bluuebunny/crossref_metadata_2025 huggingface dataset:
Penicillin-Binding Protein Transpeptidase Signatures for Tracking and Predicting β-Lactam Resistance Levels in Streptococcus pneumoniae
Authors: Li Yuan , Metcalf Benjamin J. , Chochua Sopio , Li Zhongya , Gertz Robert E. , Walker Hollis , Hawkins Paulina A. , Tran Theresa , Whitney Cynthia G. , McGee Lesley , Beall Bernard W.
Published: June 2016

β-Lactam antibiotics are the drugs of choice to treat pneumococcal infections. The spread of β-lactam-resistant pneumococci is a major concern in choosing an effective therapy for patients. Systematically tracking β-lactam resistance could benefit disease surveillance. Here we developed a classification system in which a pneumococcal isolate is assigned to a “PBP type” based on sequence signatures in the transpeptidase domains (TPDs) of the three critical penicillin-binding proteins (PBPs), PBP1a, PBP2b, and PBP2x. We identified 307 unique PBP types from 2,528 invasive pneumococcal isolates, which had known MICs to six β-lactams based on broth microdilution. We found that increased β-lactam MICs strongly correlated with PBP types containing divergent TPD sequences. The PBP type explained 94 to 99% of variation in MICs both before and after accounting for genomic backgrounds defined by multilocus sequence typing, indicating that genomic backgrounds made little independent contribution to β-lactam MICs at the population level. We further developed and evaluated predictive models of MICs based on PBP type. Compared to microdilution MICs, MICs predicted by PBP type showed essential agreement (MICs agree within 1 dilution) of >98%, category agreement (interpretive results agree) of >94%, a major discrepancy (sensitive isolate predicted as resistant) rate of <3%, and a very major discrepancy (resistant isolate predicted as sensitive) rate of <2% for all six β-lactams. Thus, the PBP transpeptidase signatures are robust indicators of MICs to different β-lactam antibiotics in clinical pneumococcal isolates and serve as an accurate alternative to phenotypic susceptibility testing.

IMPORTANCE
The human pathogen
Streptococcus pneumoniae
is a leading cause of morbidity and mortality worldwide. β-Lactam antibiotics such as penicillin and ceftriaxone are the drugs of choice to treat pneumococcal infections. Some pneumococcal strains have developed β-lactam resistance through altering their penicillin-binding proteins (PBPs) and have become a major concern in choosing effective patient therapy. To systematically track and predict β-lactam resistance, we obtained the sequence signatures of PBPs from a large collection of clinical pneumococcal isolates using whole-genome sequencing data and found that these “PBP types” were predictive of resistance levels. Our findings can benefit the current era of strain surveillance when whole-genome sequencing data often lacks detailed resistance information. Using PBP positions that we found are always substituted within highly resistant strains may lead to further refinements. Sequence-based predictions are accurate and may lead to the ability to extract critical resistance information from nonculturable clinical specimens.
Bilateral adrenal myelolipoma in Cushing's disease: a relook into the role of corticotropin in adrenal tumourigenesis
Authors: Chakraborty Partha Pratim , Bhattacharjee Rana , Mukhopadhyay Pradip , Chowdhury Subhankar
Published: June 2016

Adrenal myelolipomas are infrequently encountered benign tumours of unknown aetiology. In the majority of cases they are unilateral, and clinically and hormonally silent, only requiring periodic follow-up. However, bilateral adrenal myelolipomas are sometimes associated with endocrine disorders and warrant appropriate evaluation. Though the understanding of the pathophysiology of adrenal myelolipomas has long been elusive, adrenocorticotropic hormone (ACTH) has been proposed as the main tropic factor in a number of studies. Cushing's disease is rarely associated with bilateral and sometimes giant myelolipomas. In this article, the association of bilateral adrenal myelolipomas with Cushing's disease has been discussed and the role of ACTH in the tumourigenesis has been reviewed.
Basal insulin regime change from Lantus to Toujeo resulted in fewer hypoglycaemic episodes in a 28-year-old man with diabetes mellitus
Authors: Shields Alexandra , Sankaranarayanan Sailesh
Published: June 2016

An active 28-year-old man with type 1 diabetes mellitus reported a reduced number of hypoglycaemic episodes following change in basal regime insulin glargine from U100 Lantus to U300 Toujeo. Consequently, an improved quality of life was also reported. Flash-based glucose monitoring was utilised to record 24-hour continuous glucose levels throughout two comparable 60-day periods before and after the change in regimen. Low blood glucose was most likely between 03:00 and 08:00. Nocturnal hypoglycaemic episodes (≤3.9 mmol/L) reduced by an average of 2.5 episodes per week. Severe hypoglycaemic episodes (≤2.9 mmol/L) reduced to an average of 0.4 per week, down from 1.5 per week. Nocturnal hypoglycaemic episodes reduced in frequency and severity. Furthermore, nocturnal hypoglycaemia episodes occurred in a more predictable time window. This was especially important in the reported reduction of impact on the patient's quality of life, as the episodes tended to be associated with anxiety and low mood. Patient education needed to facilitate this change was minimal, and benefits to the patient were great, including decreased sleep disturbances and reduced risk of associated anxiety symptoms.
Effect of a hospital outreach intervention programme on decreasing hospitalisations and medical costs in patients with chronic obstructive pulmonary disease in China: protocol of a randomised controlled trial
Authors: Yan Jin , Wang Lianhong , Liu Chun , Yuan Hong , Wang Xiaowan , Yu Baorong , Luo Qian
Published: June 2016

Introduction

Patients with chronic obstructive pulmonary disease (COPD) often have multiple hospitalisations because of exacerbation. Evidence shows disease management programmes are one of the most cost-effective measures to prevent re-hospitalisation for COPD exacerbation, but lack implementation and economic appraisal in China. The aims of the proposed study are to determine whether a hospital outreach invention programme for disease management can decrease hospitalisations and medical costs in patients with COPD in China. Economic appraisal of the programme will also be carried out.

