bluuebunny/crossref_metadata_2025 huggingface dataset:
Parathyroid surgery: correlation between pre‐operative localization studies and surgical outcomes
Authors: Ebner Yaniv , Garti‐Gross Yael , Margulis Ariel , Levy Yair , Nabrisky Dan , Ophir Dov , Rotman‐Pikielny Pnina
Published: June 2015

Objective

Pre‐operative imaging techniques have enabled minimally invasive parathyroid surgery to supersede the traditional approach to hyperparathyroidism (HPT) surgery, which included cervical exploration. Cervical ultrasound (US) and sestamibi scan (MIBI) are commonly performed, but the results of these localization tests do not always match. This study correlated surgical outcomes with pre‐operative localization findings, including matched positive US and MIBI studies, one positive study (US or MIBI), conflicting studies or negative results.

Design

Retrospective medical record review.

Patients

A hundred and sixty nine consecutive patients who underwent parathyroidectomy from January 2005 to December 2012.

Measurements

Correlation between surgical outcomes and pre‐operative localization tests.

Results

All patients (134F/35M, 59·6 ± 13·5 years of age) had primary HPT. US and MIBI localization studies matched in 76%, whereas 10·7% had positive MIBI only and 8·3% US only. Studies were negative in 3·6% and contradictory in 1·8%. Minimally invasive parathyroidectomy was performed in 87% of the matched group and 89% of the MIBI‐only group. Surgical success rate, defined as postoperative normalization of calcium and PTH levels, was similar in patients with a single positive study (MIBI or US) vs double‐matched studies (MIBI and US). Patients were followed up for 6 weeks. Overall, pathology was consistent with adenoma in 95%.

Discussion

Parathyroidectomy success rate was similar in patients with primary HPT and MIBI‐only or US‐only positive localization studies compared to those with matched US/MIBI studies. The results support a clinical algorithm in which positive results from one imaging technique, either MIBI or US, are sufficient to refer a patient for parathyroid surgery.
Guidelines for the Cytopathologic Diagnosis of Epithelioid and Mixed‐Type Malignant Mesothelioma: a secondary publication
Authors: Hjerpe A. , Ascoli V. , Bedrossian C. W. M. , Boon M. E. , Creaney J. , Davidson B. , Dejmek A. , Dobra K. , Fassina A. , Field A. , Firat P. , Kamei T. , Kobayashi T. , Michael C. W. , Önder S. , Segal A. , Vielh P.
Published: June 2015

Objective

To provide practical guidelines for the cytopathologic diagnosis of malignant mesothelioma.

Data Sources

Cytopathologists with an interest in the field involved in the International Mesothelioma Interest Group (IMIG) and the International Academy of Cytology (IAC) contributed to this update. Reference material includes peer‐reviewed publications and textbooks.

Rationale

This article is the result of discussions during and after the IMIG 2012 conference in Boston, followed by thorough discussions during the 2013 IAC meeting in Paris. Additional contributions have been obtained from cytopathologists and scientists who could not attend these meetings, with final discussions and input during the IMIG 2014 conference in Cape Town.
Reference Values for Real Time Three‐Dimensional Echocardiography–Derived Left Ventricular Volumes and Ejection Fraction: Review and Meta‐Analysis of Currently Available Studies
Authors: Buccheri Sergio , Costanzo Luca , Tamburino Corrado , Monte Ines
Published: June 2015

Introduction

Current guidelines recommend three‐dimensional echocardiography (3DE) as the reference technique to assess left ventricular (LV) volumes and ejection fraction (EF). We performed a meta‐analysis to identify normative reference values by real time 3DE in healthy subjects.

Methods

We searched MEDLINE and the Cochrane Library databases using the key search terms three‐dimensional echocardiography, volumes, and healthy. Data were pooled using random‐effects meta‐analysis, and source of variation was investigated using meta‐regression. After selection, 13 articles were included (2806 subjects). Four studies were conducted in children and young adolescents; one study provided data in an independent pediatric subgroup.

Results

In adults, pooled mean value for LV EDV was 98.4 mL (95%CI, 87–110 mL), while LV ESV mean value was 37.0 mL (95%CI, 32–42 mL). LV EF mean value was 62.9% (95%CI 61.7–64.2%). Male subjects showed a significant increase in both LV EDV index (mean difference 5.3 mL/m2; P < 0.001) and LV ESV index (mean difference 3.3 mL/m2; P < 0.001). LV EF was significantly higher in female subjects (P = 0.003). In pediatric studies, LV EDV pooled mean value was 53.1 mL (95%CI, 38.1–68 mL), while for LV ESV, it was 19.8 mL (95%CI, 14.8–24.8 mL); LV EF mean value was 63.3% (95%CI, 61.6–65%). Significant heterogeneity and inconsistency were noted among studies. Age, systolic blood pressure, and heart rate were identified as a source of between‐studies variation for LV volumes. Body surface area was a predictor of nonindexed LV volumes.

