bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct‐acting antivirals combination for elderly patients with chronic hepatitis C: A cost‐effectiveness analysis
Authors: Ciaccio Antonio , Cortesi Paolo A. , Bellelli Giuseppe , Rota Matteo , Conti Sara , Okolicsanyi Stefano , Rota Monica , Cesana Giancarlo , Mantovani Lorenzo G. , Annoni Giorgio , Strazzabosco Mario
Published: December 2016

Background

Chronic hepatitis C (CHC) has been undertreated among elderly patients. Interferon‐free treatment represents an opportunity for these patients. The aim of this study was to assess the cost‐effectiveness of directly acting antivirals (DAAs) in CHC elderly patients.

Methods

A Markov model of CHC natural history was built. This study focuses on CHC patients older than 65 years, stratified according to genotype (1/4, 2 and 3), liver fibrosis (METAVIR F1 to F4), age and frailty phenotype (robust, pre‐frail and frail). DAAs combination vs no treatment was simulated for each theoretical population, assessing life years, quality‐adjusted life years (QALYs), costs, incremental cost‐effectiveness ratios (ICERs) in a lifetime time horizon and by the Healthcare System perspective.

Results

Incremental cost‐effectiveness ratio increased with age and frailty status in all fibrosis stages. For robust F3 and F4 patients ICERs remained below the willingness‐to‐pay threshold (WTP) of 40 000€/QALY up to age 75 and 86 years, respectively, depending on drug price and sustained virological response probability (sensitivity analysis). Notably, in F4 and frail subjects older than 75 years, ICER was more sensitive to non‐liver‐related mortality rate. In elderly F1 and F2 patients, ICERs were below WTP only up to 77 years old, with wide variability among frailty phenotypes.

Conclusions

Cost‐effectiveness of DAAs treatment of elderly CHC patients is solid in those with advanced fibrosis, but it depends strongly on frailty status and age, particularly in patients with milder fibrosis stages. Accurate assessment of clinical variables, including frailty, is necessary to allocate limited resources to this special population.
Time‐trends in incidence and prognosis of hepatocellular carcinoma in Denmark: A nationwide register‐based cohort study
Authors: Jepsen Peter , Andersen Mette W. , Villadsen Gerda E. , Ott Peter , Vilstrup Hendrik
Published: December 2016

Background & Aims

There are no recent data on incidence or survival of hepatocellular carcinoma (HCC) in Denmark. We examined current HCC epidemiology.

Methods

We used data from nationwide registries to identify all Danish citizens diagnosed with HCC in 1994‐2016. We computed annual standardized incidence rates for the entire 1994‐2016 period, and we compared survival for patients diagnosed in 2004‐2014; data on HCC stage were available for that period alone and coded according to the TNM classification.

Results

The incidence rate for 1994‐2016 was 3.7 (95% CI 3.6‐3.8) per 100 000 population per year. It was stable around 3.0 in 1994‐2007, climbed steadily to 5.7 in 2008‐2011, and remained high in 2012‐2016. The proportion of non‐cirrhotic patients with HCC was 21%, with a slightly decreasing time trend. Median survival time rose from 2.7 months in 2004‐2006 to 7.7 months in 2013‐2014, but only patients with early HCC (stage I or II HCC or a “probably early HCC”) saw improvements after 2007 (confounder‐adjusted mortality hazard ratio for 2013‐2014 vs 2007‐2009=0.67, 95% 0.50‐0.90). The proportion of patients with early HCC rose from 17% in 2004‐2006 to 30% in 2013‐2014.

Conclusions

HCC incidence increased between 2007 and 2011. Concurrently, the HCC stage at diagnosis and patient survival improved. The likely reasons for the changes include easier access to HCC workup, changing diagnostic criteria for HCC, increased prevalence of risk factors for HCC, and improved treatment of patients with HCC.
Adriatic ‘opisthobranchs’ (Gastropoda, Heterobranchia): shedding light on biodiversity issues
Authors: Zenetos Argyro , Mačić Vesna , Jaklin Andrej , Lipej Lovrenc , Poursanidis Dimitris , Cattaneo‐Vietti Riccardo , Beqiraj Sajmir , Betti Federico , Poloniato Diego , Kashta Lefter , Katsanevakis Stelios , Crocetta Fabio
Published: December 2016