Methods and analysis

A randomised single-blinded controlled trial will be conducted. 220 COPD patients with exacerbations will be recruited from the Third Xiangya Hospital, Central South University, China. After hospital discharge they will be randomly allocated into an intervention or a control group. Participants in the intervention group will attend a 3-month hospital-based pulmonary rehabilitation intervention and then receive a home-based programme. Both groups will receive identical usual discharge care before discharge from hospital. The primary outcomes will include rate of hospitalisation and medical cost, while secondary outcomes will include mortality, self-efficacy, self-management, health status, quality of life, exercise tolerance and pulmonary function, which will be evaluated at baseline and at 3, 12 and 24 months after the intervention. Cost-effectiveness analysis will be employed for economic appraisal.

Ethics and dissemination

The study has been approved by the institutional review board (IRB) of the Third Xiangya Hospital, Central South University (IRB2014-S159). Findings will be shared widely through conference presentations and peer-reviewed publications. Furthermore, the results of the programme will be submitted to health authorities and policy reform will be recommended.

Trial registration number

Chi CTR-TRC-14005108; Pre-results.
Associations of alcoholic beverage preference with cardiometabolic and lifestyle factors: the NQplus study
Authors: Sluik Diewertje , Brouwer-Brolsma Elske M , de Vries Jeanne H M , Geelen Anouk , Feskens Edith J M
Published: June 2016

Objectives

The preference for a specific alcoholic beverage may be related to an individual's overall lifestyle and health. The objective was to investigate associations between alcoholic beverage preference and several cardiometabolic and lifestyle factors, including adiposity, cholesterol, glycated haemoglobin (HbA1c), liver enzymes and dietary patterns.

Design

Cross-sectional study.

Setting

The Dutch Longitudinal Nutrition Questionnaires plus (NQplus) Study.

Participants

1653 men and women aged 20–77 years.

Methods

Diet, including alcohol, was assessed by Food Frequency Questionnaire. Based on the average number of reported glasses of alcoholic beverage, a person was classified as having a preference for beer, wine, spirit/no specific preference, or as a non-consumer. Mixed linear models were used to calculate crude and adjusted means of cardiometabolic and lifestyle factors across alcoholic beverage preference categories.

Primary outcome measures

Anthropometric measures, blood pressure, lipids, HbA1c, albumin, creatinine, uric acid, liver enzymes and dietary patterns.

Results

In the study population, 43% had a wine preference, 13% a beer preference, 29% had a spirit or no specific preference, and 15% did not consume alcohol. Men who preferred wine had lowest measures of adiposity; the preference for alcoholic beverages was not associated with adiposity measures in women. Wine consumers had higher high density lipoprotein-cholesterol, lower HbA1cand were more likely to follow the ‘Salad’ pattern. Beer consumers had highest levels of triglycerides and liver enzymes, and had higher scores for the ‘Meat’ and ‘Bread’ pattern.

Conclusions

Few differences in dietary patterns across alcoholic beverage preference categories were observed. Those differences in cardiometabolic parameters that were observed according to alcoholic beverage preference, suggested that wine consumers have a better health status than beer consumers.
Physicians' occupational stress, depressive symptoms and work ability in relation to their working environment: a cross-sectional study of differences among medical residents with various specialties working in German hospitals
Authors: Bernburg Monika , Vitzthum Karin , Groneberg David A , Mache Stefanie
Published: June 2016

Objectives

This study aimed to analyse and compare differences in occupational stress, depressive symptoms, work ability and working environment among residents working in various medical specialties.

Methods

435 German hospital residents in medical training working in 6 different medical specialties participated in a cross-sectional survey study. Physicians were asked about their working conditions and aspects of mental health and work ability. The Copenhagen Psychosocial Questionnaire, the Work Ability Index, the ICD-10 Symptom Rating and the Perceived Stress Questionnaire were used to measure working conditions, mental health and work ability.

Results

Results show that up to 17% of the physicians reported high levels of occupational distress and 9% reported high levels of depressive symptoms. 11% of the hospital physicians scored low in work ability. Significant differences between medical specialties were demonstrated for occupational distress, depressive symptoms, work ability, job demands and job resources. Surgeons showed consistently the highest levels of perceived distress but also the highest levels of work ability and lowest scores for depression. Depressive symptoms were rated with the highest levels by anaesthesiologists. Significant associations between physicians’ working conditions, occupational distress and mental health-related aspects are illustrated.