Conclusions

Data from available studies of normative values for 3DE were summarized. Our findings may increase the generalizability of LV normative data by 3DE.
Comparison between Regional and Local Pulse‐Wave Velocity Data
Authors: Simova Iana , Katova Tzvetana , Santoro Ciro , Galderisi Maurizio
Published: June 2015

Background

Gold standard for pulse‐wave velocity (PWV) measurement is determination of the carotid‐femoral cfPWV, reflecting regional aortic PWV. Nevertheless, in several echocardiographic laboratories, PWV is measured locally, most commonly at the common carotid artery (CCA). The aim of this study was to compare regional and local PWV values in healthy volunteers.

Methods

The study population consisted of 22 prospectively enrolled healthy subjects, mean age 38.7 ± 11.1 years, 50% male. For regional PWV measurement, we evaluated cfPWV with a standard echo scanner. Regional PWV was measured at the CCA, with semiautomated dedicated software (MyLab, EsaOte, Italy).

Results

cfPWV and local PWV values correlated significantly with high Pearson correlation coefficient (0.62, P = 0.002). Mean regional cfPWV (9.29 ± 3.73 m/s), however, was significantly higher than mean local PWV value (5.96 ± 1.08 m/s) (P < 0.001). The difference persisted in the subgroup analysis using different cfPWV cutoff values (10, 9, 8, and 7 m/s), except for subjects with cfPWV ≤7 m/s, where regional and local PWV values were similar.

Conclusion

In a group of healthy volunteers, regional and local PWV values showed a good correlation. However, regional PWV was significantly higher than local PWV. These findings should be carefully taken into account when using this technique in the clinical setting.
cati: an R package using functional traits to detect and quantify multi‐level community assembly processes
Authors: Taudiere Adrien , Violle Cyrille
Published: June 2015

Community ecologists are active in describing species by their functional traits, quantifying the functional structure of plant and animal assemblages and inferring community assembly processes with null‐model analyses of trait distribution and functional diversity indices. Intraspecific variation in traits and effects of spatial scale are potentially important in these analyses.

Here, we introduce the R package cati (Community Assembly by Traits: Individuals and beyond) available on CRAN, for the analysis of community assembly with functional traits. cati builds on a recent approach to community assembly that explicitly incorporates individual differences in community assembly analyses and decomposes phenotypic variations across scales and organizational levels, based on three phenotypic variance ratios, termed the T‐statistics. More generally, the cati package 1) calculates a variety of single‐trait and multi‐trait indices from interspecific and intraspecific trait measures; 2) it partitions functional trait variation among spatial and taxonomic levels; 3) it implements a palette of flexible null models for detecting non‐random patterns of functional traits. These patterns can be used to draw inferences about hypotheses of community assembly such as environmental filtering and species interactions.

The basic input for cati is a data frame in which columns are traits, rows are species or individuals, and entries are the measured trait values. The cati package can also incorporate a square distance matrix into analyses, which could include phylogenetic or genetic distances among individuals or species. Users select from a variety of functional trait metrics and analyze these relative to a null model that specifies trait distributions in a regional source pool.
Naming and Framing of Intersectionality in Hijab Cases — Does It Matter? An Analysis of Discrimination Cases in Scandinavia and the Netherlands
Authors: Halrynjo Sigtona , Jonker Merel
Published: June 2015

This article examines how intersectionality is recognized in hijab discrimination cases brought before the Norwegian, Swedish, Danish and Dutch equality bodies. Hijab cases are regarded as a perfect example of intersectionality, as religion and gender are interwoven in the use of the Muslim veil. The theoretical shift towards intersectionality has influenced substantial revisions of equality policies, bodies and laws. Recognizing intersectionality has become synonymous with quality in the equality architecture. We question this and argue that quality must be scrutinized empirically, including the practice of the equality bodies. Our results show that most complainants do not present their cases as intersectional discrimination, and that only the Norwegian equality body applies an intersectional approach. However, an intersectional approach seems not to be crucial to protect against discrimination in these cases. Thus, we argue that the quality of the equality architecture should be scrutinized more on the process, judgement and actual ability to promote equality, than on the naming and framing of intersectionality.
Determining the stability of complete blood count parameters in stored blood samples using the SYSMEX XE‐5000 automated haematology analyser
Authors: Joshi A. , McVicker W. , Segalla R. , Favaloro E. , Luu V. , Vanniasinkam T.
Published: June 2015

Introduction

In this study, changes that occur in various blood parameters as determined by the Sysmex XE‐5000 analyser upon storage of blood samples for 72 h were investigated.

Methods

Blood specimens (200) were processed through the SYSMEX XE‐5000 haematology analyser within 4 h of collection. Each specimen was distributed into two aliquots and one stored at 4 °C and the other at room temperature (25 ± 1 °C). Both stored aliquots were retested after 24, 48 and 72 h. The mean, mean per cent change and mean absolute difference between the value at 4 h and each time point for all parameters were calculated.

Results

Among CBC parameters tested, the white cell count, red cell count and haemoglobin levels were found to be stable for up to 72 h. The mean cell volume and haematocrit changed significantly following 24‐h storage at room temperature. Reticulocytes were stable for 72 h under both storage conditions. Among the differential parameters, results of the monocyte count displayed significant change after 24‐h storage at room temperature.

