bluuebunny/crossref_metadata_2025 huggingface dataset:
Helminth infection reactivates latent γ-herpesvirus via cytokine competition at a viral promoter
Authors: Reese T. A. , Wakeman B. S. , Choi H. S. , Hufford M. M. , Huang S. C. , Zhang X. , Buck M. D. , Jezewski A. , Kambal A. , Liu C. Y. , Goel G. , Murray P. J. , Xavier R. J. , Kaplan M. H. , Renne R. , Speck S. H. , Artyomov M. N. , Pearce E. J. , Virgin H. W.
Published: June 2014

Parasites make it hard to fight viruses

Microbial co-infections challenge the immune system—different pathogens often require different flavors of immune responses for their elimination or containment (see the Perspective by Maizels and Gause). Two teams studied what happens when parasitic worms and viruses infect mice at the same time. Reese
et al.
found that parasite co-infection woke up a dormant virus. Osborne
et al.
found that mice already infected with parasitic worms were worse at fighting off viruses. In both cases, worms skewed the immune response so that the immune cells and the molecules they secreted created an environment favorable for the worm at the expense of antiviral immunity.

Science
, this issue p.
573
and p.
578
; see also p.
517
Genome Sequence of
Pseudomonas
sp. Strain P482, a Tomato Rhizosphere Isolate with Broad-Spectrum Antimicrobial Activity
Authors: Krzyzanowska Dorota M. , Ossowicki Adam , Jafra Sylwia
Published: June 2014

The tomato rhizosphere isolate
Pseudomonas
sp. strain P482 is a member of a diverse group of fluorescent pseudomonads. P482 produces a yet unidentified broad-spectrum antimicrobial compound(s), active
inter alia
(i.a.) against
Dickeya
spp. Here, we present a nearly complete genome of P482 obtained by a hybrid assembly of Illumina and PacBio sequencing data.
Full Genome Sequence of a Bovine Enterovirus Isolated in China
Authors: Peng Xiao-wei , Dong Hao , Wu Qing-min , Lu Yan-li
Published: June 2014

We report the full genome sequence of an isolate of bovine enterovirus type B from China. The virus (BEV-BJ001) was isolated from Beijing, China, from fecal swabs of cattle suffering from severe diarrhea. This genome sequence will give useful insight for future molecular epidemiological studies in China.
Two women with recurrent falls: La maladie des genoux bleus alias cryptogenic drop attacks
Authors: Butsch Raphael , Schneemann Markus
Published: June 2014

Two women, aged 79 and 56, reported recurrent falls for several years without any prodromes or residues, without any known features of either syncope or seizure, without any detectable causative condition and seemingly without revealing any pathognomonic signs in the clinical examination. In both cases, the falls occurred only while walking and without loss of consciousness. These falls resulted always in dropping forward with pouncing on the knees. There had never been an injury other than contusions of the knees. Indeed, inspection of the knees of one of these patients showed signs of contusion with erosions and scars of different ages, whereas on the whole body no other wounds or dermatological lesions could be detected. What could that be? Cryptogenic drop attacks—or in French and more descriptively: La maladie des genoux bleues!
Incidental central tear in Descemet membrane endothelial complex during Descemet membrane endothelial keratoplasty
Authors: Mittal Vikas , Mittal Ruchi , Jain Rajat , Sangwan Virender S
Published: June 2014

Descemet membrane endothelial keratoplasty (DMEK) was performed in a 70-year-old man diagnosed with pseudophakic bullous keratopathy. During Descemet endothelial complex (DEC) preparation, a central tear was noticed in the DMEK graft. However, the surgery was continued. On sixth postoperative day, a small fluid pocket was observed between the DEC and the posterior host stroma in inferior third of the graft area. It was, however, decided to observe it for spontaneous attachment. At 2 weeks, the inferior DEC detachment had increased with overlying corneal oedema. Descemetopexy with 100% air was performed the same day which reattached the DEC. Subsequently, DEC remained attached and at the last follow-up of 2 months, DEC was well opposed with a clear overlying cornea. The final best-corrected Snellen's visual acuity was 20/60. A small tear in the DEC does not necessitate tissue replacement and a good anatomical and visual outcome can be achieved in such cases.
Paranasal sinus metastasis of breast cancer
Authors: Pittoni P , Di Lascio S , Conti-Beltraminelli M , Valli MC , Espeli V , Bongiovanni M , Richetti A , Pagani O
Published: June 2014