Conclusions

Study results demonstrated significant differences in specific job stressors, demands and resources. Relevant relations between work factors and physicians' health and work ability are discussed. These findings should be reinvestigated in further studies, especially with a longitudinal study design. This work suggests that to ensure physicians' health, hospital management should plan and implement suitable mental health promotion strategies. In addition, operational efficiency through resource planning optimisation and work process improvements should be focused by hospital management.
The enhanced knowledge translation and exchange framework for road safety: a brief report on its development and potential impacts
Authors: Hinchcliff Reece , Senserrick Teresa , Travaglia Joanne , Greenfield David , Ivers Rebecca
Published: June 2016

Knowledge translation and exchange (KTE) can enable evidence-informed road safety policy and practice by reducing the gap between what is known to be effective and what actually occurs. A quality improvement project, undertaken within a government policy frame, was implemented in 2015 to produce an enhanced KTE framework for road safety (the framework). Information was collected from 35 road safety stakeholders in the UK, the Netherlands, Norway and Sweden. Thirteen KTE facilitators were identified that covered research funding and production, the expertise of knowledge users and dissemination practices. The framework was subsequently developed, which separated facilitators seen as essential for a KTE system, from others perceived as aspirational due to their lesser influence and the considerable time and resources required for their implementation. The framework provides a heuristic device to enable policy agencies to holistically assess and improve current KTE systems for road safety, to encourage evidence-informed policy and practice.
Endovascular therapy for Acute ischemic Stroke Trial (EAST): study protocol for a prospective, multicentre control trial in China
Authors: Miao Zhongrong , Huo Xiaochuan , Gao Feng , Liao Xiaoling , Wang Chunjuan , Peng Ya , Cao Yibin , Chen Shengli , Zhang Meng , Jiang Changchun , Peng Xiaoxiang , Song Cunfeng , Wei Liping , Zhu Qiyi , Guo Zaiyu , Liu Li , Lin Hang , Yang Hua , Wu Wei , Liang Hui , Xu Anding , Chen Kangning , Zhao Xingquan , Pan Yuesong , Li Hao , Liu Liping , Wang Yilong , Wang Yongjun ,   EAST investigators
Published: June 2016

Background and purpose

5 recent trials have shown the benefit of endovascular treatment for acute ischaemic stroke (AIS) due to large vessel occlusion of the anterior circulation. This study aims to evaluate the safety and efficacy of Solitaire thrombectomy in patients with moderate-to-severe stroke in the Chinese population, which has a high prevalence of intracranial atherosclerosis.

Methods and analysis

This multicentre prospective control study will involve 17 stroke centres in China, and plans to recruit 150 patients in the intervention group, and 150 patients in the medical group, in which patients meet enrolment criteria but refuse intervention. Patients with AIS due to large vessel occlusion indicated for treatment with Solitaire stent retriever within 12 hours of symptom onset, and who meet the inclusion and exclusion criteria, will be enrolled in this study. The primary efficacy endpoint is functional independence as defined by a modified Rankin Scale (mRS) score ≤2 at 90 days or by functional improvement as defined by mRS, using shift analysis. The procedural efficacy endpoint is arterial recanalisation of the occluded target vessel measured by a modified Thrombolysis in Cerebral Infarction (mTICI) score equal or superior to 2b right following the use of the study device. The primary safety endpoint is symptomatic intracranial haemorrhage (sICH) within 24±3 hours postprocedure.

Ethics and dissemination

The protocol was approved by the Ethics Committee at the coordinating centre and by the local Institutional Review Board of each participating centre.

Trial registration number

NCT02350283.
Clinical findings and treatment outcomes for cats diagnosed with patent ductus arteriosus in the UK: a retrospective study of 19 cases (2004–2012)
Authors: Wustefeld‐Janssens B. G. , Burrow R. , Mõtsküla P. , Martin M. , Dukes‐McEwan J.
Published: June 2016

Patent ductus arteriosus (PDA) is infrequently reported in cats and represents between 1–7.3 per cent of left to right shunting cardiac congenital anomalies. The objective of this study was to report the presenting complaints, clinical examination findings, diagnostic findings, treatment outcomes and survival times in cats diagnosed with a PDA in the UK. Medical records from three major UK referral centres were searched for cats that were diagnosed with PDA from January 2004 to December 2012. Data obtained for analysis included: signalment, clinical examination findings including murmur characteristics, diagnostic imaging findings, treatment outcomes and survival times. Nineteen cats were included in the analysis. The most common reason for referral was investigation of an incidentally detected heart murmur without clinical signs (13/19; 68 per cent). Pulmonary arterial hypertension (PAH) was diagnosed in seven (37 per cent) cats and those cats with PAH were significantly more likely to present with signs of disease (P=0.004). Median survival time in cats that were diagnosed with PDA and died due to cardiac causes was 898 days (interquartile range 459–1011 days). The median survival time of those cats that had an additional congenital anomaly was significantly shorter to those cats without a congenital anomaly (P=0.008).
Comparing the effects of first‐line antiepileptic drugs on the gait of dogs with idiopathic epilepsy
Authors: Suiter E. J. , Packer R. M. A. , Volk H. A.
Published: June 2016