Conclusion

The data presented suggest that clinically reliable results for some CBC parameters can be obtained from specimens that are stored at 4 °C for up to 72 h.
Parenting style influences bullying: a longitudinal study comparing children with and without behavioral problems
Authors: Rajendran Khushmand , Kruszewski Edyta , Halperin Jeffrey M.
Published: June 2015

Background

More optimal parenting has been linked with lower rates of bullying. However, it is not clear whether parenting can alter the trajectories of bullying among children diagnosed with ADHD or ODD as well as those who are not so diagnosed. This study examined whether parenting at age 4–5 years was associated with changes in bullying over the next 4 years among children with Attention‐deficit/Hyperactivity Disorder (ADHD) with and without comorbid Oppositional Defiant Disorder (ODD) relative to children without these disorders.

Method

Children from the New York metropolitan area (n = 162) were prospectively studied over six annual assessment points between preschool and 9 years of age. Parenting was assessed by laboratory observations of the parent and child; teachers rated child bullying, and parents reported on children's diagnostic status (Neither ADHD nor ODD, ADHD but not ODD, both ADHD and ODD).

Results

Children with comorbid ADHD and ODD were more likely to bully than the other two groups. Hierarchical linear modeling revealed a fall in bullying over five years. Diagnostic status was significantly associated with initial levels of bullying. Irrespective of diagnostic group, children receiving more parent support for child autonomy at age 4 to 5 years showed a significantly greater decline in bullying than those provided with little support for autonomy. There was no longitudinal link between parent negative affect, emotionally supportive parenting and quality of parent–child interactions with bullying.

Conclusions

Greater parent support for child autonomy at age 4–5 years is related to reduced bullying. Interventions that encourage parent support for child autonomy at the time of entry into school may reduce bullying during early school years.
Lack of Oestrogenic Inhibition of the Nuclear Factor‐κB Pathway in Somatolactotroph Tumour Cells
Authors: Eijo G. , Gottardo M. F. , Jaita G. , Magri M. L. , Moreno Ayala M. , Zárate S. , Candolfi M. , Pisera D. , Seilicovich A.
Published: June 2015

Activation of nuclear factor (NF)‐κB promotes cell proliferation and inhibits apoptosis. We have previously shown that oestrogens sensitise normal anterior pituitary cells to the apoptotic effect of tumour necrosis factor (TNF)‐α by inhibiting NF‐κB nuclear translocation. In the present study, we examined whether oestrogens also modulate the NF‐κB signalling pathway and apoptosis in GH3 cells, a rat somatolactotroph tumour cell line. As determined by Western blotting, 17β‐oestradiol (E2) (10−9 m) increased the nuclear concentration of NF‐κB/p105, p65 and p50 in GH3 cells. However, E2 did not modify the expression of Bcl‐xL, a NF‐κB target gene. TNF‐α induced apoptosis of GH3 cells incubated in either the presence or absence of E2. Inhibition of the NF‐kB pathway using BAY 11‐7082 (BAY) (5 μm) decreased the viability of GH3 cells and increased the percentage of terminal deoxynucleotidyl transferase dUTP nick end labelling (TUNEL)‐positive GH3 cells. BAY also increased TNF‐α‐induced apoptosis of GH3 cells, an effect that was further increased by an inhibitor of the c‐Jun N‐terminal protein kinase pathway, SP600125 (10 μm). We also analysed the role of the NF‐κB signalling pathway on proliferation and apoptosis of GH3 tumours in vivo. The administration of BAY to nude mice bearing GH3 tumours increased the number of TUNEL‐positive cells and decreased the number of proliferating GH3 cells. These findings suggest that GH3 cells lose their oestrogenic inhibitory action on the NF‐κB pathway and that the pro‐apoptotic effect of TNF‐α on these tumour pituitary cells does not require sensitisation by oestrogens as occurs in normal pituitary cells. NF‐κB was required for the survival of GH3 cells, suggesting that pharmacological inhibition of the NF‐κB pathway could interfere with pituitary tumour progression.
Assessment of acute kidney injury at hospital admission in cirrhosis: estimating baseline serum creatinine is not the answer
Authors: Solà Elsa , Ginès Pere
Published: June 2015

See Article on Page 2108
Health disparities in liver disease in sub‐Saharan Africa
Authors: Spearman C. Wendy , Sonderup Mark W.
Published: June 2015

