bluuebunny/crossref_metadata_2025 huggingface dataset:
Hepatitis C virus infection: opportunities for an earlier detection in primary care
Authors: Lapi Francesco , Capogrosso Sansone Alice , Mantarro Stefania , Simonetti Monica , Tuccori Marco , Blandizzi Corrado , Rossi Alessandro , Corti Giampaolo , Bartoloni Alessandro , Bellia Alfonso , Baiocchi Leonardo , Cricelli Iacopo , Cricelli Claudio
Published: November 2016

Background/aim

In the era of direct-acting antiviral medications, which can cure the hepatitis C virus (HCV) infection, the actual epidemiology of this condition in the general population is still unclear. We therefore aimed to estimate the prevalence rate of HCV and assess the determinants for incident cases of HCV in primary care in Italy.

Methods

We identified outpatients aged at least 15 years registered in the Italian Health Search IMS Health Longitudinal Patient Database from 1 January 2002 to 30 June 2013. The annual trend of HCV prevalence was estimated. The candidate determinants for the risk of incident HCV infection included geographical area of residence, sex, age, infections by the HIV, hepatitis B virus (HBV), or other forms of hepatitis, and abuse of illicit substances or drugs.

Results

The eligible cohort included 826 300 patients (53.5% women, mean age 48.1±19.1 years). The prevalence rate of HCV increased over the 11-year study period, ranging from 0.24 to 0.50%, with a small increase in men versus women. Patients aged more than 24 years had a higher risk than those aged 14–24 years, with up to a five-fold increase among patients aged 65–74 years. Being resident of Southern/Islands Italy, concurrent diagnosis HBV or HIV, and drug or illicit substance abuse were significant determinants for HCV infection.

Conclusion

Our study shows that the prevalence of HCV in Italy has doubled over the last decade. Patients with certain demographics and clinical characteristics are more prone to be infected by HCV. In this scenario, general practitioners may play a crucial role in screening, early identification, and therapy of high-risk patients.
Neonatal nonimmune hemolytic anemia
Authors: Yaish Hassan M. , Christensen Robert D. , Lemons Richard S.
Published: November 2016

Purpose of review

As in adults and older children, anemia in newborn infants can be the result of erythropoietic failure, hemorrhage, or hemolysis. When hemolysis is the prime consideration, it can be challenging for physicians caring for neonates to choose from the wide variety of available diagnostic tests. This review describes the authors’ opinions regarding rational, consistent, and cost-effective means of making an exact diagnosis of a neonatal hemolytic condition.

Recent findings

Two recent advances in the diagnosis of neonatal nonimmune hemolytic disorders are highlighted in this review: introduction of flow cytometry-based Eosin-5-maleimide (EMA) uptake as a screening test to identify RBC membrane defects and next-generation sequencing (NGS)-based panels to uncover exact mutations causing hemolysis.

The availability of newer tools such as EMA and NGS to diagnose specific hemolytic conditions, which might otherwise remain unknown, enables neonatal practitioners not only to identify the exact cause of hemolysis but also to discover novel mutations that can be implicated in the cause of neonatal hemolytic processes.
Telephone Follow-Up by Nurse After Total Knee Arthroplasty
Authors: Szöts Kirsten , Konradsen Hanne , Solgaard Søren , Østergaard Birte
Published: November 2016

BACKGROUND/PURPOSE:

Because of shorter hospitalizations, patients now have to take responsibility for their recovery period at a very early stage. We evaluated the effects of structured, nurse-managed telephone follow-up (TFU) after discharge from the hospital following total knee arthroplasty (TKA).

METHOD/DESIGN:

The design was a single-center, unblinded, parallel-group randomized clinical trial. The primary outcome was self-reported physical function according to the Western Ontario and McMaster Universities Osteoarthritis (WOMAC) Index. Secondary outcomes were stiffness and pain according to the WOMAC Index; health-related quality of life, measured with the Medical Outcomes Study Short Form (SF-36); general self-efficacy, measured with the General Self-Efficacy Scale; and number of acute visits to the orthopaedic outpatient clinic. In total, 117 patients were randomized to 2 groups: an intervention group receiving TFU 4 and 14 days after discharge in addition to conventional treatment, and a control group receiving conventional treatment. The TFUs were structured by key subjects for health status, as defined by the VIPS model (the Swedish acronym for the concepts of Well-being, Integrity, Prevention, and Safety). The effect was measured 1 and 3 months postsurgery.

RESULTS:

No significant effects on physical function in the disease-specific WOMAC Index were identified. However, significant differences in scores were identified in favor of the intervention group on general self-efficacy (p = .014) and physical function (p = .031), measured with the Medical Outcomes Study Short Form 1 month after TKA, but this effect was not seen at 3 months. A positive improvement in several dimensions of health status and health-related quality of life was identified in favor of the intervention group, but patients who had TFU had more unscheduled visits to the outpatient clinic.