Idiopathic epilepsy (IE) is a common chronic neurological disease of the dog. Previous studies of anti‐epileptic drug (AED) treatment have indicated that acceptable AED adverse effects are as important to owners as reductions in seizure frequency. AEDs in both dogs and human beings are frequently associated with the adverse‐effect ataxia. The aim of this study was to compare ataxia levels in dogs with IE treated chronically with phenobarbitone or imepitoin, the two currently available first‐line AED treatments. The gait of 6 imepitoin‐treated dogs, 8 phenobarbitone‐treated dogs and 10 age‐matched healthy control dogs were compared. Fifty strides from a walking gait were analysed for each dog, quantifying ataxia via the variability in six established gait parameters. Three variables differed significantly between groups: lateral distance between (i) pelvic paw placements, (ii) thoracic paw placements and (iii) stance time, which were significantly more variable in the phenobarbitone‐treated dogs than imepitoin‐treated or control dogs. These results indicate that dogs treated with phenobarbitone experience ataxia compared with controls and imepitoin‐treated dogs. Conversely, there was no difference between imepitoin‐treated dogs and controls. These results along with further research are needed to quantify AEDs adverse effects, to help vets and owners make more informed drug‐choices.
Guillardia theta gen. et sp.nov. (Cryptophyceae)
Authors: Hill David R. A. , Wetherbee Richard
Published: June 2016

Guillardia theta gen. et sp.nov. is proposed as a new name for a cryptomonad that is well known in the literature as Cryptomonas sp. θ. Guillardia is small and can be distinguished from other cryptomonad genera by a combination of features of the plastidial complex, the furrow-gullet system, and a distinct periplast structure. Its fine structure is known from several previous reports and is only summarized here.
Effects of the isoetid macrophytes Eriocaulon septangulare and Lobelia dortmanna on the periphyton of littoral sediments
Authors: Howell E. T.
Published: June 2016

Plants of an isoetid form are common in soft-water lakes and can increase surface area available for periphyton development. The effects of the macrophytes Eriocaulon septangulare With. and Lobelia dortmanna L. on the productivity of periphyton overlying sediments were evaluated by comparing periphyton from macrophyte-sediment treatments with periphyton from sediment treatments in four lakes. Areal productivity (expressed on the basis of underlying sediment area), chlorophyll a standardized productivity, and chlorophyll a biomass of a loosely associated component of the epiphyton of Eriocaulon and Lobelia were similar and not significantly different from that measured for periphyton on sediments. The areal productivity (expressed on the basis of leaf area) of an attached epiphyton component was only 10–20% of rates measured for the loosely associated component. The concentration of leaf area over sediments did not appear to affect areal production rates of epiphyton components over the range 1:0.4 and 1:3.8 sediment area to leaf area. Periphyton productivity is likely higher in areas of isoetid macrophytes than in areas of sediment alone because of the contribution of the attached component of the epiphyton, which is proportional to the leaf area present. Key words: periphyton, isoetid, soft water, productivity, Eriocaulon, Lobelia.
Cytological studies on the infection of barley cultivars with known resistance genotypes by Rhynchosporium secalis
Authors: Lehnackers H. , Knogge W.
Published: June 2016

Seven races of Rhynchosporium secalis were screened for their virulence on a variety of barley cultivars. Four races were identified as virulent on cultivar Atlas 46 (resistance loci Rrs1 and Rrs2) but virulent on the near-isogenic cultivar Atlas (Rrs2). For one of these races, US238.1, the fungal infection cycle was followed on the susceptible cultivar by means of light and scanning electron microscopy. From a comparative analysis of fungal development on the susceptible and resistant cultivars, two lines of plant defense emerged: (i) inhibition of spore germination on the leaf surface and (ii) prevention of the establishment of the subcuticular stroma. Investigations of the development of race US238.1 on different barley cultivars with and without Rrs1 and on F1 individuals from different crosses excluded involvement of Rrs1 in the inhibition of spore germination. Possible pathogenicity mechanisms are discussed. Key words: leaf scald, microscopy, plant resistance.
Characterization of mussel H2A.Z.2: a new H2A.Z variant preferentially expressed in germinal tissues fromMytilus
Authors: Rivera-Casas Ciro , González-Romero Rodrigo , Vizoso-Vazquez Ángel , Cheema Manjinder S. , Cerdán M. Esperanza , Méndez Josefina , Ausió Juan , Eirin-Lopez Jose M.
Published: June 2016

Histones are the fundamental constituents of the eukaryotic chromatin, facilitating the physical organization of DNA in chromosomes and participating in the regulation of its metabolism. The H2A family displays the largest number of variants among core histones, including the renowned H2A.X, macroH2A, H2A.B (Bbd), and H2A.Z. This latter variant is especially interesting because of its regulatory role and its differentiation into 2 functionally divergent variants (H2A.Z.1 and H2A.Z.2), further specializing the structure and function of vertebrate chromatin. In the present work we describe, for the first time, the presence of a second H2A.Z variant (H2A.Z.2) in the genome of a non-vertebrate animal, the mussel Mytilus. The molecular and evolutionary characterization of mussel H2A.Z.1 and H2A.Z.2 histones is consistent with their functional specialization, supported on sequence divergence at promoter and coding regions as well as on varying gene expression patterns. More precisely, the expression of H2A.Z.2 transcripts in gonadal tissue and its potential upregulation in response to genotoxic stress might be mirroring the specialization of this variant in DNA repair. Overall, the findings presented in this work complement recent reports describing the widespread presence of other histone variants across eukaryotes, supporting an ancestral origin and conserved role for histone variants in chromatin.
By-product of passion fruit seed (Passiflora edulis) in the diet of commercial laying hens
Authors: Zanetti Leonardo Henrique , Murakami Alice Eiko , Diaz-Vargas Mayra , Flávia Quiles Garcia Guerra Ana , Ospina-Rojas Ivan Camilo , Matumoto Pintro Paula Toshimi , Cruz-Polycarpo Valquíria Cação
Published: June 2016