Disparities in health reflect the differences in the incidence, prevalence, burden of disease and access to care determined by socio‐economic and environmental factors. With liver disease, these disparities are exacerbated by a combination of limited awareness and preventable causes of morbidity and mortality in addition to the diagnostic and management costs. Sub‐Saharan Africa, comprising 11% of the world's population, disproportionately has 24% of the global disease burden, yet allocates <1% of global spend on health. It has 3% of the global healthcare workforce with a mean of 0.8 healthcare workers per 1000 population. Barriers to healthcare access are many and compounded by limited civil registration data, socio‐economic inequalities, discrepancies in private and public healthcare services and geopolitical strife. The UN 2014 report on the Millennium Development Goals suggest that sub‐Saharan Africa will probably not meet several goals, however with HIV/AIDS and Malaria (goal 6), many successes have been achieved. A 2010 Global Burden of Disease study demonstrated that cirrhosis mortality in sub‐Saharan Africa doubled between 1980 and 2010. Aetiologies included hepatitis B (34%), hepatitis C (17%), alcohol (18%) and unknown in 31%. Hepatitis B, C and alcohol accounted for 47, 23 and 20% of hepatocellular carcinoma respectively. In 10%, the underlying aetiology was not known. Liver disease reflects the broader disparities in healthcare in sub‐Saharan Africa. However, many of these challenges are not insurmountable as vaccines and new therapies could comprehensively deal with the burden of viral hepatitis. Access to and affordability of therapeutics remains the major barrier.
Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana
Authors: Chen Yuan , Litvintseva Anastasia P. , Frazzitta Aubrey E. , Haverkamp Miriam R. , Wang Liuyang , Fang Charles , Muthoga Charles , Mitchell Thomas G. , Perfect John R.
Published: June 2015

Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub‐Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MATa allele were observed in both clinical and environmental isolates; however, the mating‐type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MATa and MATα mating types were observed among all clinical isolates and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.
Linking demographic responses and life history tactics from longitudinal data in mammals
Authors: Gamelon Marlène , Gaillard Jean‐Michel , Gimenez Olivier , Coulson Tim , Tuljapurkar Shripad , Baubet Eric
Published: June 2015

In stochastic environments, a change in a demographic parameter can influence the population growth rate directly or via a resulting impact on age structure. Stochastic elasticity of the long‐run stochastic growth rate λsto a demographic parameter offers a suitable way to measure the overall demographic response because it includes both the direct effect of changing the demographic parameter and its indirect effect through changes in the age structure. From 25 mammalian populations with contrasting life histories, we investigated how pace of life and population growth rate influence the demographic responses (measured as the relative contributions of the direct and indirect components of stochastic elasticity on λs). We found that in short‐lived species, the change in population structure resulting from an increase in yearling survival leads to an additional increase in λs, whereas in long‐lived species, the same change in population structure leads to a decrease. Short‐lived species thus display a boom‐bust life history strategy contrary to long‐lived species, for which the long lifespan dampens the demographic consequences of changing age structure. Irrespective of the species’ life history strategy, the change in population age structure resulting from an increase in adult survival leads to an additional increase in λsdue to an increase of the proportion of mature individuals in the population. On the contrary, a change in population age structure resulting from an increase of reproductive performance leads to a decrease in λsthat is due to the increase of the proportion of immature individuals in the population. Our comparative analysis of stochastic elasticity patterns in mammals shows the existence of different demographic responses to changes in age structure between short‐ and long‐lived species, which improves our understanding of population dynamics in variable environments in relation to the species‐specific pace of life.
Emotion Dysregulation and Affective Intensity Mediate the Relationship Between Childhood Abuse and Suicide‐Related Behaviors Among Women with Bulimia Nervosa
Authors: Gordon Kathryn H. , Simonich Heather , Wonderlich Stephen A. , Dhankikar Swati , Crosby Ross D. , Cao Li , Kwan Mun Yee , Mitchell James E. , Engel Scott G.
Published: June 2015

Self‐harm and suicide attempts occur at elevated rates among individuals with bulimia nervosa, particularly among those who have experienced childhood abuse. This study investigated the potential mediating roles of emotion dysregulation and affective intensity in the relationship between these variables in 125 women with bulimia nervosa. Analyses revealed that emotion dysregulation mediated the relationship between sexual and emotional abuse with both self‐harm and suicide attempts. Negative affective intensity mediated the relationship between abuse and suicide attempts. The findings may advance the understanding of mechanisms underlying suicide‐related behaviors in women with bulimia nervosa who experienced abuse and suggest potential clinical targets.
Skin substitute‐assisted repair shows reduced dermal fibrosis in acute human wounds validated simultaneously by histology and optical coherence tomography
Authors: Greaves Nicholas S. , Iqbal Syed A. , Hodgkinson Tom , Morris Julie , Benatar Brian , Alonso‐Rasgado Teresa , Baguneid Mohamed , Bayat Ardeshir
Published: June 2015