CONCLUSIONS:

Telephone follow-up did not improve physical function compared with conventional treatment, as measured with the WOMAC Index. A short-term effect was identified, improving general self-efficacy and physical function as dimensions of health-related quality of life.
Healthcare Access and PrEP Continuation in San Francisco and Miami After the US PrEP Demo Project
Authors: Doblecki-Lewis Susanne , Liu Albert , Feaster Daniel , Cohen Stephanie E. , Cardenas Gabriel , Bacon Oliver , Andrew Erin , Kolber Michael A.
Published: November 2016

Background:

Pre-exposure prophylaxis (PrEP) for prevention of HIV infection has demonstrated efficacy in randomized controlled trials and in demonstration projects. For PrEP implementation to result in significant reductions in HIV incidence for men who have sex with men in the United States, sufficient access to PrEP care and continued engagement outside of demonstration projects is required.

Methods:

We report the results of a follow-up survey of 173 former participants from the Miami and San Francisco sites of the US PrEP Demo Project, administered 4–6 months after study completion.

Results:

Survey respondents continued to frequently access medical care and had a high incidence of sexually transmitted infections after completion of the Demo Project, indicating ongoing sexual risk behavior. Interest in continuing PrEP was high with 70.8% indicating that they were “very interested” in continuing PrEP. Among respondents, 39.9% reported continuation of PrEP after completion of the Demo Project, largely through their primary care providers and frequently at low or no cost. Variability in access and engagement was seen, with participants from the San Francisco site, those with medical insurance, and those with a primary care provider at the end of the Demo Project more likely to successfully obtain PrEP medication. Two respondents reported HIV seroconversion in the period between study completion and the follow-up survey.

Conclusions:

Additional effort to increase equitable access to PrEP outside of demonstration projects is needed to realize the potential impact of this evidence-based prevention intervention.
Brief Report: Psychosocial Predictors of Engagement in Sexual Risk Behavior Among Trans*female Youth Aged 16–24 Years in San Francisco
Authors: Turner Caitlin M. , Santos Glenn-Milo , Arayasirikul Sean , Wilson Erin C.
Published: November 2016

Background:

Trans*female youth (TFY) carry a disproportionate burden of HIV. Few longitudinal studies have analyzed both proximal and upstream predictors of changes in HIV-related risk behaviors for TFY. The aim of the present analysis was to identify psychosocial predictors of changes in sexual risk behavior over time for TFY in the San Francisco Bay Area.

Methods:

Data come from the SHINE cohort study conducted at the San Francisco Department of Public Health from 2012 to 2014 (n = 263). The relationship between hypothesized psychosocial factors and changes in engagement in condomless receptive anal intercourse over 12-month follow-up was modeled using generalized estimating equations, after adjusting for participant age, race/ethnicity, and education level.

Results:

TFY who were ever in a serious relationship since identifying as trans* [adjusted odds ratio (aOR) = 1.89, 95% confidence interval (CI): 1.16 to 3.08], those who reported recent crack/cocaine use (aOR = 2.01, 95% CI: 1.05 to 3.85), and those with a monthly income of more than $500 (aOR = 0.55, 95% CI: 0.35 to 0.85) had significantly higher odds of condomless receptive anal intercourse over the 12-month study period compared to TFY without these exposures. Those who reported high exposure to gender-based discrimination had increased adjusted odds of engagement in condomless receptive anal intercourse compared to those who had low exposure over the study period (aOR = 1.70, 95% CI: 1.10 to 2.63).

Conclusions:

Both proximal and structural factors predicted increased engagement in sexual risk behavior among TFY. Results demonstrate the need for a multilevel approach to HIV prevention strategies for this population.
Complementary Feeding and Diarrhea and Respiratory Infection Among HIV-Exposed Tanzanian Infants
Authors: Kamenju Pili , Liu Enju , Hertzmark Ellen , Spiegelman Donna , Kisenge Rodrick R. , Kupka Roland , Aboud Said , Manji Karim , Duggan Christopher , Fawzi Wafaie W.
Published: November 2016

Objective:

To examine the association between complementary feeding and risks of diarrhea and acute respiratory infection (ARI) among HIV-exposed infants aged 6–24 months.

Design:

We prospectively used an Infant and Child Feeding Index (ICFI) to measure complementary feeding practices (breastfeeding status, food consistency, dietary diversity, food group frequency, and meal frequency). We determined the association of ICFI and each of its components with the risk of diarrhea and ARI. Generalized estimating equations were used to estimate the relative risks for morbidity episodes.

Setting:

Dar es Salaam, Tanzania.

Subjects:

A total of 2092 HIV-exposed infants followed from 6 months of age to 24 months of age.

Results:

The ICFI score ranged from 0 to 9; the median score was 6 (interquartile range = 4–7). Low ICFI scores were likely associated with increased risk of dysentery [low vs. high tertile risk ratio (RR): 1.40; 95% confidence interval (CI): 0.93 to 2.10; P for trend = 0.02] and respiratory infection (low vs. high tertile RR: 1.16; 95% CI: 0.96 to 1.41; P for trend = 0.01). Low dietary diversity scores were likely associated with higher risk of dysentery (low vs. high tertile RR: 1.47; 95% CI: 0.92 to 2.35; P for trend = 0.03) and respiratory infection (low vs. high tertile RR: 1.41; 95% CI: 1.13 to 1.76; P for trend = 0.01). Low food consistency scores were associated with higher risk of respiratory infection (RR: 1.77; 95% CI: 1.40 to 2.26; P < 0.01).