This study evaluated the effects of the inclusion of the by-product passion fruit seed (BPFS) in the diet of laying hens on performance, blood variables, quality, and lipid oxidation in eggs. A total of 384 Hy-line W36 layers (32 wk old) were distributed in a completely randomized design, with six treatments (control, 2.5%, 5.0%, 7.5%, 10.0%, and 12.5% inclusion of BPFS), eight replicates and eight birds each. The productive performance was evaluated for three cycles of 28 d each. There was no difference (P > 0.05) in egg production and feed conversion. However, feed intake showed increased linearly (P < 0.05). The egg weight, egg mass, percentage of eggshell, eggshell thickness, and Haugh unit did not differ (P > 0.05); however, the specific gravity of eggs increased (P < 0.05). Total cholesterol and blood triglycerides decreased linearly (P < 0.05). To evaluate the lipid yolk oxidation, a 6 × 5 × 2 factorial design (six levels of BPFS × five storage periods × two temperatures) was used. There was an interaction (P < 0.05) among the levels of BPFS, time, and storage temperature with the lowest oxidation level of 12.5% when eggs were refrigerated. The BPFS can be included at a level up to 5.0% without compromising bird performance and 12.5% for egg quality, and this level reduced yolk lipid oxidation.
Comparison of apparent ileal and total tract digestibility of calcium in calcium sources for pigs
Authors: Zhang F. , Ragland D. , Adeola O.
Published: June 2016

Two experiments were conducted to compare apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of calcium (Ca) in pigs. In experiment 1, three semipurified diets with soybean meal, canola meal, or sunflower meal as the sole source of Ca were formulated. Eighteen cannulated pigs (initial BW = 66 ± 5 kg) were assigned in a randomized complete block design to three treatments and six replicates per treatment. Results indicated that for either Ca or phosphorus (P), the ATTD was not different from the AID in the three diets (Psite = 0.16 and 0.81, respectively). In experiment 2, diets with four Ca concentrations were formulated with calcium carbonate as the Ca source. Sixteen cannulated pigs (initial BW = 73 ± 4 kg) were assigned in a randomized complete block design to four treatments in two experimental periods. The results indicated that the ATTD of Ca was not different from the AID for all diets. Furthermore, the Ca digestibility was not affected by dietary treatments, but the P digestibility was linearly improved (P < 0.01) as dietary Ca and P concentrations increased. Thus, it is concluded that both AID and ATTD can be used to describe the digestibility of Ca for growing–finishing pigs.
Sediment addition reduces the importance of predation on ecosystem functions in experimental stream channels
Authors: Louhi Pauliina , Richardson John S. , Muotka Timo
Published: June 2016

Sedimentation is a pervasive cause of biological impairment in streams, and predation exerts strong control over lower trophic levels. However, studies combining these two factors are lacking. In a factorial experiment in flow-through channels, addition of sand (<0.5 mm) and predatory stoneflies (Perlidae) caused independent effects on benthic invertebrates, algal biomass, and leaf breakdown. Sand reduced invertebrate density by 55% and also reduced leaf breakdown and algal biomass. Predators reduced invertebrate densities by 40%, with the strongest impact on algal-feeding invertebrates. Predators also decreased densities of leaf-shredding invertebrates and reduced leaf breakdown, thereby inducing a trophic cascade via detritus-based food web. The two treatments exhibited an antagonistic interaction whereby sand obscured any effect of predators on algae, indicating that an abiotic stress may modify a trophic cascade. By contrast, we found no support for synergistic interactions between sand and predation. The strong effects of sedimentation on key ecosystem processes illustrate that stream management needs to exploit riparian and in-stream measures to reduce sediment inputs to headwater streams.
Condition dependence in the marine exit timing of sockeye salmon (Oncorhynchus nerka) returning to Copper Creek, Haida Gwaii
Authors: Katinić Peter J. , Patterson David A. , Ydenberg Ronald C.
Published: June 2016

We examined a small population of sockeye salmon (Oncorhynchus nerka) that enters their natal stream, to hold in their natal lake, months (>130 days) prior to spawning. This effectively decouples the influence of spawn timing requirements and behaviours from river entry (alternately referred to as “marine exit”) timing and is therefore a good model to study the migration strategies specifically associated with marine exit. We found individuals with early marine exit had higher growth rates in the months prior to river entry, had greater lipid density, were more likely male, more likely of the 2.2 versus 1.2 age class, had smaller gonads, and (if female) had more and smaller eggs. Body size at river entry did not vary seasonally. These patterns are explained using a life history model proposing that individual fish exit the sea when the marginal fitness benefits of further growth are outweighed by the marginal fitness cost of further marine residence. This point is reached at different times depending on body size, sex, lipid reserves, and the growth rate.
Soil microbial properties during decomposition of pulse crop and legume green manure residues in three consecutive subsequent crops
Authors: Lupwayi Newton Z. , Soon Yoong K.
Published: June 2016