A 76-year-old woman presented with symptoms suggestive of acute sinusitis. Previously, her breast carcinoma was treated with right lumpectomy, adjuvant chemotherapy and breast radiotherapy. She remained free from recurrence for the following 8 years. After initial treatment with antibiotics, the local symptom worsened with exophthalmos, eye blindness and development of an ulceration of the hard palate. MRI showed irregular enhancement of the nasal cavity extended to the maxillary sinus and ethmoidal lamina and concomitant infiltration of the orbit and skull base. A biopsy of the palatal ulcer showed a poorly differentiated adenocarcinoma and was compared with the histology of the primary breast tumour and it was concluded for the same morphology. After discussion at the multidisciplinary team, a specific chemotherapy has been activated with an initial local response. Further surgical resection was not thought appropriate and the patient has subsequently undergone palliative radiotherapy to the right paranasal lesions to improve local disease control.
Recruitment feasibility to a cohort study of endocrine and metabolic health among survivors of childhood brain tumours: a report from the Canadian study of Determinants of Endometabolic Health in ChIlDrEn (CanDECIDE)
Authors: Samaan M Constantine , Scheinemann Katrin , Burrow Sarah , Dillenburg Rejane F , Barr Ronald D , Wang Kuan-Wen , Valencia Marlie , Thabane Lehana
Published: June 2014

Objectives

The aim of this study was to test the feasibility of recruitment and performance of study procedures of the Canadian Study of Determinants of Endometabolic Health in ChIlDrEn (CanDECIDE) study, which was designed to assess the determinants of endocrine and metabolic health in survivors of childhood brain tumours.

Setting

A single paediatric tertiary care centre in Hamilton, Ontario, Canada.

Participants

We included boys and girls, aged 5 years and older, who were lean (body mass index (BMI) below 85th centile for age and gender) or overweight/obese (BMI 85th centile or above for age and gender). We excluded children on steroids or immunosuppressant therapy, smokers and those who had an active infection for the 2 weeks prior to participation.

Outcomes

Feasibility targets included recruitment rate of at least 50%, the consenting of 80% of participants to provide biological samples, 90% questionnaire completion rate and the ability to process biological samples from at least 80% of participants.

Results

We approached 210 potential participants, and of the 112 (53%) who agreed to participate, 30 (26.8%) completed the study visit over 7 months. All participants agreed to fast, provide biological samples and complete the questionnaires. Sample collection was successful in 97% (29/30) of participants and laboratory procedures were feasible in 100% of collected samples. We also tested resources required for the conduct of the full study including personnel, space, laboratory equipment and procedures and determined that they are all feasible.

Conclusions

Recruitment and consenting of patients for the CanDECIDE study may be feasible. However, we are considering prolonging recruitment duration and collaboration with other centres to meet recruitment targets due to lower than expected recruitment rate. Completion of questionnaires and implementation of sample processing protocols are feasible.
A cross-sectional comparison study on the iodine nutritional status between rural and urban residents in Zhejiang Province, China
Authors: Zou Yan , Lou Xiaoming , Ding Gangqiang , Mo Zhe , Zhu Wenming , Mao Guangming
Published: June 2014

Objectives

To evaluate the difference of iodine nutritional status between rural and urban residents under the universal salt iodisation policy.

Setting

A multistage cluster sampling technique was employed in the present cross-sectional study. In total, 3300 rural and 3300 urban households were selected where the investigation was conducted.

Participants

A total of 8553 rural and 8909 urban residents participated in this provincial survey.

Primary and secondary outcome measures

Spot urine samples were collected and the iodine concentration in urine was determined by the modified acid-digestion method.

Results

The median urinary iodine concentration of rural residents was 170.1 μg/L, which was higher than that of urban residents with 153.5 μg/L. For school-aged children, middle-aged people and older people, the median urinary iodine concentration of rural residents was 191.2, 160.2 and 154.0 μg/L, respectively, which was higher than that of urban residents with 166.2, 153.8 and 129.5 μg/L, respectively. Risk factors for urinary concentration of rural residents were age (OR=0.99), terrain (OR=0.83), usual intake of pickled products (OR=1.45) and non-iodised salt intake (OR=0.39), while those for urban residents were age (OR=0.99), terrain (OR=0.83), usual intake of aquatic products (OR=1.24) and non-iodised salt intake (OR=0.27) compared with iodised table salt intake.

Conclusions

The median urinary iodine concentration of rural residents was higher than that of urban residents although they were both falls in optimal iodine status as recommended by WHO/UNICEF/International Council for the Control of Iodine Deficiency Disorders. Iodised salt intake is the major factor which influences the iodine nutritional status mostly for rural and urban residents. The ongoing monitoring of population iodine status remains crucially important.
Discussing prognosis and end-of-life care in the final year of life: a randomised controlled trial of a nurse-led communication support programme for patients and caregivers
Authors: Walczak Adam , Butow Phyllis N , Clayton Josephine M , Tattersall Martin H N , Davidson Patricia M , Young Jane , Epstein Ronald M
Published: June 2014

Introduction

Timely communication about life expectancy and end-of-life care is crucial for ensuring good patient quality-of-life at the end of life and a good quality of death. This article describes the protocol for a multisite randomised controlled trial of a nurse-led communication support programme to facilitate patients’ and caregivers’ efforts to communicate about these issues with their healthcare team.