Conclusions:

In this setting, low ICFI, dietary diversity, and food consistency scores were likely associated with increased risk of diarrhea and ARI among HIV-exposed infants.
Violence From a Sexual Partner is Significantly Associated With Poor HIV Care and Treatment Outcomes Among Female Sex Workers in the Dominican Republic
Authors: Mendoza Carlisdania , Barrington Clare , Donastorg Yeycy , Perez Martha , Fleming Paul J. , Decker Michele R. , Kerrigan Deanna
Published: November 2016

Background:

Female sex workers (FSWs) experience high rates of violence from their sexual partners. Although violence is associated with HIV risk behaviors among FSWs, there is limited evidence on the association between violence and HIV treatment outcomes.

Methods:

We analyzed data from a socio-behavioral survey with a cohort of FSWs living with HIV in the Dominican Republic (n = 268) to describe the burden of violence from a sexual partner in the last 6 months. We assessed the relationship between violence and HIV treatment outcomes, comparing findings across 2 types of sexual partners: intimate partners and clients.

Results:

Nearly one-fifth of women (18.3%) experienced violence in the last 6 months. More women experienced violence from an intimate partner (12.3%) than a client (8.3%), with some (2.6%) reporting both. Although violence from an intimate partner was significantly associated with not currently being on antiretroviral treatment [ART; adjusted odds ratio (AOR): 4.05, 95% confidence interval (CI): 1.00 to 16.36] and missing an ART dose in the last 4 days (AOR: 5.26, 95% CI: 1.91 to 14.53), violence from a client was associated with never having received HIV care (AOR: 2.85, 95% CI: 1.03 to 7.92) and ever interrupting ART (AOR: 5.45, 95% CI: 1.50 to 19.75).

Conclusions:

Violence from a sexual partner is associated with poor HIV treatment outcomes among FSWs. Different patterns by type of partner reflect how relationship dynamics may influence these associations. Violence prevention and support services should be tailored based on type of partner. Violence screening and referrals should be integrated into HIV care services for FSWs to improve their health and reduce ongoing transmission.
Role of APOE ε4 Allele and Incident Stroke on Cognitive Decline and Mortality
Authors: Rajan Kumar B. , Aggarwal Neelum T. , Schneider Julie A. , Wilson Robert S. , Everson-Rose Susan A. , Evans Denis A.
Published: November 2016

Background:

The apolipoprotein E (APOE) ε4 allele and stroke increase the risk of cognitive decline. However, the association of the APOE ε4 allele before and after stroke is not well understood.

Methods:

Using a prospective sample of 3444 (66% African Americans, 61% females, mean age=71.9 y) participants, we examined cognitive decline relative to stroke among those with and without the APOE ε4 allele.

Results:

In our sample, 505 (15%) had incident stroke. Among participants without stroke, the ε4 allele was associated with increased cognitive decline compared to noncarriers (0.080 vs. 0.036 units/year; P<0.0001). Among participants without the ε4 allele, cognitive decline increased significantly after stroke compared to before stroke (0.115 vs. 0.039 units/year; P<0.0001). Interestingly, cognitive decline before and after stroke was not significantly different among those with the ε4 allele (0.091 vs. 0.102 units/year; P=0.32). Poor cognitive function was associated with higher risk of stroke (hazard ratio=1.41, 95% confidence interval, 1.25-1.58), but the APOE ε4 allele was not (P=0.66). The APOE ε4 allele, cognitive function, and incident stroke were associated with mortality.

Conclusions:

The association of stroke with cognitive decline appears to differ by the presence of the APOE ε4 allele, but no such interaction was observed for mortality.
Mechanical tuning of mammalian sperm behaviour by hyperactivation, rheology and substrate adhesion: a numerical exploration
Authors: Ishimoto Kenta , Gaffney Eamonn A.
Published: November 2016

The great mammalian sperm race encounters numerous microenvironments to which sperm must adapt and a fundamental sperm response is the change in its waveform owing to both fluid rheology and capacitation, with the latter associated with a hyperactivated beat pattern. Hence, in this modelling study, we examine the effect of different flagellar waveforms for sperm behaviour near adhesive substrates, which are representative of epithelia in female tract sperm reservoirs and the zona pellucida (ZP), which surrounds the mammalian egg. On contact with an adhesive surface, virtual sperm rotate to become nearly tangential with the surface, as generally observed. Hyperactivation also induces many effects: sperm exert greater forces on the substrate and periodically tug way from adhesions under circumstances reflecting binding at sperm reservoirs, but with extensive fluid elasticity, as found in the cumulus surrounding the ZP, sperm instead continually push into the substrate. Furthermore, with weak adhesion, rheological media increase the duration hyperactivated sperm remain in the proximity of a substrate. More generally, such results predict that changes owing to both hyperactivation of the flagellar waveform and the rheology of the surrounding medium provide a means of tuning sperm behaviour near, or attached to, adhesive substrates.
SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells
Authors: Benabdallah Nezha S. , Gautier Philippe , Hekimoglu-Balkan Betul , Lettice Laura A. , Bhatia Shipra , Bickmore Wendy A.
Published: November 2016