Crop residue decomposition not only is mainly driven by, but also affects, soil microorganisms. However, soil microbial responses to legume crops are usually studied only in one subsequent crop. We compared the soil microbial effects of pea (Pisum sativa L.) and faba bean (Vicia faba L.) pulse crops (grown for seed) with faba green manure (GM) and chickling vetch (Lathyrus sativus L.) GM crops in three subsequent crops. Soil microbial biomass C (MBC), β-glucosidase enzyme activity, and bacterial physiological (C substrate utilization) diversity were measured in the summer (rhizosphere and bulk soil) and fall (bulk soil) in all subsequent crops: wheat (Triticum aestivum L.), canola (Brassica napus L.), and barley (Hordeum vulgare L.). Residues of faba bean (grown for GM, herein called faba GM, or for seed, herein called faba bean) usually resulted in the most soil MBC and β-glucosidase activity relative to the other residues. Faba and vetch GM residues increased bulk soil MBC or β-glucosidase enzyme activity more than pulse crop residues in the first and (or) third subsequent crops. Soil MBC and β-glucosidase activities were often positively correlated with initial crop residue N concentrations and negatively correlated with initial C:N ratios or C concentrations. Bacterial physiological diversity was the least responsive to crop residues and was affected differently by sampling time. β-Glucosidase activity was always greater in the fall after crop harvest than in summer. Therefore, β-glucosidase activity was a more sensitive and consistent biological indicator of crop residue effects, and perhaps soil health, than MBC or bacterial physiological diversity.
Intestinal parasites of gray wolves (Canis lupus) in northern and western Canada
Authors: Schurer Janna M. , Pawlik Michael , Huber Anna , Elkin Brett , Cluff H. Dean , Pongracz Jodie D. , Gesy Karen , Wagner Brent , Dixon Brent , Merks Harriet , Bal Mandeep S. , Jenkins Emily J.
Published: June 2016

Gray wolves (Canis lupus L., 1758) are mobile opportunistic predators that can be infected by a wide range of parasites, with many acquired via predator–prey relationships. Historically, many of these parasites were identified only to genus or family, but genetic tools now enable identification of parasite fauna to species and beyond. We examined 191 intestines from wolves harvested for other purposes from regions in the Northwest Territories, British Columbia, Saskatchewan, and Manitoba. Adult helminths were collected from intestinal contents for morphological and molecular identification, and for a subset of wolves, fecal samples were also analyzed to detect helminth eggs and protozoan (oo)cysts. Using both detection methods, we found that 83% of 191 intestines contained one or more parasite species, including cestodes (Taenia spp., Echinococcus spp., and Diphyllobothrium sp.), nematodes (Uncinaria stenocephala Railliet, 1884, Trichuris spp., Physaloptera spp., and Toxascaris leonina (von Linstow, 1902)), a trematode (Alaria sp.), and protozoa (Sarcocystis spp., Giardia sp., and Cryptosporidium spp.). Molecular characterization identified one species of Diphyllobothrium (Diphyllobothrium latum (L., 1758) Cobbold, 1858), three species of Taenia (Taenia krabbei Moniez, 1879, Taenia hydatigena Pallas, 1766, and Taenia multiceps Leske, 1786), and two Giardia duodenalis (Davaine) Deschiens, 1921 assemblages (B and C). These results demonstrate the diverse diet of wolves and illustrate the possibility of parasite spillover among wildlife, domestic animals, and people.
Hierarchical k-Nearest Neighbor with GPUs and a High Performance Cluster: Application to Handwritten Character Recognition
Authors: Cecotti Hubert
Published: June 2016

The accelerating progress and availability of low cost computers, high speed networks, and software for high performance distributed computing allow us to reconsider computationally expensive techniques in image processing and pattern recognition. We propose a two-level hierarchical [Formula: see text]-nearest neighbor classifier where the first level uses graphics processor units (GPUs) and the second level uses a high performance cluster (HPC). The system is evaluated on the problem of character recognition with nine databases (Arabic digits, Indian digits (Bangla, Devnagari, and Oriya), Bangla characters, Indonesian characters, Arabic characters, Farsi characters and digits). Contrary to many approaches that tune the model for different scripts, the proposed image classification method is unchanged throughout the evaluation on the nine databases. We show that a hierarchical combination of decisions based on two distances, using GPUs and a HPC provides state-of-the-art performances on several scripts, and provides a better accuracy than more complex systems.
DFT CALCULATIONS OF THE ELECTRONIC STRUCTURE AND INTERLAYER INTERACTION IN THE Li-INTERCALATED GRAPHENE BILAYER
Authors: PETROVA N. V. , YAKOVKIN I. N.
Published: June 2016