Methods and analysis

This NHMRC-sponsored trial is being conducted at medical oncology clinics located at/affiliated with major teaching hospitals in Sydney, Australia. Patients with advanced, incurable cancer and life expectancy of less than 12 months will participate together with their primary informal caregiver where possible. Guided by the self-determination theory of health-behaviour change, the communication support programme pairs a purpose-designed Question Prompt List (QPL—an evidence-based list of questions patients/caregivers can ask clinicians) with nurse-led exploration of QPL content, communication challenges, patient values and concerns and the value of early discussion of end-of-life issues. Oncologists are also cued to endorse patient and caregiver question asking and use of the QPL. Behavioural and self-report data will be collected from patients/caregivers approximately quarterly for up to 2.5 years or until patient death, after which patient medical records will be examined. Analyses will examine the impact of the intervention on patients’ and caregivers’ participation in medical consultations, their self-efficacy in medical encounters, quality-of-life, end-of-life care receipt and quality-of-death indicators.

Ethics and dissemination

Approvals have been granted by the human ethics review committee of Royal Prince Alfred Hospital and governance officers at each participating site. Results will be reported in peer-reviewed publications and conference presentations.

Trial registration number

Australian New Zealand Clinical Trials Registry ACTRN12610000724077.
Endoscopic management of peripancreatic fluid collections
Authors: Goyal Jatinder , Ramesh Jayapal
Published: June 2014

Peripancreatic fluid collections are a well-known complication of pancreatitis and can vary from fluid-filled collections to entirely necrotic collections. Although most of the fluid-filled pseudocysts tend to resolve spontaneously with conservative management, intervention is necessary in symptomatic patients. Open surgery has been the traditional treatment modality of choice though endoscopic, laparoscopic and transcutaneous techniques offer alternative drainage approaches. During the last decade, improvement in endoscopic ultrasound technology has enabled real-time access and drainage of fluid collections that were previously not amenable to blind transmural drainage. This has initiated a trend towards use of this modality for treatment of pseudocysts. In this review, we have summarised the existing evidence for endoscopic drainage of peripancreatic fluid collections from published studies.
Physical health and gender as risk factors for usage of services for mental illness
Authors: Matheson Flora I , Smith Katherine L W , Fazli Ghazal S , Moineddin Rahim , Dunn James R , Glazier Richard H
Published: June 2014

Background

People with comorbid mental and physical illness (PI) experience worse health, inadequate care and increased mortality relative to those without mental illness (MI). The role of gender in this relationship is not fully understood. This study examined gender differences in onset of mental health service usage among people with physical illness (COPD, asthma, hypertension and type II diabetes) compared with a control cohort.

Methods

We used a unique linked dataset consisting of the 2000–2001 Canadian Community Health Survey and medical records (n=17 050) to examine risk of onset of MI among those with and without PI among Ontario residents (18–74 years old) over a 10-year period (2002–2011). Adjusted COX proportional survival analysis was conducted.

Results

Unadjusted use of MI medical services in the PI cohort was 55.6% among women and 44.7% (p=0.0001) among men; among controls 48.1% of the women and 36.7% of the men used MI medical services (p=0.0001). The relative risk of usage among women in the PI group relative to controls was 1.16. Among men, the relative risk was 1.22. Women were 1.45 times more likely to use MI medical services relative to men (HR=1.45, CI 1.35 to 1.55). Respondents in the PI cohort were 1.32 times more likely to use MI medical services (HR=1.32, CI 1.23 to 1.42) relative to controls. Women in the PI cohort used MI medical services 6.4 months earlier than PI males (p=0.0059). In the adjusted model, women with PI were most likely to use MI medical services, followed by women controls, men with PI and men controls. There was no significant interaction between gender and PI cohort.

Conclusions

Further, gender-based research focusing on onset of usage of MI services among those with and without chronic health problems will enable better understanding of gender-based health disparities to improve healthcare quality, delivery and public health policy.
Persistent and occasional poverty and children's food consumption: evidence from a longitudinal Québec birth cohort
Authors: Kakinami Lisa , Gauvin Lise , Séguin Louise , Lambert Marie , Nikiema Béatrice , Paradis Gilles
Published: June 2014

Background

Childhood poverty is associated with poorer food consumption but longitudinal data are limited. The objective was to assess if food consumption differs depending on age (6, 7, 10 and 12 years) and pattern of poverty.

Methods

Participants were from the 1998–2010 ‘Quebec Longitudinal Study of Child Development’ birth cohort. Poverty was defined as income below the low-income thresholds established by Statistics Canada which adjusts for household size and geographic region. Multiple imputation was used for missing data, and latent class growth analysis identified poverty trajectories. Multivariable ordinal logistic regression assessed the association between poverty and greater consumption of milk, cheese, fruits, vegetables, sweets and sugar-sweetened beverages (SSB).