The expression of genes with key roles in development is under very tight spatial and temporal control, mediated by enhancers. A classic example of this is the sonic hedgehog gene (Shh), which plays a pivotal role in the proliferation, differentiation and survival of neural progenitor cells bothin vivoandin vitro. Shhexpression in the brain is tightly controlled by several known enhancers that have been identified through genetic, genomic and functional assays. Using chromatin profiling during the differentiation of embryonic stem cells to neural progenitor cells, here we report the identification of a novel long-range enhancer for Shh—Shh-brain-enhancer-6 (SBE6)—that is located 100 kb upstream ofShhand that is required for the proper induction ofShhexpression during this differentiation programme. This element is capable of driving expression in the vertebrate brain. Our study illustrates how a chromatin-focused approach, coupled toin vivotesting, can be used to identify new cell-type specificcis-regulatory elements, and points to yet further complexity in the control ofShhexpression during embryonic brain development.
Depth and substratum differentiations among coexisting herbivorous cichlids in Lake Tanganyika
Authors: Hata Hiroki , Ochi Haruki
Published: November 2016

Cichlid fish in Lake Tanganyika represent a system of adaptive radiation in which eight ancestral lineages have diversified into hundreds of species through adaptation to various niches. However, Tanganyikan cichlids have been thought to be oversaturated, that is, the species number exceeds the number of niches and ecologically equivalent and competitively even species coexist. However, recent studies have shed light on niche segregation on a finer scale among apparently equivalent species. We observed depth and substratum preferences of 15 herbivorous cichlids from four ecomorphs (i.e. grazer, browser, scraper and scooper) on a rocky littoral slope for 14 years. Depth differentiation was detected among grazers that defended feeding territories and among browsers with feeding territories. Cichlid species having no feeding territory also showed specificity on depth and substratum, resulting in habitat segregation among species that belong to the same ecomorph. Phylogenetically close species did not occupy adjacent depths, nor the opposite depth zones. Our findings suggest that apparently equivalent species of the same ecomorph coexist parapatrically along depth on a few-metre scale, or coexist with different substratum preferences on the rocky shore, and this niche segregation may have been acquired by competition between encountering equivalent species through repetitive lake-level fluctuations.
Sensitivity of marine protected area network connectivity to atmospheric variability
Authors: Fox Alan D. , Henry Lea-Anne , Corne David W. , Roberts J. Murray
Published: November 2016

International efforts are underway to establish well-connected systems of marine protected areas (MPAs) covering at least 10% of the ocean by 2020. But the nature and dynamics of ocean ecosystem connectivity are poorly understood, with unresolved effects of climate variability. We used 40-year runs of a particle tracking model to examine the sensitivity of an MPA network for habitat-forming cold-water corals in the northeast Atlantic to changes in larval dispersal driven by atmospheric cycles and larval behaviour. Trajectories of
Lophelia pertusa
larvae were strongly correlated to the North Atlantic Oscillation (NAO), the dominant pattern of interannual atmospheric circulation variability over the northeast Atlantic. Variability in trajectories significantly altered network connectivity and source–sink dynamics, with positive phase NAO conditions producing a well-connected but asymmetrical network connected from west to east. Negative phase NAO produced reduced connectivity, but notably some larvae tracked westward-flowing currents towards coral populations on the mid-Atlantic ridge. Graph theoretical metrics demonstrate critical roles played by seamounts and offshore banks in larval supply and maintaining connectivity across the network. Larval longevity and behaviour mediated dispersal and connectivity, with shorter lived and passive larvae associated with reduced connectivity. We conclude that the existing MPA network is vulnerable to atmospheric-driven changes in ocean circulation.
How self-organization can guide evolution
Authors: Glancy Jonathan , Stone James V. , Wilson Stuart P.
Published: November 2016

Self-organization and natural selection are fundamental forces that shape the natural world. Substantial progress in understanding how these forces interact has been made through the study of abstract models. Further progress may be made by identifying a model system in which the interaction between self-organization and selection can be investigated empirically. To this end, we investigate how the self-organizing thermoregulatory huddling behaviours displayed by many species of mammals might influence natural selection of the genetic components of metabolism. By applying a simple evolutionary algorithm to a well-established model of the interactions between environmental, morphological, physiological and behavioural components of thermoregulation, we arrive at a clear, but counterintuitive, prediction: rodents that are able to huddle together in cold environments should evolve a lower thermal conductance at a faster rate than animals reared in isolation. The model therefore explains how evolution can be accelerated as a consequence ofrelaxed selection, and it predicts how the effect may be exaggerated by an increase in the litter size, i.e. by an increase in the capacity to use huddling behaviours for thermoregulation. Confirmation of these predictions in future experiments with rodents would constitute strong evidence of a mechanism by which self-organization can guide natural selection.
Globalization and pollution: tele-connecting local primary PM
2.5
emissions to global consumption
Authors: Meng Jing , Liu Junfeng , Xu Yuan , Guan Dabo , Liu Zhu , Huang Ye , Tao Shu
Published: November 2016