The electronic band structure, density of states (DOS) and interlayer interaction in Li-intercalated graphene bilayers are studied by means of density functional theory (DFT) calculations. It has been found that for a pristine bilayer, the relative shift of graphene layers from AB stacking configuration, pertinent to a bulk graphite, to AA configuration results in the opening of the bandgap at Fermi level, so that the bilayer becomes a semiconductor. The Li intercalation of the graphene bilayer significantly increases the density of states at Fermi level, which can be considered as an increased metallicity. The electronic density in the space between graphene layers also substantially increases and leads to related increase of the interlayer interaction. We hope that the obtained results of calculations will be useful for various applications of Li-intercalated graphene layers in nanoelectronics.
Voting with Intensity of Preferences
Authors: Vargas Luis G.
Published: June 2016

In this paper, we develop a method based on the idea of pairwise voting to rank projects or candidates and incorporate in the ranking process how strongly the referees/voters feel about the comparisons they make. Voting is a modified form of ranking and all the votes are equally important. However, there are situations similar to voting in which the votes are not just ordinal but each voter expresses an intensity of preference for the different candidates, e.g., ranking projects for funding. We show that our method yields the same results as ordinal voting in large populations when the intensity of preferences becomes extreme. Voting with intensity of preferences does not violate democracy but soften the stand of voters and allows for consideration of the diversity of issues involved in voting.
The Development of a KIM Behavioural Framework to Support Science and Technology Knowledge Transfer in the UK Defence Sector. A Case Study Approach
Authors: Darby R. , Kirke C.
Published: June 2016

A framework is presented for investigating and understanding human behaviour connected with knowledge and information management (KIM), developed from a case study in the UK defence sector. Qualitative research was undertaken in three organisations within the wider defence and security sector. The research showed that particular areas of sensitivity leading to resistance to change when KIM systems were introduced include a perceived lack of usability of KIM IT systems, the length of time required to learn how to use them, their perceived lack of reliability and the users’ consequent lack of trust in them. These issues led to the widespread use of “work arounds” to cope with the demands of the job without using the KIM systems as designed. The framework’s purpose is to contribute to the current field of knowledge about how organisations can best approach and implement required KIM changes, taking these human issues into account.
A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features
Authors: Li Liqi , Luo Qifa , Xiao Weidong , Li Jinhui , Zhou Shiwen , Li Yongsheng , Zheng Xiaoqi , Yang Hua
Published: June 2016

Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, organelle localization, and functions, therefore plays an important role in a variety of cell biological processes. Identification of palmitoylation sites is necessary for understanding protein–protein interaction, protein stability, and activity. Since conventional experimental techniques to determine palmitoylation sites in proteins are both labor intensive and costly, a fast and accurate computational approach to predict palmitoylation sites from protein sequences is in urgent need. In this study, a support vector machine (SVM)-based method was proposed through integrating PSI-BLAST profile, physicochemical properties, [Formula: see text]-mer amino acid compositions (AACs), and [Formula: see text]-mer pseudo AACs into the principal feature vector. A recursive feature selection scheme was subsequently implemented to single out the most discriminative features. Finally, an SVM method was implemented to predict palmitoylation sites in proteins based on the optimal features. The proposed method achieved an accuracy of 99.41% and Matthews Correlation Coefficient of 0.9773 for a benchmark dataset. The result indicates the efficiency and accuracy of our method in prediction of palmitoylation sites based on protein sequences.
On conformally related spherically symmetric Finsler metrics
Authors: Maleki Maryam , Sadeghzadeh Nasrin , Rajabi Tahereh
Published: June 2016

In this paper, we study the projective invariant quantities in Finsler geometry which remain invariant under the conformal change of metrics. In particular, we obtain the necessary and sufficient conditions of a given Douglas and Weyl and generalized Douglas–Weyl (GDW) metric to be invariant under the conformal transformations. Finally, we introduce some explicit examples of these metrics. Also, some of these [Formula: see text]-conformal transformations of Einstein metrics are considered.
Sample Compression Schemes for VC Classes
Authors: Moran Shay , Yehudayoff Amir
Published: June 2016

Sample compression schemes were defined by Littlestone and Warmuth (1986) as an abstraction of the structure underlying many learning algorithms. Roughly speaking, a sample compression scheme of size
k
means that given an arbitrary list of labeled examples, one can retain only
k
of them in a way that allows us to recover the labels of all other examples in the list. They showed that compression implies probably approximately correct learnability for binary-labeled classes and asked whether the other direction holds. We answer their question and show that every concept class
C
with VC dimension
d
has a sample compression scheme of size exponential in
d
.
A Rank Lower Bound for Cutting Planes Proofs of Ramsey’s Theorem
Authors: Lauria Massimo
Published: June 2016

Ramsey’s Theorem is a cornerstone of combinatorics and logic. In its simplest formulation it says that for every
k
> 0 and
s
> 0, there is a minimum number
r
(
k
,
s
) such that any simple graph with at least
r
(
k
,
s
) vertices contains either a clique of size
k
or an independent set of size
s
. We study the complexity of proving upper bounds for the number
r
(
k
,
k
). In particular, we focus on the propositional proof system cutting planes; we show that any cutting plane proof of the upper bound “
r
(
k
,
k
) ⩽ 4

k

” requires high rank. In order to do that we show a protection lemma which could be of independent interest.
Improved Algorithms for Constructing Consensus Trees
Authors: Jansson Jesper , Shen Chuanqi , Sung Wing-Kin
Published: June 2016