Results

Four poverty trajectories were identified: 1 reference category (stable non-poor) and 3 higher-risk categories (stable poor, increasing and decreasing risk). The probability of more frequent consumption was lower among children from stable poor households compared to children from stable non-poor households for fruit (6, 10 and 12 years), milk and vegetables (6, 7, 10 and 12 years) but was higher for SSB (10 and 12 years). Among children from increasing and decreasing poverty households compared to stable non-poor households, the probability of greater consumption of fruits and vegetables was lower and greater consumption of SSB was higher by the age of 12 years.

Conclusions

While experiencing continual exposure to poverty has detrimental effects on food consumption throughout childhood, the association for milk, fruits and vegetables does not differ across age. Intermittent exposure to poverty may also have long-lasting effects.
Population genetics and phylogenetic analysis of thevrs1nucleotide sequence in wild and cultivated barley
Authors: Ren Xifeng , Wang Yonggang , Yan Songxian , Sun Dongfa , Sun Genlou
Published: June 2014

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.
Low-energy positron scattering from gas-phase uracil
Authors: Franz Jan , Gianturco Franco A. , Baccarelli Isabella
Published: June 2014

Quantum scattering calculations are presented for the interaction of low energy positrons with the uracil molecule, an important component of biological systems. The rotational elastic and inelastic cross sections and vibrational inelastic cross sections are reported and compared with existing experiments, indicating a general trend of the cross sections different from the experimental findings and in line with what should be expected from the behavior of the total cross sections in similar polar targets. Some specific considerations can be drawn on the reliability of existing experiments, as to their size vis-à-vis to the computed integral cross sections over the same range of energies.
Futures and Option Contracts of the Supply Chain Influenced by e-Business Market
Authors: Dong Junfeng , Shi Ye , Liang Liang
Published: June 2014

We consider a supply chain consisting of a retailer and a supplier, which is influenced by e-business market. To control the uncertainty in demand, the retailer can purchase futures or options from the supplier. Futures or options can be exercised by the retailer to replenish inventory in the season. Moreover, redundant futures or options might be traded in the e-business market. The retailer's equilibrium ordering decision and the supplier's equilibrium pricing decision are analyzed under each kind of contracts. In addition, a comparison of futures and options is also presented and the conditions under which futures (or options) are superior are also identified. Our research shows that both the supplier and the retailer can be better off comparing with the newsvendor cases by using the two contracts. Furthermore, due to superior flexibility of the options, channel coordination can be achieved by using options. However, more cost needs to be paid to replenish by options, which may hurt the retailer. Hence, if the cost of replenishing by options is not overly high, the options are recommended to use; otherwise, the futures are recommended to choose.
FUZZY LOGIC AND NEURAL NETWORK BASED INDOOR FINGERPRINT POSITIONING ALGORITHMS IN WiFi
Authors: LI YIBO , LIU XITING
Published: June 2014

In this paper, a method that uses RBF-BP neural network to generate fingerprint database (FD) is proposed to improve the quality. The reference points in the database present regular tetrahedron distribution in three-dimensional space. To improve the accuracy of selecting which points are considered to locate currently and estimating their weights, two positioning algorithms based on signal strength difference values (SSDV) are proposed through analyzing the characteristic of difference values between mobile receiver and reference points. The first one is fuzzy logic algorithm (FLA). It uses different fuzzy logic models to calculate the weights of considered points. The second one is RBF-BP neural network algorithm (NNA). It uses different neural network models to estimate the spatial distances between mobile receiver and reference points. The points which have small sum of distances are considered. Their weights are calculated by a newly proposed method. The proposed algorithms use more than one weight to describe the distance to one considered point, which is more accurate. The test results demonstrate the improvement and effectiveness of proposed methods by comparing with other existing methods.
BINARY PSO AND ROUGH SET THEORY FOR FEATURE SELECTION: A MULTI-OBJECTIVE FILTER BASED APPROACH
Authors: XUE BING , CERVANTE LIAM , SHANG LIN , BROWNE WILL N. , ZHANG MENGJIE
Published: June 2014