Globalization pushes production and consumption to geographically diverse locations and generates a variety of sizeable opportunities and challenges. The distribution and associated effects of short-lived primary fine particulate matter (PM
2.5
), a representative of local pollution, are significantly affected by the consumption through global supply chain. Tele-connection is used here to represent the link between production and consumption activity at large distances. In this study, we develop a global consumption-based primary PM
2.5
emission inventory to track primary PM
2.5
emissions embodied in the supply chain and evaluate the extent to which local PM
2.5
emissions are triggered by international trade. We further adopt consumption-based accounting and identify the global original source that produced the emissions. We find that anthropogenic PM
2.5
emissions from industrial sectors accounted for 24 Tg globally in 2007; approximately 30% (7.2 Tg) of these emissions were embodied in export of products principally from Brazil, South Africa, India and China (3.8 Tg) to developed countries. Large differences (up to 10 times) in the embodied emissions intensity between net importers and exporters greatly increased total global PM
2.5
emissions. Tele-connecting production and consumption activity provides valuable insights with respect to mitigating long-range transboundary air pollution and prompts concerted efforts aiming at more environmentally conscious globalization.
Pointwise gradient bounds for degenerate semigroups (of UFG type)
Authors: Crisan D. , Ottobre M.
Published: November 2016

In this paper, we consider diffusion semigroups generated by second-order differential operators of degenerate type. The operators that we consider
do not
, in general, satisfy the Hörmander condition and are
not
hypoelliptic. In particular, instead of working under the Hörmander paradigm, we consider the so-called UFG (uniformly finitely generated) condition, introduced by Kusuoka and Strook in the 1980s. The UFG condition is weaker than the uniform Hörmander condition, the smoothing effect taking place only in certain directions (rather than in every direction, as it is the case when the Hörmander condition is assumed). Under the UFG condition, Kusuoka and Strook deduced sharp
small
time asymptotic bounds for the derivatives of the semigroup in the directions where smoothing occurs. In this paper, we study the
large
time asymptotics for the gradients of the diffusion semigroup in the same set of directions and under the same UFG condition. In particular, we identify conditions under which the derivatives of the diffusion semigroup in the smoothing directions decay exponentially in time. This paper constitutes, therefore, a stepping stone in the analysis of the long-time behaviour of diffusions which do not satisfy the Hörmander condition.
Buckling of spherical shells revisited
Authors: Hutchinson John W.
Published: November 2016

A study is presented of the post-buckling behaviour and imperfection sensitivity of complete spherical shells subject to uniform external pressure. The study builds on and extends the major contribution to spherical shell buckling by Koiter in the 1960s. Numerical results are presented for the axisymmetric large deflection behaviour of perfect spheres followed by an extensive analysis of the role axisymmetric imperfections play in reducing the buckling pressure. Several types of middle surface imperfections are considered including dimple-shaped undulations and sinusoidal-shaped equatorial undulations. Buckling occurs either as the attainment of a maximum pressure in the axisymmetric state or as a non-axisymmetric bifurcation from the axisymmetric state. Several new findings emerge: the abrupt mode localization that occurs immediately after the onset of buckling, the existence of an apparent lower limit to the buckling pressure for realistically large imperfections, and comparable reductions of the buckling pressure for dimple and sinusoidal equatorial imperfections.
Analytic materials
Authors: Milton Graeme W.
Published: November 2016

The theory of inhomogeneous analytic materials is developed. These are materials where the coefficients entering the equations involve analytic functions. Three types of analytic materials are identified. The first two types involve an integerp. Ifptakes its maximum value, then we have a complete analytic material. Otherwise, it is incomplete analytic material of rankp. For two-dimensional materials, further progress can be made in the identification of analytic materials by using the well-known fact that a 90°rotation applied to a divergence-free field in a simply connected domain yields a curl-free field, and this can then be expressed as the gradient of a potential. Other exact results for the fields in inhomogeneous media are reviewed. Also reviewed is the subject of metamaterials, as these materials provide a way of realizing desirable coefficients in the equations.
Optimal frequency of rabies vaccination campaigns in Sub-Saharan Africa
Authors: Bilinski Alyssa M. , Fitzpatrick Meagan C. , Rupprecht Charles E. , Paltiel A. David , Galvani Alison P.
Published: November 2016

Rabies causes more than 24 000 human deaths annually in Sub-Saharan Africa. The World Health Organization recommends annual canine vaccination campaigns with at least 70% coverage to control the disease. While previous studies have considered optimal coverage of animal rabies vaccination, variation in the frequency of vaccination campaigns has not been explored. To evaluate the cost-effectiveness of rabies canine vaccination campaigns at varying coverage and frequency, we parametrized a rabies virus transmission model to two districts of northwest Tanzania, Ngorongoro (pastoral) and Serengeti (agro-pastoral). We found that optimal vaccination strategies were every 2 years, at 80% coverage in Ngorongoro and annually at 70% coverage in Serengeti. We further found that the optimality of these strategies was sensitive to the rate of rabies reintroduction from outside the district. Specifically, if a geographically coordinated campaign could reduce reintroduction, vaccination campaigns every 2 years could effectively manage rabies in both districts. Thus, coordinated campaigns may provide monetary savings in addition to public health benefits. Our results indicate that frequency and coverage of canine vaccination campaigns should be evaluated simultaneously and tailored to local canine ecology as well as to the risk of disease reintroduction from surrounding regions.
Enhanced macroboring and depressed calcification drive net dissolution at high-CO
2
coral reefs
Authors: Enochs Ian C. , Manzello Derek P. , Kolodziej Graham , Noonan Sam H. C. , Valentino Lauren , Fabricius Katharina E.
Published: November 2016