We herein review the Adriatic opisthobranch fauna, provide an updated checklist of 223 species and assess their distribution at regional and country levels. New Adriatic records are provided for 67 opisthobranch taxa, adding three new records for the Italian coastline, five new records for Albania, eight for Croatia and 15 for Montenegro. The presence of Hermaea bifida (Montagu, 1815), Hermaea variopicta (Costa A., 1869) and Facelina annulicornis (Chamisso & Eysenhardt, 1821) is reported for the first time from anywhere in the Adriatic Sea. Including the new findings, our inventory includes 28 species from Albania, 163 from Croatia, 178 from the Italian coastline of the Adriatic, 41 from Montenegro and 74 from Slovenia. No records were available from Bosnia and Hercegovina. Ninety species (40.4%) are widespread, and were recorded from all three main divisions (Northern, Western and Eastern Adriatic), whilst 79 species (35.4%) were reported from only one of them. At sub‐division levels, the Albanian inventory is the most dissimilar to the other country/regional lists, presumably because of the lack of targeted field surveys. The highest similarity is observed amongst the Western Adriatic, Croatia and the Italian Ionian coastline. Seven alien, one possible alien and three cryptogenic opisthobranchs were reliably recorded from the Adriatic Sea. The first Mediterranean records of five species were in the Adriatic Sea, of which four species have not been found elsewhere in the Mediterranean. Shipping and aquaculture are the probable pathways for most of the alien species. A steady rate of one to two alien introductions per decade since the 1970s was evident. The Northern Adriatic coasts are the most affected by alien invasions, probably due to repeated local introductions along with shellfish transfers (oysters, mussels, Manila clams), and heavy maritime transport.
Staple crops biofortified with increased vitamins and minerals: considerations for a public health strategy
Authors: Garcia‐Casal Maria Nieves , Peña‐Rosas Juan Pablo , Giyose Boitshepo ,   consultation working groups
Published: December 2016

Biofortification of staple crops has been proposed as a strategy to address micronutrient malnutrition, particularly with respect to insufficient intake of vitamin A, iron, zinc, and folate. The World Health Organization, in collaboration with the Food and Agriculture Organization of the United Nations and the Sackler Institute for Nutrition Science at the New York Academy of Sciences, convened a technical consultation entitled “Staple Crops Biofortified with Vitamins and Minerals: Considerations for a Public Health Strategy” in April 2016. Participants of the consultation reviewed the definition of biofortification of staple crops, patterns of crops production, processing, consumption, seed varieties, and micronutrient stability and bioavailability, as well as farmers’ adoption and acceptability of the modified crops. Also discussed were economic, environmental, safety, and equity aspects of biofortified crops, as well as legal, policy, regulatory, and ethical issues for the implementation of biofortification strategies in agriculture and nutrition. Consultation working groups identified important and emerging technical issues, lessons learned, and research priorities to better support the evidence of improved nutrition and unintended adverse effects of biofortification. This paper provides the background and rationale of the technical consultation, synopsizes the presentations, and provides a summary of the main considerations proposed by the working groups.
A Nonfluoroscopic Technique for Coronary Arteries Three‐Dimensional Mapping during Epicardial Ventricular Tachycardia Ablation
Authors: CALZOLARI VITTORIO , BARBATO GAETANO , CROSATO MARTINO , DE MATTIA LUCA , DANIOTTI ALESSANDRO , INDIANI STEFANO , SQUASI PAOLO ANTONIO MARIA , OLIVARI ZORAN
Published: December 2016

When performing epicardial ablation of ventricular tachycardia (VT), caution must be taken not to damage the coronary arteries. We report a case in which a new, nonfluoroscopic technique for incorporating an accurate, real‐time reconstruction of the main coronary vessels into a three‐dimensional electroanatomic map was used for epicardial VT ablation.
Clinical Significance of J Waves in Patients Undergoing Therapeutic Hypothermia for Out‐of‐Hospital Cardiac Arrest
Authors: HARHASH AHMED , GUSSAK IHOR , CASSUTO JAMES , WINTERS STEPHEN L.
Published: December 2016

Background

Hypothermia is associated with the development of J waves. However, little is known about the impact of these electrocardiogram (ECG) findings on the development of ventricular arrhythmias and patient outcomes during therapeutic hypothermia (TH) postresuscitation from out‐of‐hospital cardiac arrest (OHCA). We investigated the prevalence of J waves in OHCA patients prior to and during TH. Additionally, we explored the incidence of atrial and ventricular arrhythmias and in‐hospital mortality for patients with and without J waves either at baseline, during TH, or both.

Methods

We conducted a retrospective analysis of patients who suffered OHCA and underwent TH (goal temperature of 32–34°C). Fifty‐nine patients were stratified dependent upon the presence of or the development of J waves on surface ECGs. Descriptive analysis and logistic regression modeling were used to assess the population differences and mortality, respectively, between patients who developed J waves during TH and those who did not.

Results

There was no difference in the development of in‐hospital atrial or ventricular arrhythmias between patients with J waves present during TH (16%) and those without (17.6%, P = 0.834). Compared to patients without J waves at baseline and during TH, those with J waves present both at baseline and during TH had significantly worse survival (hazard ratio = 12.42, P = 0.046).