A
consensus tree
is a single phylogenetic tree that summarizes the branching structure in a given set of conflicting phylogenetic trees. Many different types of consensus trees have been proposed in the literature; three of the most well-known and widely used ones are
the majority rule consensus tree
,
the loose consensus tree
, and
the greedy consensus tree
. This article presents new deterministic algorithms for constructing them that are faster than all the previously known ones. Given
k
phylogenetic trees with
n
leaves each and with identical leaf label sets, our algorithms run in
O
(
nk
) time (majority rule consensus tree),
O
(
nk
) time (loose consensus tree), and
O
(
n
2
k
) time (greedy consensus tree). Our algorithms for the majority rule consensus and the loose consensus trees are optimal since the input size is Ω(
nk
). Experimental results show that the algorithms are fast in practice.
Identification of human sympathetic neurovascular control using multivariate wavelet decomposition analysis
Authors: Saleem Saqib , Teal Paul D. , Kleijn W. Bastiaan , Ainslie Philip N. , Tzeng Yu-Chieh
Published: June 2016

The dynamic regulation of cerebral blood flow (CBF) is thought to involve myogenic and chemoreflex mechanisms, but the extent to which the sympathetic nervous system also plays a role remains debated. Here we sought to identify the role of human sympathetic neurovascular control by examining cerebral pressure-flow relations using linear transfer function analysis and multivariate wavelet decomposition analysis that explicitly accounts for the confounding effects of dynamic end-tidal Pco2 (PetCO2) fluctuations. In 18 healthy participants randomly assigned to the α1-adrenergic blockade group ( n = 9; oral Prazosin, 0.05 mg/kg) or the placebo group ( n = 9), we recorded blood pressure, middle cerebral blood flow velocity, and breath-to-breath PetCO2. Analyses showed that the placebo administration did not alter wavelet phase synchronization index (PSI) values, whereas sympathetic blockade increased PSI for frequency components ≤0.03 Hz. Additionally, three-way interaction effects were found for PSI change scores, indicating that the treatment response varied as a function of frequency and whether PSI values were PetCO2 corrected. In contrast, sympathetic blockade did not affect any linear transfer function parameters. These data show that very-low-frequency CBF dynamics have a composite origin involving, not only nonlinear and nonstationary interactions between BP and PetCO2, but also frequency-dependent interplay with the sympathetic nervous system.
A new experimental model of acid- and endotoxin-induced acute lung injury in rats
Authors: Puig F. , Herrero R. , Guillamat-Prats R. , Gómez M. N. , Tijero J. , Chimenti L. , Stelmakh O. , Blanch L. , Serrano-Mollar A. , Matthay M. A. , Artigas A.
Published: June 2016

The majority of the animal models of acute lung injury (ALI) are focused on the acute phase. This limits the studies of the mechanisms involved in later phases and the effects of long-term treatments. Thus the goal of this study was to develop an experimental ALI model of aspiration pneumonia, in which diffuse alveolar damage continues for 72 h. Rats were intratracheally instilled with one dose of HCl (0.1 mol/l) followed by another instillation of one dose of LPS (0, 10, 20, 30, or 40 μg/g body weight) 2 h later, which models aspiration of gastric contents that progresses to secondary lung injury from bacteria or bacterial products. The rats were euthanized at 24, 48, and 72 h after the last instillation. The results showed that HCl and LPS at all doses caused activation of inflammatory responses, increased protein permeability and apoptosis, and induced mild hypoxemia in rat lungs at 24 h postinstillation. However, this lung damage was present at 72 h only in rats receiving HCl and LPS at the doses of 30 and 40 μg/g body wt. Mortality (∼50%) occurred in the first 48 h and only in the rats treated with HCl and LPS at the highest dose (40 μg/g body wt). In conclusion, intratracheal instillation of HCl followed by LPS at the dose of 30 μg/g body wt results in severe diffuse alveolar damage that continues at least 72 h. This rat model of aspiration pneumonia-induced ALI will be useful for testing long-term effects of new therapeutic strategies in ALI.
Cardiovascular control during whole body exercise
Authors: Volianitis Stefanos , Secher Niels H.
Published: June 2016

It has been considered whether during whole body exercise the increase in cardiac output is large enough to support skeletal muscle blood flow. This review addresses four lines of evidence for a flow limitation to skeletal muscles during whole body exercise. First, even though during exercise the blood flow achieved by the arms is lower than that achieved by the legs (∼160 vs. ∼385 ml·min−1·100 g−1), the muscle mass that can be perfused with such flow is limited by the capacity to increase cardiac output (42 l/min, highest recorded value). Secondly, activation of the exercise pressor reflex during fatiguing work with one muscle group limits flow to other muscle groups. Another line of evidence comes from evaluation of regional blood flow during exercise where there is a discrepancy between flow to a muscle group when it is working exclusively and when it works together with other muscles. Finally, regulation of peripheral resistance by sympathetic vasoconstriction in active muscles by the arterial baroreflex is critical for blood pressure regulation during exercise. Together, these findings indicate that during whole body exercise muscle blood flow is subordinate to the control of blood pressure.