Ocean acidification (OA) impacts the physiology of diverse marine taxa; among them corals that create complex reef framework structures. Biological processes operating on coral reef frameworks remain largely unknown from naturally high-carbon-dioxide (CO
2
) ecosystems. For the first time, we independently quantified the response of multiple functional groups instrumental in the construction and erosion of these frameworks (accretion, macroboring, microboring, and grazing) along natural OA gradients. We deployed blocks of dead coral skeleton for roughly 2 years at two reefs in Papua New Guinea, each experiencing volcanically enriched CO
2
, and employed high-resolution micro-computed tomography (micro-CT) to create three-dimensional models of changing skeletal structure. OA conditions were correlated with decreased calcification and increased macroboring, primarily by annelids, representing a group of bioeroders not previously known to respond to OA. Incubation of these blocks, using the alkalinity anomaly methodology, revealed a switch from net calcification to net dissolution at a pH of roughly 7.8, within Intergovernmental Panel on Climate Change's (IPCC) predictions for global ocean waters by the end of the century. Together these data represent the first comprehensive experimental study of bioerosion and calcification from a naturally high-CO
2
reef ecosystem, where the processes of accelerated erosion and depressed calcification have combined to alter the permanence of this essential framework habitat.
Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw
Authors: Ma Shichun , Huang Yan , Wang Cong , Fan Hui , Dai Lirong , Zhou Zheng , Liu Xing , Deng Yu
Published: November 2016

A thermophilic, anaerobic, fermentative bacterium, strain A6T, was obtained from an anaerobic batch digester treating animal manure and rice straw. Cells were Gram-stain-positive, slightly curved rods with a size of 0.6–1×2.5–8.2 µm, non-motile and produced terminal spores. The temperature, pH and NaCl concentration ranges for growth were 40–60 °C, 6.5–8.0 and 0–15.0 g l−1, with optimum growth noted at 50–55 °C, pH 7.5 and in the absence of NaCl, respectively. Yeast extract was required for growth. d-Glucose, maltose, d-xylose, d-galactose, d-fructose, d-ribose, lactose, raffinose, sucrose, d-arabinose, cellobiose, d-mannose and yeast extract were used as carbon and energy sources. The fermentation products from glucose were ethanol, lactate, acetate, propionate, butyrate, valerate, iso-butyrate, iso-valerate, H2 and CO2. The G+C content of the genomic DNA was 36.6 mol%. The predominant fatty acids were C16 : 0, iso-C17 : 1, C14 : 0, C16 : 1
ω7c, C16 : 0 N-alcohol and C13 : 0 3-OH. Respiratory quinones were not detected. The polar lipid profile comprised phosphoglycolipids, phospholipids, glycolipids, a diphosphatidylglycerol, a phosphatidylglycerol and an unidentified lipid. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was closely related to

Defluviitalea saccharophila

DSM 22681T with a similarity of 96.0 %. Based on the morphological, physiological and taxonomic characterization, strain A6T is considered to represent a novel species of the genus

Defluviitalea

, for which the name Defluviitalea raffinosedens sp. nov. is proposed. The type strain is A6T (=DSM 28090T=ACCC 19951T).
Deciphering the genic basis of environmental adaptations by simultaneous forward and reverse genetics inSaccharomyces cerevisiae
Authors: Maclean Calum J. , Metzger Brian P.H. , Yang Jian-Rong , Ho Wei-Chin , Moyers Bryan , Zhang Jianzhi
Published: November 2016

The budding yeastSaccharomyces cerevisiaeis the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of natural phenotypic variation is limited by the inefficiency of association mapping owing to strong and complex population structure. To facilitate association mapping, we analyzed 190 high-quality genomes of diverse strains, including 85 newly sequenced ones, to uncover yeast’s population structure that varies substantially among genomic regions. We identified 181 yeast genes that are absent from the reference genome and demonstrated their expression and role in important functions such as drug resistance. We then simultaneously measured the growth rates of over 4500 lab strains each deficient of a nonessential gene and 81 natural strains across multiple environments using unique DNA barcode present in each strain. We combined the genome-wide reverse genetic information with genome-wide association analysis to determine potential genomic regions of importance to environmental adaptations, and for a subset experimentally validated their role by reciprocal hemizygosity tests. The resources provided permit efficient and reliable association mapping in yeast and significantly enhances its value as a model for understanding the genetic mechanisms of phenotypic polymorphism and evolution.
An overview on the DNA nucleotide compositions across kingdoms
Authors: Guo Yabin
Published: November 2016

The DNA nucleotide compositions vary among species. This fascinating phenomenon has been studied for decades with some interesting questions remaining unclear. Recent years, thousands of genomes have been sequenced, but general evaluations on the nucleotide compositions across different phylogenetic groups are still absent. In this letter, I analyzed 371 genomes from different kingdoms and provided an overview on DNA nucleotide compositions. A number of important topics were discussed, including GC content, DNA strand symmetricity, CDS purine content, codon usage, thermophilicity in prokaryotes and non-coding RNA genes. I also gave explanations to two long debated questions: 1) both genome GC content and CDS purine content are correlated with the thermophilicity in archaea, but not in bacteria; 2) the purine rich pattern of CDS in most species is mainly a consequence of coding requirement, but not mRNA interaction dynamics. This study provides valuable information and ideas for future investigations.
Automatic Tracing of Ultra-Volume of Neuronal Images
Authors: Peng Hanchuan , Zhou Zhi , Meijering Erik , Zhao Ting , Ascoli Giorgio A. , Hawrylycz Michael
Published: November 2016