Skin substitutes are heterogeneous biomaterials designed to accelerate wound healing through provision of replacement extracellular matrix. Despite growing evidence for their use in chronic wounds, the role of skin substitutes in acute wound management and their influence on fibrogenesis remains unclear. Skin substitute characteristics including biocompatibility, porosity, and elasticity strongly influence cellular behavior during wound healing. Thus, we hypothesize that structural and biomechanical variation between biomaterials may induce differential scar formation after cutaneous injury. The following human prospective cohort study was designed to investigate this premise. Four 5‐mm full thickness punch biopsies were harvested from 50 volunteers. In all cases, site 1 healed by secondary intention, site 2 was treated with collagen‐GAG scaffold (CG), and decellularised dermis (DCD) was applied to site 3 while tissue extracted from site 4 was replaced (autograft). Healing tissue was assessed weekly with optical coherence tomography (OCT), before being excised on days 7, 14, 21, or 28 depending on study group allocation for later histological and immunohistochemical evaluation. Extracted RNA was used in microarray analysis and polymerase chain reaction of highlighted genes. Autograft treatment resulted in minimal fibrosis confirmed immunohistochemically and with OCT through significantly lower collagen I levels (p = 0.047 and 0.03) and reduced mean grayscale values (p = 0.038 and 0.015), respectively. DCD developed intermediate scar formation with partial rete ridge reformation and reduced fasiculonodular fibrosis. It was uniquely associated with late up‐regulation of matrix metalloproteinases 1 and 3, oncostatin M, and interleukin‐10 (p = 0.007, 0.04, 0.019, 0.019). Regenerated dermis was significantly thicker in DCD and autografts 28 days post‐injury compared with control and CG samples (p = 0.003 and <0.0001). In conclusion, variable fibrotic outcomes were observed in skin substitute‐treated wounds with reduced scarring in autograft and DCD samples compared with controls. OCT enabled concurrent assessment of wound morphology and quantification of dermal fibrosis.
Pivotal role of ATP in macrophages fast tracking wound repair and regeneration
Authors: Kotwal Girish J. , Sarojini Harshini , Chien Sufan
Published: June 2015

Chronic wounds occurring during aging or diabetes pose a significant burden to patients. The classical four‐phase wound healing process has a 3–6 day lag before granulation starts to appear and it requires an intermediate step of activation of resident fibroblasts during the remodeling phase for production of collagen. This brief communication discusses published articles that demonstrate how the entire wound healing process can be fast tracked by intracellular ATP delivery, which triggers a novel pathway where alternatively activated macrophages play absolutely critical and central roles. This novel pathway involves an increase in proinflammatory cytokines (TNF, IL‐1β, IL‐6) and a chemokine (MCP‐1) release. This is followed by activation of purinergic receptor (a family of plasma membrane receptors found in almost all mammalian cells), production of platelets and platelet microparticles, and activation of ATP‐dependent chromatin remodeling enzymes. The end result is a massive influx and in situ proliferation of macrophages, increases in vascular endothelial growth factors that promote neovascularization, and most prominently, the direct production of collagen.
Antimicrobial Resistance Profiles of Campylobacter spp. Isolated from Broiler Chicken Meat of Estonian, Latvian and Lithuanian Origin at Estonian Retail Level and from Patients with Severe Enteric Infections in Estonia
Authors: Mäesaar M. , Kramarenko T. , Meremäe K. , Sõgel J. , Lillenberg M. , Häkkinen L. , Ivanova M. , Kovalenko K. , Hörman A. , Hänninen M.‐L. , Roasto M.
Published: June 2015

The resistance patterns of Campylobacter spp. isolated from retail broiler chicken meat originating either from Estonia, Lithuania or Latvia collected in Estonia were determined. Additionally, in collaboration with the laboratories of several Estonian hospitals, antimicrobial susceptibility patterns were determined for Campylobacter isolates from patients with severe Campylobacter enteric infections. The isolates were identified at the species level by the PCR method. Respectively, 88.8% of the isolates were C. jejuni, and 11.2% were C. coli. In total, 126 Campylobacter isolates of broiler chicken meat and human origin were tested for minimal inhibitory concentrations (MICs) with the broth microdilution VetMICTH method (National Veterinary Institute; Uppsala, Sweden) for a total of six antimicrobials. Resistance to one or more antimicrobials was detected in 62 (63.3%) of Campylobacter broiler chicken meat isolates and in 20 (71.4%) of human‐origin isolates. Large proportions of the broiler chicken meat isolates were resistant to ciprofloxacin (60.2%). Multidrug resistance (i.e. to three or more unrelated antimicrobials) was detected in five (5.1%) C. jejuni isolates. Among the human isolates, 20 (71.4%) were resistant to fluoroquinolones, and two (7.1%) C. jejuni isolates exhibited multidrug resistance. The chicken meat isolates of Estonian origin were the most susceptible. However, a high proportion of fluoroquinolone‐resistant C. jejuni isolates were found in Latvian and Lithuanian products. The results of this study indicate that the problems caused by the inappropriate use of antimicrobials extend beyond the country in which a food originates; therefore, both domestic and international interventions and agreements are required to implement common policies on antimicrobial usage and to minimize the emergence of Campylobacter drug resistance.
Staphylococcus aureus
and the ecology of the nasal microbiome
Authors: Liu Cindy M. , Price Lance B. , Hungate Bruce A. , Abraham Alison G. , Larsen Lisbeth A. , Christensen Kaare , Stegger Marc , Skov Robert , Andersen Paal Skytt
Published: June 2015

Nasal turf wars may provide the secrets to stopping staph.
Facultative Anaerobe Caldibacillus debilis GB1: Characterization and Use in a Designed Aerotolerant, Cellulose-Degrading Coculture with Clostridium thermocellum
Authors: Wushke Scott , Levin David B. , Cicek Nazim , Sparling Richard
Published: June 2015

