado Health system. Descriptive statistics were utilized for analysis.

Results

Of 59 patients screened, 56 were included: mean age 47 years, 59% male and 30% injection drug users/polysubstance abusers (dalbavancin, 71%; oritavancin, 25%; both, 4%). Most common indications for laLGP: ABSSSIs (36%), osteomyelitis (27%) and endocarditis (9%). Most common isolated pathogens: MSSA and MRSA (25% and 19%, respectively), Enterococcus faecalis (11%) and CoNS (11%). Previous antibiotics were administered for a median of 13 days (IQR = 7.0–24.5 days) and laLGPs for a median of one dose (IQR = 1–2 doses). Ten (18%) patients were lost to follow-up. Clinical failure was found in 7/47 (15%) cases with adequate follow-up. Mild adverse effects occurred in six (11%) patients. Projected reduction in hospital LOS and health-system costs were 514 days (9.18 days/person average) and $963456.72 ($17204.58/person average), respectively.

Conclusions

Prospective trials are needed to validate the use of these antibiotics for Gram-positive infections in practice, with the hope that they will reduce hospital LOS and the need for daily antibiotic infusions to provide alternative options for patients not qualifying for outpatient parenteral antimicrobial therapy.
Learning to detect and understand drug discontinuation events from clinical narratives
Authors: Liu Feifan , Pradhan Richeek , Druhl Emily , Freund Elaine , Liu Weisong , Sauer Brian C , Cunningham Fran , Gordon Adam J , Peters Celena B , Yu Hong
Published: March 2019

Objective

Identifying drug discontinuation (DDC) events and understanding their reasons are important for medication management and drug safety surveillance. Structured data resources are often incomplete and lack reason information. In this article, we assessed the ability of natural language processing (NLP) systems to unlock DDC information from clinical narratives automatically.

Materials and Methods

We collected 1867 de-identified providers’ notes from the University of Massachusetts Medical School hospital electronic health record system. Then 2 human experts chart reviewed those clinical notes to annotate DDC events and their reasons. Using the annotated data, we developed and evaluated NLP systems to automatically identify drug discontinuations and reasons at the sentence level using a novel semantic enrichment-based vector representation (SEVR) method for enhanced feature representation.

Results

Our SEVR-based NLP system achieved the best performance of 0.785 (AUC-ROC) for detecting discontinuation events and 0.745 (AUC-ROC) for identifying reasons when testing this highly imbalanced data, outperforming 2 state-of-the-art non–SEVR-based models. Compared with a rule-based baseline system for discontinuation detection, our system improved the sensitivity significantly (57.75% vs 18.31%, absolute value) while retaining a high specificity of 99.25%, leading to a significant improvement in AUC-ROC by 32.83% (absolute value).

Conclusion

Experiments have shown that a high-performance NLP system can be developed to automatically identify DDCs and their reasons from providers’ notes. The SEVR model effectively improved the system performance showing better generalization and robustness on unseen test data. Our work is an important step toward identifying reasons for drug discontinuation that will inform drug safety surveillance and pharmacovigilance.
Endocrine and Metabolic Diseases Among Colorectal Cancer Survivors in a Population-Based Cohort
Authors: Hawkins Makenzie L , Blackburn Brenna E , Rowe Kerry , Snyder John , Deshmukh Vikrant G , Newman Michael , Fraser Alison , Smith Ken , Herget Kimberly , Ganz Patricia A , Samadder N Jewel , Hashibe Mia
Published: March 2019

Background

There are an estimated 1.4 million colorectal cancer (CRC) survivors in the United States. Research on endocrine and metabolic diseases over the long term in CRC survivors is limited. Obesity is a risk factor for CRC; thus it is of interest to investigate diseases that may share this risk factor, such as diabetes, for long-term health outcomes among CRC survivors.

Methods

A total of 7114 CRC patients were identified from the Utah Population Database and matched to a general population cohort of 25 979 individuals on birth year, sex, and birth state. Disease diagnoses (assessed over three time periods of 1–5 years, 5–10 years, and >10 years) were identified using electronic medical records and statewide ambulatory and inpatient discharge data. Cox proportional hazard models were used to estimate the risk of endocrine and metabolic disease.

Results

Across all three time periods, risks for endocrine and metabolic diseases were statistically significantly greater for CRC survivors compared with the general population cohort. At 1–5 years postdiagnosis, CRC survivors’ risk for diabetes mellitus with complications was statistically significantly elevated (hazard ratio [HR] = 1.36, 99% confidence interval [CI] = 1.09 to 1.70). CRC survivors also experienced a 40% increased risk of obesity at 1–5 years postcancer diagnosis (HR= 1.40, 99% CI= 1.66 to 2.18) and a 50% increased risk at 5–10 years postdiagnosis (HR = 1.50, 99% CI= 1.16 to 1.95).

Conclusions

Endocrine and metabolic diseases were statistically significantly higher in CRC survivors throughout the follow-up periods of 1–5 years, 5–10 years, and more than 10 years postdiagnosis. As the number of CRC survivors increases, understanding the long-term trajectory is critical for improved survivorship care.
Meta-Analysis of Anxiety in Parents of Young People with Chronic Health Conditions
Authors: Pinquart Martin
Published: March 2019

Objective

Chronic health conditions are often associated with uncertainty and threats which may cause anxiety in the family members. The present meta-analysis analyzed whether parents of children with chronic physical diseases and/or sensory/physical disabilities show higher anxiety levels than parents of healthy/nondisabled children or test norms.

Methods

The databases PSYCINFO, MEDLINE, Google Scholar, CINAHL, and PSYNDEX were searched for relevant studies. In total, 486 studies were identified that fulfilled the inclusion criteria.

Results

We found moderate elevations of anxiety symptoms in parents of young people with chronic conditions (g = .54 standard deviation units). About 16% of the parents fulfilled the criteria for an anxiety disorder. Parents of young people with neuromuscular disorders, HIV-infection/AIDS, and cancer during active treatment showed large elevations of anxiety symptoms. Elevations of anxiety symptoms were smaller in the cases of longer lasting chronic conditions, longer time since the end of active treatment, in families of older children, in samples with lower percentages of mothers, and in studies from economically developed countries compared to less developed countries.

Conclusion

Measures for preventing and reducing anxiety symptoms in parents of young people with neuromuscular disorders, HIV-infection/AIDS, and those undergoing cancer treatments are particularly needed.