Feature selection is a multi-objective problem, where the two main objectives are to maximize the classification accuracy and minimize the number of features. However, most of the existing algorithms belong to single objective, wrapper approaches. In this work, we investigate the use of binary particle swarm optimization (BPSO) and probabilistic rough set (PRS) for multi-objective feature selection. We use PRS to propose a new measure for the number of features based on which a new filter based single objective algorithm (PSOPRSE) is developed. Then a new filter-based multi-objective algorithm (MORSE) is proposed, which aims to maximize a measure for the classification performance and minimize the new measure for the number of features. MORSE is examined and compared with PSOPRSE, two existing PSO-based single objective algorithms, two traditional methods, and the only existing BPSO and PRS-based multi-objective algorithm (MORSN). Experiments have been conducted on six commonly used discrete datasets with a relative small number of features and six continuous datasets with a large number of features. The classification performance of the selected feature subsets are evaluated by three classification algorithms (decision trees, Naïve Bayes, and k-nearest neighbors). The results show that the proposed algorithms can automatically select a smaller number of features and achieve similar or better classification performance than using all features. PSOPRSE achieves better performance than the other two PSO-based single objective algorithms and the two traditional methods. MORSN and MORSE outperform all these five single objective algorithms in terms of both the classification performance and the number of features. MORSE achieves better classification performance than MORSN. These filter algorithms are general to the three different classification algorithms.
ARTIFICIAL BEE COLONY ALGORITHM WITH IMPROVED EXPLORATIONS: A NOVEL APPROACH FOR NUMERICAL OPTIMIZATION
Authors: ALAM MD. SHAFIUL , ISLAM MD. MONIRUL , MURASE KAZUYUKI
Published: June 2014

The Artificial Bee Colony (ABC) algorithm is a recently introduced swarm intelligence algorithm that has been successfully applied on numerous and diverse optimization problems. However, one major problem with ABC is its premature convergence to local optima, which often originates from its insufficient degree of explorative search capability. This paper introduces ABC with Improved Explorations (ABC-IX), a novel algorithm that modifies both the selection and perturbation operations of the basic ABC algorithm in an explorative way. First, an explorative selection scheme based on simulated annealing allows ABC-IX to probabilistically accept both better and worse candidate solutions, whereas the basic ABC can accept better solutions only. Second, a self-adaptive strategy enables ABC-IX to automatically adapt the perturbation rate, separately for each candidate solution, to customize the degree of explorations and exploitations around it. ABC-IX is evaluated on several benchmark numerical optimization problems and results are compared with a number of state-of-the-art evolutionary and swarm intelligence algorithms. Results show that ABC-IX often performs better optimization than most other algorithms in comparison on most of the problems.
Anthropology and Voice
Authors: Weidman Amanda
Published: June 2014

Voice is both a set of sonic, material, and literary practices shaped by culturally and historically specific moments and a category invoked in discourse about personal agency, communication and representation, and political power. This review focuses on scholarship produced since the 1990s in a variety of fields, addressing the status of the voice within Euro-Western modernity, voice as sound and embodied practice, technological mediation, and voicing. It then turns to the ways in which anthropology and related fields have framed the relationship between voice and identity, status, subjectivity, and publics. The review suggests that attending to voice in its multiple registers gives particular insight into the intimate, affective, and material/embodied dimensions of cultural life and sociopolitical identity. Questions of voice are implicated in many issues of concern to contemporary anthropology and can lend theoretical acuity to broader concepts of more general concern to social theory as well.
Physical Models of Plant Development
Authors: Ali Olivier , Mirabet Vincent , Godin Christophe , Traas Jan
Published: June 2014

The definition of shape in multicellular organisms is a major issue of developmental biology. It is well established that morphogenesis relies on genetic regulation. However, cells, tissues, and organism behaviors are also bound by the laws of physics, which limit the range of possible deformations organisms can undergo but also define what organisms must do to achieve specific shapes. Besides experiments, theoretical models and numerical simulations of growing tissues are powerful tools to investigate the link between genetic regulation and mechanics. Here, we provide an overview of the main mechanical models of plant morphogenesis developed so far, from subcellular scales to whole tissues. The common concepts and discrepancies between the various models are discussed.
Discrete Element Method Simulations for Complex Granular Flows
Authors: Guo Yu , Curtis Jennifer Sinclair
Published: June 2014

This review article focuses on the modeling of complex granular flows employing the discrete element method (DEM) approach. The specific topic discussed is the application of DEM models for the study of the flow behavior of nonspherical, flexible, or cohesive particles, including particle breakage. The major sources of particle cohesion—liquid induced, electrostatics, van der Waals forces—and their implementation into DEM simulations are covered. These aspects of particle flow are of great importance in practical applications and hence are the significant foci of research at the forefront of current DEM modeling efforts. For example, DEM simulations of nonspherical grains can provide particle stress information needed to develop constitutive models for continuum-based simulations of large-scale industrial processes.
Determinants of Mutation Rate Variation in the Human Germline
Authors: Ségurel Laure , Wyman Minyoung J. , Przeworski Molly
Published: June 2014