Development of a designed coculture that can achieve aerotolerant ethanogenic biofuel production from cellulose can reduce the costs of maintaining anaerobic conditions during industrial consolidated bioprocessing (CBP). To this end, a strain of
Caldibacillus debilis
isolated from an air-tolerant cellulolytic consortium which included a
Clostridium thermocellum
strain was characterized and compared with the
C. debilis
type strain. Characterization of isolate
C. debilis
GB1 and comparisons with the type strain of
C. debilis
revealed significant physiological differences, including (i) the absence of anaerobic metabolism in the type strain and (ii) different end product synthesis profiles under the experimental conditions used. The designed cocultures displayed unique responses to oxidative conditions, including an increase in lactate production. We show here that when the two species were cultured together, the noncellulolytic facultative anaerobe
C. debilis
GB1 provided respiratory protection for
C. thermocellum
, allowing the synergistic utilization of cellulose even under an aerobic atmosphere.
Paenibacilluslarvae-Directed Bacteriophage HB10c2 and Its Application in American Foulbrood-Affected Honey Bee Larvae
Authors: Beims Hannes , Wittmann Johannes , Bunk Boyke , Spröer Cathrin , Rohde Christine , Günther Gabi , Rohde Manfred , von der Ohe Werner , Steinert Michael
Published: June 2015

Paenibacillus
larvae
is the causative agent of American foulbrood (AFB), the most serious honey bee brood bacterial disease. We isolated and characterized
P. larvae
-directed bacteriophages and developed criteria for safe phage therapy. Whole-genome analysis of a highly lytic virus of the family
Siphoviridae
(HB10c2) provided a detailed safety profile and uncovered its lysogenic nature and a putative beta-lactamase-like protein. To rate its antagonistic activity against the pathogens targeted and to specify potentially harmful effects on the bee population and the environment,
P. larvae
genotypes ERIC I to IV, representatives of the bee gut microbiota, and a broad panel of members of the order
Bacillales
were analyzed for phage HB10c2-induced lysis. Breeding assays with infected bee larvae revealed that the
in vitro
phage activity observed was not predictive of the real-life scenario and therapeutic efficacy. On the basis of the disclosed
P. larvae
-bacteriophage coevolution, we discuss the future prospects of AFB phage therapy.
Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling
Authors: Ceapa Corina , Lambert Jolanda , van Limpt Kees , Wels Michiel , Smokvina Tamara , Knol Jan , Kleerebezem Michiel
Published: June 2015

Lactobacillus rhamnosus
is a bacterial species commonly colonizing the gastrointestinal (GI) tract of humans and also frequently used in food products. While some strains have been studied extensively, physiological variability among isolates of the species found in healthy humans or their diet is largely unexplored. The aim of this study was to characterize the diversity of carbohydrate utilization capabilities of human isolates and food-derived strains of
L. rhamnosus
in relation to their niche of isolation and genotype. We investigated the genotypic and phenotypic diversity of 25 out of 65
L. rhamnosus
strains from various niches, mainly human feces and fermented dairy products. Genetic fingerprinting of the strains by amplified fragment length polymorphism (AFLP) identified 11 distinct subgroups at 70% similarity and suggested niche enrichment within particular genetic clades. High-resolution carbohydrate utilization profiling (OmniLog) identified 14 carbon sources that could be used by all of the strains tested for growth, while the utilization of 58 carbon sources differed significantly between strains, enabling the stratification of
L. rhamnosus
strains into three metabolic clusters that partially correlate with the genotypic clades but appear uncorrelated with the strain's origin of isolation. Draft genome sequences of 8 strains were generated and employed in a gene-trait matching (GTM) analysis together with the publicly available genomes of
L. rhamnosus
GG (ATCC 53103) and HN001 for several carbohydrates that were distinct for the different metabolic clusters:
l
-rhamnose, cellobiose,
l
-sorbose, and α-methyl-
d
-glucoside. From the analysis, candidate genes were identified that correlate with
l
-sorbose and α-methyl-
d
-glucoside utilization, and the proposed function of these genes could be confirmed by heterologous expression in a strain lacking the genes. This study expands our insight into the phenotypic and genotypic diversity of the species
L. rhamnosus
and explores the relationships between specific carbohydrate utilization capacities and genotype and/or niche adaptation of this species.
Anaerobic Oxidation of Methane Coupled to Nitrite Reduction by Halophilic Marine NC10 Bacteria
Authors: He Zhanfei , Geng Sha , Cai Chaoyang , Liu Shuai , Liu Yan , Pan Yawei , Lou Liping , Zheng Ping , Xu Xinhua , Hu Baolan
Published: June 2015

Anaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA and
pmoA
gene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescence
in situ
hybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite.
Extracellular Glycoside Hydrolase Activities in the Human Oral Cavity
Authors: Inui Taichi , Walker Lauren C. , Dodds Michael W. J. , Hanley A. Bryan
Published: June 2015