Despite substantial advancement in the automatic tracing of neurons' morphology in recent years, it is challenging to apply the existing algorithms to very large image datasets containing billions or more voxels. We introduceUltraTracer, a solution designed to extend any base neuron-tracing algorithm to be able to trace virtually unlimited data volumes. We applied this approach to neuron-tracing algorithms with completely different design principles and tested on challenging human and mouse neuron datasets that have hundreds of billions of voxels. Results indicate thatUltraTraceris scalable, accurate, and about 3 to 6 times more efficient compared to other state-of-the-art approaches.
PI3-kinase cascade has a differential role in acquisition and extinction of conditioned fear memory in juvenile and adult rats
Authors: Slouzkey Ilana , Maroun Mouna
Published: November 2016

The basolateral amygdala (BLA), medial prefrontal cortex (mPFC) circuit, plays a crucial role in acquisition and extinction of fear memory. Extinction of aversive memories is mediated, at least in part, by the phosphoinositide-3 kinase (PI3K)/Akt pathway in adult rats. There is recent interest in the neural mechanisms that mediate fear and extinction in juvenile animals and whether these mechanisms are distinctive from those in adult animals. In the present study, we examined (1) changes in phosphorylation of Akt in the BLA and mPFC after fear conditioning and extinction in juvenile and adult rats and (2) the effect of BLA and mPFC localized inhibition of the PI3K following acquisition and extinction of contextual fear memory. Our results show that Akt phosphorylation is increased following acquisition of contextual fear learning in the BLA but not in the mPFC in adult and juvenile rats. Extinction learning was not associated with changes in Akt phosphorylation. Although there were no differences in the pattern of phosphorylation of Akt either in adult or juvenile rats, microinjection of the PI3K inhibitor, LY294002, into the BLA or mPFC elicited differential effects on fear memory acquisition and extinction, depending on the site and timing of the microinjection, as well as on the age of the animal. These results suggest that PI3K/Akt has a differential role in formation, retrieval, and extinction of contextual fear memory in juvenile and adult animals, and point to developmental differences between adult and juvenile rats in mechanisms of extinction.
Constraint-induced direct phasing method
Authors: Xu Hongliang
Published: November 2016

The best and most detailed structural information is obtained when the diffraction pattern of a single crystal a few tenths of a millimetre in each dimension is analyzed, but growing high-quality crystals of this size is often difficult, sometimes impossible. However, many crystallization experiments that do not yield single crystals do yield showers of randomly oriented microcrystals that can be exposed to X-rays simultaneously to produce a powder diffraction pattern. Although single-crystal diffraction data consist of discrete spots or X-ray reflections, the diffraction of microcrystals in a powder forms rings so that the reflections overlap. Thus, the analysis is more challenging due to unavoidable errors in the structure-factor amplitudes and the low-resolution data available for structure determination. This paper introduces a constraint-induced phasing method that (i) improves structure solutions measured by success rate, quality of solutions and various figures of merit, and (ii) extends low-resolution powder diffraction data to atomic resolution by adding unmeasured reflections. Application results have shown clearly that the constraint-induced phasing method is an effective way to produce initial structure models that are suitable for further structural refinement and completion.
Vaccinia virus Western Reserve induces rapid surface expression of a host molecule detected by the antibody 4C7 that is distinct from CLEC2D
Authors: Williams Kinola J.N. , Eaton Heather E. , Jones Lena , Rengan Supraja , Burshtyn Deborah N.
Published: November 2016

In this study, the effect of active infection with vaccinia virus Western Reserve (VACV WR) on expression of C‐type lectin domain family 2 (CLEC2D), a ligand of the human NK cell inhibitory receptor NKR‐P1, was examined. As predicted, VACV infection led to a loss of CLEC2D mRNA in 221 cells, a B cell lymphoma line. Surprisingly, VACV infection of 221 cells caused a dramatic increase in cell surface staining for one CLEC2D‐specific antibody, 4C7. There were no changes in other antibodies specific for CLEC2D and no indication that NK cells with NKR‐P1A were inhibited, suggesting 4C7 detects a non‐CLEC2D molecule following infection. The rapid increase in 4C7 signal requires virus attachment and is disrupted by UV treatment, but does not depend on new transcription or translation of either cellular or viral proteins. 4C7 does react with intracellular compartments, suggesting the molecule that is detected at the surface following infection is derived from an intracellular store. The phenomenon extends beyond lymphoid cells: it was observed in the non‐human primate cell line Cos‐7, but not with myxoma, a poxvirus distinct from VACV. To our knowledge, this is the first report of VACV or any poxvirus leading to rapid externalization of a host molecule. Among the VACV strains tested, the phenomenon was restricted to VACV WR and IHD‐W, suggesting it has a virulence‐, as opposed to a replication‐related, function.
Re‐evaluating strategies for pollinator‐dependent crops: How useful is parthenocarpy?
Authors: Knapp Jessica L. , Bartlett Lewis J. , Osborne Juliet L.
Published: November 2016

Whilst most studies reviewing the reliance of global agriculture on insect pollination advocate increasing the ‘supply’ of pollinators (wild or managed) to improve crop yields, there has been little focus on altering a crop's ‘demand’ for pollinators.