Because germline mutations are the source of all evolutionary adaptations and heritable diseases, characterizing their properties and the rate at which they arise across individuals is of fundamental importance for human genetics. After decades during which estimates were based on indirect approaches, notably on inferences from evolutionary patterns, it is now feasible to count de novo mutations in transmissions from parents to offspring. Surprisingly, this direct approach yields a mutation rate that is twofold lower than previous estimates, calling into question our understanding of the chronology of human evolution and raising the possibility that mutation rates have evolved relatively rapidly. Here, we bring together insights from studies of human genetics and molecular evolution, focusing on where they conflict and what the discrepancies tell us about important open questions. We begin by outlining various methods for studying the properties of mutations in humans. We review what we have learned from their applications about genomic factors that influence mutation rates and the effects of sex, age, and other sources of interindividual variation. We then consider the mutation rate as a product of evolution and discuss how and why it may have changed over time in primates.
The Tiniest Tiny Genomes
Authors: Moran Nancy A. , Bennett Gordon M.
Published: June 2014

Starting in 2006, surprisingly tiny genomes have been discovered from numerous bacterial symbionts of insect hosts. Despite their size, each retains some genes that enable provisioning of limiting nutrients or other capabilities required by hosts. Genome sequence analyses show that genome reduction is an ongoing process, resulting in a continuum of sizes, with the smallest genome currently known at 112 kilobases. Genome reduction is typical in host-restricted symbionts and pathogens, but the tiniest genomes are restricted to symbionts required by hosts and restricted to specialized host cells, resulting from long coevolution with hosts. Genes are lost in all functional categories, but core genes for central informational processes, including genes encoding ribosomal proteins, are mostly retained, whereas genes underlying production of cell envelope components are especially depleted. Thus, these entities retain cell-like properties but are heavily dependent on coadaptation of hosts, which continuously evolve to support the symbionts upon which they depend.
Friend Turned Foe: Evolution of Enterococcal Virulence and Antibiotic Resistance
Authors: Van Tyne Daria , Gilmore Michael S.
Published: June 2014

The enterococci are an ancient genus that evolved along with the tree of life. These intrinsically rugged bacteria are highly adapted members of the intestinal consortia of a range of hosts that spans the animal kingdom. Enterococci are also leading opportunistic hospital pathogens, causing infections that are often resistant to treatment with most antibiotics. Despite the importance of enterococci as hospital pathogens, the vast majority live outside of humans, and nearly all of their evolutionary history took place before the appearance of modern humans. Because hospital infections represent evolutionary end points, traits that exacerbate human infection are unlikely to have evolved for that purpose. However, clusters of traits have converged in specific lineages that are well adapted to colonize the antibiotic-perturbed gastrointestinal tracts of patients and that thrive in the hospital environment. Here we discuss these traits in an evolutionary context, as well as how comparative genomics is providing new insights into the evolution of the enterococci.
Recombination Promoted by DNA Viruses: Phage λ to Herpes Simplex Virus
Authors: Weller Sandra K. , Sawitzke James A.
Published: June 2014

The purpose of this review is to explore recombination strategies in DNA viruses. Homologous recombination is a universal genetic process that plays multiple roles in the biology of all organisms, including viruses. Recombination and DNA replication are interconnected, with recombination being essential for repairing DNA damage and supporting replication of the viral genome. Recombination also creates genetic diversity, and viral recombination mechanisms have important implications for understanding viral origins as well as the dynamic nature of viral-host interactions. Both bacteriophage λ and herpes simplex virus (HSV) display high rates of recombination, both utilizing their own proteins and commandeering cellular proteins to promote recombination reactions. We focus primarily on λ and HSV, as they have proven amenable to both genetic and biochemical analysis and have recently been shown to exhibit some surprising similarities that will guide future studies.
Effects of Antibiotics on Human Microbiota and Subsequent Disease
Authors: Keeney Kristie M. , Yurist-Doutsch Sophie , Arrieta Marie-Claire , Finlay B. Brett
Published: June 2014

Although antibiotics have significantly improved human health and life expectancy, their disruption of the existing microbiota has been linked to significant side effects such as antibiotic-associated diarrhea, pseudomembranous colitis, and increased susceptibility to subsequent disease. By using antibiotics to break colonization resistance against Clostridium, Salmonella, and Citrobacter species, researchers are now exploring mechanisms for microbiota-mediated modulation against pathogenic infection, revealing potential roles for different phyla and family members as well as microbiota-liberated sugars, hormones, and short-chain fatty acids in regulating pathogenicity. Furthermore, connections are now being made between microbiota dysbiosis and a variety of different diseases such as rheumatoid arthritis, inflammatory bowel disease, type 1 diabetes, atopy, and obesity. Future advances in the rapidly developing field of microbial bioinformatics will enable researchers to further characterize the mechanisms of microbiota modulation of disease and potentially identify novel therapeutics against disease.
Fungal Membrane Organization: The Eisosome Concept
Authors: Douglas Lois M. , Konopka James B.
Published: June 2014