Carbohydrate availability shifts when bacteria attach to a surface and form biofilm. When salivary planktonic bacteria form an oral biofilm, a variety of polysaccharides and glycoproteins are the primary carbon sources; however, simple sugar availabilities are limited due to low diffusion from saliva to biofilm. We hypothesized that bacterial glycoside hydrolase (GH) activities would be higher in a biofilm than in saliva in order to maintain metabolism in a low-sugar, high-glycoprotein environment. Salivary bacteria from 13 healthy individuals were used to grow
in vitro
biofilm using two separate media, one with sucrose and the other limiting carbon sources to a complex carbohydrate. All six GHs measured were higher
in vitro
when grown in the medium with complex carbohydrate as the sole carbon source. We then collected saliva and overnight dental plaque samples from the same individuals and measured
ex vivo
activities for the same six enzymes to determine how oral microbial utilization of glycoconjugates shifts between the planktonic phase in saliva and the biofilm phase in overnight dental plaque. Overall higher GH activities were observed in plaque samples, in agreement with
in vitro
observation. A similar pattern was observed in GH activity profiles between
in vitro
and
ex vivo
data. 16S rRNA gene analysis showed that plaque samples had a higher abundance of microorganisms with larger number of GH gene sequences. These results suggest differences in sugar catabolism between the oral bacteria located in the biofilm and those in saliva.
EGFR mutant allelic-specific imbalance assessment in routine samples of non-small cell lung cancer
Authors: Malapelle Umberto , Vatrano Simona , Russo Stefania , Bellevicine Claudio , de Luca Caterina , Sgariglia Roberta , Rocco Danilo , de Pietro Livia , Riccardi Fernando , Gobbini Elisa , Righi Luisella , Troncone Giancarlo
Published: June 2015

In non-small cell lung cancer (NSCLC), the epidermal growth factor receptor (EGFR) gene may undergo both mutations and copy number gains. EGFR mutant allele-specific imbalance (MASI) occurs when the ratio of mutant-to-wild-type alleles increases significantly. In this study, by using a previously validated microfluidic-chip-based technology, EGFR-MASI occurred in 25/67 mutant cases (37%), being more frequently associated with EGFR exon 19 deletions (p=0.033). In a subset of 49 treated patients, we assessed whether MASI is a modifier of anti-EGFR treatment benefit. The difference in progression-free survival and overall survival between EGFR-MASI-positive and EGFR-MASI-negative groups of patients did not show a statistical significance. In conclusion, EGFR-MASI is a significant event in NSCLC, specifically associated with EGFR exon 19 deletions. However, EGFR-MASI does not seem to play a role in predicting the response to first-generation EGFR small molecules inhibitors.
Inequalities in non-small cell lung cancer treatment and mortality
Authors: Nur Ula , Quaresma Manuela , De Stavola Bianca , Peake Michael , Rachet Bernard
Published: June 2015

Background

Non-small cell lung cancer (NSCLC) comprises approximately 85% of all lung cancer cases, and surgery is the preferred treatment for patients. The National Health Service established Primary Care Trusts (PCTs) in 2002 to manage local health needs. We investigate whether PCTs with a lower uptake of surgical treatment are those with above-average mortality 1 year after diagnosis. The applied methods can be used to monitor the performance of any administrative bodies responsible for the management of patients with cancer.

Methods

All adults diagnosed with NSCLC lung cancer during 1998–2006 in England were identified. We fitted mixed effect logistic models to predict surgical treatment within 6 months after diagnosis, and mortality within 1 year of diagnosis.

Results

Around 10% of the NCSLC patients received curative surgery. Older deprived patients and those who did not receive surgery had much higher odds of death 1 year after being diagnosed with cancer. In total, 69% of the PCTs were below the lower control limit of surgery and have predicted random intercepts above the mean value of zero of the random effect for mortality, whereas 40% were above the upper control limit of mortality within 1 year.

Conclusions

Our main results suggest the presence of clear geographical variation in the use of surgical treatment of NSCLC and mortality. Mixed-effects models combined with the funnel plot approach were useful for assessing the performance of PCTs that were above average in mortality and below average in surgery.
The outlook of physician histories: J. Marion Sims and ‘The Discovery of Anaesthesia’
Authors: Rosenbloom Julia M , Schonberger Robert B
Published: June 2015

The fact that doctors have a long tradition of writing medical history to interpret and direct their profession is well established. But readers (particularly modern physician readers) can also understand physician-authored histories as offering commentary and analysis of the world beyond medicine. In this essay, we offer a reading (perhaps a modern one) of J. Marion Sims's 1877 article, ‘The Discovery of Anaesthesia’ which exemplifies the stance of looking both inward and outward from the medical field. We begin by discussing Sims, including the complicated legacy he left as a physician. Next, we review late 19th-century history with a focus on Reconstruction. Finally, we show how the modern reader can use Sims's article both to trace the first use of ether and nitrous oxide for surgical anaesthesia and to provide a window into the 19th-century medical profession and the post-Civil War period. Through this study, we hope to show how to read both medicine and the world around it in physician histories.
Highways in the Sky: Scales of Atmospheric Transport of Plant Pathogens
Authors: Schmale David G. , Ross Shane D.
Published: June 2015