Parthenocarpy (fruit set in the absence of fertilization) is a trait which can increase fruit quantity and quality from pollinator‐dependent crops by removing the need for pollination.

Here we present a meta‐analysis of studies examining the extent and effectiveness of parthenocarpy‐promoting techniques (genetic modification, hormone application and selective breeding) currently being used commercially, or experimentally, on pollinator‐dependent crops in different test environments (no pollination, hand pollination, open pollination).

All techniques significantly increased fruit quantity and quality in 18 pollinator‐dependent crop species (not including seed and nut crops as parthenocarpy causes seedlessness). The degree to which plants experienced pollen limitation in the different test environments could not be ascertained, so the absolute effect of parthenocarpy relative to optimal pollination could not be determined.

Synthesis and applications. Parthenocarpy has the potential to lower a crop's demand for pollinators, whilst extending current geographic and climatic ranges of production. Thus, growers may wish to use parthenocarpic crop plants, in combination with other environmentally considerate practices, to improve food security and their economic prospects.
Critical catchments for freshwater biodiversity conservation in Europe: identification, prioritisation and gap analysis
Authors: Carrizo Savrina F. , Lengyel Szabolcs , Kapusi Felícia , Szabolcs Márton , Kasperidus Hans D. , Scholz Mathias , Markovic Danijela , Freyhof Jörg , Cid Núria , Cardoso Ana C. , Darwall William
Published: November 2016

The conservation of freshwater ecosystems has lagged behind that of marine and terrestrial ecosystems and often requires the integration of large‐scale approaches and transboundary considerations. This study aims to set the foundations of a spatial conservation strategy by identifying the most important catchments for the conservation of freshwater biodiversity in Europe.

Using data on 1296 species of fish, mollusc, odonate and aquatic plant, and the key biodiversity area criteria (species Red List status, range restriction and uniqueness of species assemblages), we identified a network of Critical Catchments for the conservation of freshwater biodiversity. Applying spatial prioritisation, we show how the prioritised network differs from the ideal case of protecting all Critical Catchments and how it changes when protected areas are included, and we also identify gaps between the prioritised network and existing protected areas.

Critical Catchments (n = 8423) covered 45% of the area of Europe, with 766 qualifying (‘trigger’) species located primarily in southern Europe. The prioritised network, limited to 17% of the area of Europe, comprised 3492 catchments mostly in southern and eastern Europe and species targets were met for at least 96% of the trigger species.

We found the majority of Critical Catchments to be inadequately covered by protected areas. However, our prioritised network presents a possible solution to augment protected areas to meet policy targets while also achieving good species coverage.

Policy implications. While Critical Catchments cover almost half of Europe, priority catchments are mostly in southern and eastern Europe where the current level of protection is not sufficient. This study presents a foundation for a Europe‐wide systematic conservation plan to ensure the persistence of freshwater biodiversity. Our study provides a powerful new tool for optimising investment on the conservation of freshwater biodiversity and for meeting targets set forth in international biodiversity policies, conventions and strategies.
Effects of high‐sodium intake on systemic blood pressure and vascular responses in spontaneously diabetic WBN/Kob‐Leprfa/fa rats
Authors: Takagi Yoshiichi , Kadowaki Haruno , Kobayashi Ikumi , Ito Kaoru , Ito Katsuaki , Shirai Mitsuyuki , Asai Fumitoshi
Published: November 2016

The prevalence of type 2 diabetes mellitus (T2DM) and hypertension has markedly increased worldwide. The purpose of the present study was to examine the effects of a high‐salt intake on the systolic blood pressure (SBP) and vascular responses in WBN/Kob‐Leprfa/fa (WBKDF) rats, a new spontaneous animal model of T2DM. Male WBKDF rats and age‐matched Wistar rats at 6 weeks of age were each divided into two groups and fed either a normal‐sodium (NS, 0.26%) diet or high‐sodium (HS, 8%) diet for 14 weeks: (i) Wistar rats on NS diet (Wistar‐NS); (ii) Wistar rats on HS diet (Wistar‐HS); (iii) WBKDF rats on NS diet (WBKDF‐NS); (iv) WBKDF rats on HS diets (WBKDF‐HS). Neither WBKDF‐NS nor Wistar‐NS rats showed significant changes in SBP throughout the experiment, but both WBKDF‐HS and Wistar‐HS exhibited significant elevation of SBP, which was more prominent (P<.01) in WBKDF‐HS than in Wistar‐HS. Phenylephrine‐induced contractions of isolated thoracic aortic rings were significantly (P<.01) enhanced in WBKDF‐HS and Wistar‐HS compared with the respective strain of rats on the NS diet. In contrast, acetylcholine‐ and nitroprusside‐induced relaxation were significantly (P<.01) diminished in both WBKDF‐HS and Wistar‐HS, and these HS diet‐induced changes were more profound (P<.01) in WBKDF rats than in Wistar rats. Significantly (P<.05) higher plasma concentrations of 8‐iso‐prostaglandin F2α and sodium ions were observed in WBKDF‐HS than in Wistar‐HS. The current study demonstrated that WBKDF‐HS rats developed salt‐sensitive hypertension associated with vascular dysfunction. The WBKDF rat may be a useful model for investigating the etiology of hypertension with T2DM.