The fungal plasma membrane is organized into specialized domains that vary in size, stability, and composition. Membrane compartment of Can1(MCC)/eisosome domains that were recently discovered in the budding yeast Saccharomyces cerevisiae are interesting because they represent a novel type of membrane domain that is important for plasma membrane organization, sphingolipid homeostasis, and cell wall morphogenesis. The MCC portion was identified as stable punctate patches that correspond to furrows in the plasma membrane that are about 300 nm long and 50 nm deep. These domains contain integral membrane proteins, including the tetraspan proteins Sur7 and Nce102. The eisosome portion includes proteins peripherally associated with the cytoplasmic side of the MCC, including the Bin/amphiphysin/Rvs-domain proteins Pil1 and Lsp1, which assemble into filaments that curve the membrane to form the furrows. By comparing MCC/eisosome domains in diverse fungi, researchers are identifying common features that further our understanding of their unique biogenesis, structure, and function.
Regulation of Virulence ofEntamoeba histolytica
Authors: Marie Chelsea , Petri William A.
Published: June 2014

Entamoeba histolytica is the third-leading cause of parasitic mortality globally. E. histolytica infection generally does not cause symptoms, but the parasite has potent pathogenic potential. The origins, benefits, and triggers of amoebic virulence are complex. Amoebic pathogenesis entails depletion of the host mucosal barrier, adherence to the colonic lumen, cytotoxicity, and invasion of the colonic epithelium. Parasite damage results in colitis and, in some cases, disseminated disease. Both host and parasite genotypes influence the development of disease, as do the regulatory responses they govern at the host-pathogen interface. Host environmental factors determine parasite transmission and shape the colonic microenvironment E. histolytica infects. Here we highlight research that illuminates novel links between host, parasite, and environmental factors in the regulation of E. histolytica virulence.
Biomass Utilization by Gut Microbiomes
Authors: White Bryan A. , Lamed Raphael , Bayer Edward A. , Flint Harry J.
Published: June 2014

Mammals rely entirely on symbiotic microorganisms within their digestive tract to gain energy from plant biomass that is resistant to mammalian digestive enzymes. Especially in herbivorous animals, specialized organs (the rumen, cecum, and colon) have evolved that allow highly efficient fermentation of ingested plant biomass by complex anaerobic microbial communities. We consider here the two most intensively studied, representative gut microbial communities involved in degradation of plant fiber: those of the rumen and the human large intestine. These communities are dominated by bacteria belonging to the Firmicutes and Bacteroidetes phyla. In Firmicutes, degradative capacity is largely restricted to the cell surface and involves elaborate cellulosome complexes in specialized cellulolytic species. By contrast, in the Bacteroidetes, utilization of soluble polysaccharides, encoded by gene clusters (PULs), entails outer membrane binding proteins, and degradation is largely periplasmic or intracellular. Biomass degradation involves complex interplay between these distinct groups of bacteria as well as (in the rumen) eukaryotic microorganisms.
Bacterial Type III Secretion Systems: Specialized Nanomachines for Protein Delivery into Target Cells
Authors: Galán Jorge E. , Lara-Tejero Maria , Marlovits Thomas C. , Wagner Samuel
Published: June 2014

One of the most exciting developments in the field of bacterial pathogenesis in recent years is the discovery that many pathogens utilize complex nanomachines to deliver bacterially encoded effector proteins into target eukaryotic cells. These effector proteins modulate a variety of cellular functions for the pathogen's benefit. One of these protein-delivery machines is the type III secretion system (T3SS). T3SSs are widespread in nature and are encoded not only by bacteria pathogenic to vertebrates or plants but also by bacteria that are symbiotic to plants or insects. A central component of T3SSs is the needle complex, a supramolecular structure that mediates the passage of the secreted proteins across the bacterial envelope. Working in conjunction with several cytoplasmic components, the needle complex engages specific substrates in sequential order, moves them across the bacterial envelope, and ultimately delivers them into eukaryotic cells. The central role of T3SSs in pathogenesis makes them great targets for novel antimicrobial strategies.
Generating Human Neurons In Vitro and Using Them to Understand Neuropsychiatric Disease
Authors: Paşca Sergiu P. , Panagiotakos Georgia , Dolmetsch Ricardo E.
Published: June 2014

Recent advances in cell reprogramming enable investigators to generate pluripotent stem cells from somatic cells. These induced pluripotent cells can subsequently be differentiated into any cell type, making it possible for the first time to obtain functional human neurons in the lab from control subjects and patients with psychiatric disorders. In this review, we survey the progress made in generating various neuronal subtypes in vitro, with special emphasis on the characterization of these neurons and the identification of unique features of human brain development in a dish. We also discuss efforts to uncover neuronal phenotypes from patients with psychiatric disease and prospects for the use of this platform for drug development.
Chemogenetic Tools to Interrogate Brain Functions
Authors: Sternson Scott M. , Roth Bryan L.
Published: June 2014