Many high-risk plant pathogens are transported over long distances (hundreds of meters to thousands of kilometers) in the atmosphere. The ability to track the movement of these pathogens in the atmosphere is essential for forecasting disease spread and establishing effective quarantine measures. Here, we discuss the scales of atmospheric dispersal of plant pathogens along a transport continuum (pathogen scale, farm scale, regional scale, and continental scale). Growers can use risk information at each of these dispersal scales to assist in making plant disease management decisions, such as the timely application of appropriate pesticides. Regional- and continental-scale atmospheric features known as Lagrangian coherent structures (LCSs) may shuffle plant pathogens along highways in the sky. A promising new method relying on overlapping turbulent back-trajectories of pathogen-laden parcels of air may assist in localizing potential inoculum sources, informing local and/or regional management efforts such as conservation tillage. The emergence of unmanned aircraft systems (UASs, or drones) to sample plant pathogens in the lower atmosphere, coupled with source localization efforts, could aid in mitigating the spread of high-risk plant pathogens.
Sharka Epidemiology and Worldwide Management Strategies: Learning Lessons to Optimize Disease Control in Perennial Plants
Authors: Rimbaud Loup , Dallot Sylvie , Gottwald Tim , Decroocq Véronique , Jacquot Emmanuel , Soubeyrand Samuel , Thébaud Gaël
Published: June 2015

Many plant epidemics that cause major economic losses cannot be controlled with pesticides. Among them, sharka epidemics severely affect prunus trees worldwide. Its causal agent, Plum pox virus (PPV; genus Potyvirus), has been classified as a quarantine pathogen in numerous countries. As a result, various management strategies have been implemented in different regions of the world, depending on the epidemiological context and on the objective (i.e., eradication, suppression, containment, or resilience). These strategies have exploited virus-free planting material, varietal improvement, surveillance and removal of trees in orchards, and statistical models. Variations on these management options lead to contrasted outcomes, from successful eradication to widespread presence of PPV in orchards. Here, we present management strategies in the light of sharka epidemiology to gain insights from this worldwide experience. Although focused on sharka, this review highlights more general levers and promising approaches to optimize disease control in perennial plants.
Range-Expanding Pests and Pathogens in a Warming World
Authors: Bebber Daniel Patrick
Published: June 2015

Crop pests and pathogens (CPPs) present a growing threat to food security and ecosystem management. The interactions between plants and their natural enemies are influenced by environmental conditions and thus global warming and climate change could affect CPP ranges and impact. Observations of changing CPP distributions over the twentieth century suggest that growing agricultural production and trade have been most important in disseminating CPPs, but there is some evidence for a latitudinal bias in range shifts that indicates a global warming signal. Species distribution models using climatic variables as drivers suggest that ranges will shift latitudinally in the future. The rapid spread of the Colorado potato beetle across Eurasia illustrates the importance of evolutionary adaptation, host distribution, and migration patterns in affecting the predictions of climate-based species distribution models. Understanding species range shifts in the framework of ecological niche theory may help to direct future research needs.
Leaf Rust of Cultivated Barley: Pathology and Control
Authors: Park Robert F. , Golegaonkar Prashant G. , Derevnina Lida , Sandhu Karanjeet S. , Karaoglu Haydar , Elmansour Huda M. , Dracatos Peter M. , Singh Davinder
Published: June 2015

Leaf rust of barley is caused by the macrocyclic, heteroecious rust pathogen Puccinia hordei, with aecia reported from selected species of the genera Ornithogalum, Leopoldia, and Dipcadi, and uredinia and telia occurring on Hordeum vulgare, H. vulgare ssp. spontaneum, Hordeum bulbosum, and Hordeum murinum, on which distinct parasitic specialization occurs. Although Puccinia hordei is sporadic in its occurrence, it is probably the most common and widely distributed rust disease of barley. Leaf rust has increased in importance in recent decades in temperate barley-growing regions, presumably because of more intensive agricultural practices. Although total crop loss does not occur, under epidemic conditions yield reductions of up to 62% have been reported in susceptible varieties. Leaf rust is primarily controlled by the use of resistant cultivars, and, to date, 21 seedling resistance genes and two adult plant resistance (APR) genes have been identified. Virulence has been detected for most seedling resistance genes but is unknown for the APR genes Rph20 and Rph23. Other potentially new sources of APR have been reported, and additivity has been described for some of these resistances. Approaches to achieving durable resistance to leaf rust in barley are discussed.
Nontariff Measures and Standards in Trade and Global Value Chains
Authors: Beghin John C. , Maertens Miet , Swinnen Johan
Published: June 2015

We assess the literature on public and private quality standards and their impact in food markets, international trade, and global supply chains. We focus on their effects on welfare, trade, industrial organization, and labor markets and with special attention to the North-South context. We also attempt to better characterize when these measures constitute protectionism, a complicated task. We look at studies investigating public and private standards and across various quantitative approaches and countries. These standards have complex effects. The evidence is mixed regarding standards as catalyst for or as impediment against trade and development, reflecting the complexity of these effects and their specificity to industries and countries. The analysis of standard-like nontariff measures and their impacts does not lead to sweeping prescriptions for policy reforms. We identify more modest prescriptions and make some recommendations for fruitful research directions.