Elucidating the roles of neuronal cell types for physiology and behavior is essential for understanding brain functions. Perturbation of neuron electrical activity can be used to probe the causal relationship between neuronal cell types and behavior. New genetically encoded neuron perturbation tools have been developed for remotely controlling neuron function using small molecules that activate engineered receptors that can be targeted to cell types using genetic methods. Here we describe recent progress for approaches using genetically engineered receptors that selectively interact with small molecules. Called “chemogenetics,” receptors with diverse cellular functions have been developed that facilitate the selective pharmacological control over a diverse range of cell-signaling processes, including electrical activity, for molecularly defined cell types. These tools have revealed remarkably specific behavioral physiological influences for molecularly defined cell types that are often intermingled with populations having different or even opposite functions.
IceCube
Authors: Gaisser Thomas , Halzen Francis
Published: June 2014

IceCube is the first kilometer-scale neutrino detector. Built primarily for neutrino astronomy, it has recently discovered events with energies above 100 TeV that are likely to be from distant sources beyond the solar system. Among the events are three with deposited energies of more than 1 PeV, the highest-energy neutrinos ever detected. We review the astrophysical arguments that motivate such a large detector, and we describe how it works and how the high-energy events are reconstructed and identified above the background of atmospheric neutrinos. We also describe the broad range of neutrino physics and particle astrophysics topics addressed by IceCube, as well as its potential for the future.
A Life in High-Energy Physics: Success Beyond Expectations
Authors: Cronin James W.
Published: June 2014

The author describes in some technical detail his career in experimental particle physics. It began in 1955, when he joined Brookhaven National Laboratory, and ended in 1985, when he moved to the field of cosmic-ray physics. The author discusses not only his successes but also his failures and his bad judgments. This period was the golden age of particle physics, when the experimental possibilities were abundant and one could carry out experiments with a small team of colleagues and students.
Localizing Viruses in Their Insect Vectors
Authors: Blanc Stéphane , Drucker Martin , Uzest Marilyne
Published: June 2014

The mechanisms and impacts of the transmission of plant viruses by insect vectors have been studied for more than a century. The virus route within the insect vector is amply documented in many cases, but the identity, the biochemical properties, and the structure of the actual molecules (or molecule domains) ensuring compatibility between them remain obscure. Increased efforts are required both to identify receptors of plant viruses at various sites in the vector body and to design competing compounds capable of hindering transmission. Recent trends in the field are opening questions on the diversity and sophistication of viral adaptations that optimize transmission, from the manipulation of plants and vectors ultimately increasing the chances of acquisition and inoculation, to specific “sensing” of the vector by the virus while still in the host plant and the subsequent transition to a transmission-enhanced state.
Networks and Plant Disease Management: Concepts and Applications
Authors: Shaw M.W. , Pautasso M.
Published: June 2014

A network is a natural structure with which to describe many aspects of a plant pathosystem. The article seeks to set out in a nonmathematical way some of the network concepts that promise to be useful in managing plant disease. The field has been stimulated by developments designed to help understand and manage animal and human disease, and by technical infrastructures, such as the internet. It overlaps partly with landscape ecology. The study of networks has helped identify likely ways to reduce the flow of disease in traded plants, to find the best sites to monitor as warning sites for annually reinvading diseases, and to understand the fundamentals of how a pathogen spreads in different structures. A tension between the free flow of goods or species down communication channels and free flow of pathogens down the same pathways is highlighted.
Payment for Ecosystem Services from Forests
Authors: Alix-Garcia Jennifer , Wolff Hendrik
Published: June 2014

Every year from 2000 to 2010, our planet lost native forests roughly the size of Costa Rica ( FAO 2010 ). This rapid deforestation has dramatically changed the chemical composition of the world’s atmosphere, the level of biodiversity, and the presence of vegetation key to maintaining watershed function and preventing landslides. There has been a boom in the design of local and international policy instruments to prevent further deforestation and to encourage forest growth. This article reviews the theory and evidence surrounding forest-related payment for ecosystem services (PES) schemes intended to slow and reverse deforestation. We cover the most recent work touching on a range of issues related to PES programs, including research on targeting, contract design, environmental effectiveness, challenges to program implementation, spillovers, and distributional considerations of conditional cash transfers. We also highlight areas of potential future research.
Immigrants and African Americans
Authors: Waters Mary C. , Kasinitz Philip , Asad Asad L.
Published: June 2014

We examine how recent immigration to the United States has affected African Americans. We first review the research on the growing diversity within the black population, driven largely by the presence of black immigrants from the Caribbean and Africa. As their children and grandchildren come of age, relations between immigrants and African Americans are complicated by the fact that a growing portion of the African American community has origins in both groups. We then review literature on both new destinations and established gateway cities to illustrate the patterns of cooperation, competition, and avoidance between immigrants of diverse races and African Americans in neighborhoods, the labor market, and politics. We explore the implications of the population's increasing racial diversity owing to immigration for policies that aim to promote racial equality but that are framed in terms of diversity. We conclude with suggestions for new areas of research.