Conclusions

While J waves are common ECG findings during TH in patients resuscitated from OHCA, our study demonstrated an increase in mortality for patients with J waves present both at baseline and during TH.
ICD‐ON Registry for Perioperative Management of CIEDs: Most Require No Change
Authors: GIFFORD JANET , LARIMER KAREN , THOMAS CELIA , MAY PATRICIA
Published: December 2016

Background

There is significant variability in the perioperative management of patients with cardiac implanted electronic devices (CIEDs) undergoing procedures requiring electrosurgery.

Methods

We performed a multicenter registry from February 2014 to August 2015 at three suburban Chicago hospitals. Patients with transvenous CIEDs undergoing procedures requiring electrosurgery were assigned to one of three groups: (1) reprogram, (2) magnet, or (3) no change. Subjects with implantable cardioverter defibrillators (ICDs) or those pacemaker dependent having surgical procedures within 6 inches of their CIED were assigned to the reprogram group, whereby ICD therapies were programmed off with asynchronous pacing if pacemaker dependent. Subjects with ICDs ≥ 6 inches from their surgical site but above the iliac crest were assigned to the magnet group. All others were in the no change group. We evaluated electromagnetic interference (EMI) and postoperative device reset based on surgical location.

Results

All patients (n = 331) had pectoral CIEDs with mean age 73 years, 65% male, ejection fraction 56% for pacemaker subjects, 35% for ICD subjects with 22% pacemaker dependent. Assignments were n = 52 (16%) reprogram group, n = 51 (15%) magnet group, and n = 228 (69%) no change. There was EMI in 45% of thoracic cases, 35% of head/neck, 15% of upper extremity, and 3% of abdominal cases above iliac crest. There was no EMI in procedures below the iliac crest. There were no inappropriate therapies or device reset.

Conclusion

Results of the ICD‐ON protocol demonstrate safe and efficient management of patients with CIEDs based on electrosurgery location, with 69% requiring no reprogramming or magnet application.
New insights of red light‐induced development
Authors: Viczián András , Klose Cornelia , Ádám Éva , Nagy Ferenc
Published: December 2016

The red/far‐red light absorbing photoreceptors phytochromes regulate development and growth and thus play an essential role in optimizing adaptation of the sessile plants to the ever‐changing environment. Our understanding of how absorption of a red/far‐red photon by phytochromes initiates/modifies diverse physiological responses has been steadily improving. Research performed in the last 5 years has been especially productive and led to significant conceptual changes about the mode of action of these photoreceptors. In this review, we focus on the phytochrome B photoreceptor, the major phytochrome species active in light‐grown plants. We discuss how its light‐independent inactivation (termed dark/thermal reversion), post‐translational modification, including ubiquitination, phosphorylation and sumoylation, as well as heterodimerization with other phytochrome species modify red light‐controlled physiological responses. Finally, we discuss how photobiological properties of phytochrome B enable this photoreceptor to function also as a thermosensor.
Distinct physiological and metabolic reprogramming by highbush blueberry (Vaccinium corymbosum) cultivars revealed during long‐term UV‐B radiation
Authors: Luengo Escobar Ana , Alberdi Miren , Acevedo Patricio , Machado Mariana , Nunes‐Nesi Adriano , Inostroza‐Blancheteau Claudio , Reyes‐Díaz Marjorie
Published: December 2016

Despite the Montreal protocol and the eventual recovery of the ozone layer over Antarctica, there are still concerns about increased levels of ultraviolet‐B (UV‐B) radiation in the Southern Hemisphere. UV‐B induces physiological, biochemical and morphological stress responses in plants, which are species‐specific and different even for closely related cultivars. In woody plant species, understanding of long‐term mechanisms to cope with UV‐B‐induced stress is limited. Therefore, a greenhouse UV‐B daily course simulation was performed for 21 days with two blueberry cultivars (Legacy and Bluegold) under UV‐BBE irradiance doses of 0, 0.07 and 0.19 W m−2. Morphological changes, photosynthetic performance, antioxidants, lipid peroxidation and metabolic features were evaluated. We found that both cultivars behaved differently under UV‐B exposure, with Legacy being a UV‐B‐resistant cultivar. Interestingly, Legacy used a combined strategy: initially, in the first week of exposure its photoprotective compounds increased, coping with the intake of UV‐B radiation (avoidance strategy), and then, increasing its antioxidant capacity. These strategies proved to be UV‐B radiation dose dependent. The avoidance strategy is triggered early under high UV‐B radiation in Legacy. Moreover, the rapid metabolic reprogramming capacity of this cultivar, in contrast to Bluegold, seems to be the most relevant contribution to its UV‐B stress‐coping strategy.
Can Conversational Interviewing Improve Survey Response Quality Without Increasing Interviewer Effects?
Authors: West Brady T. , Conrad Frederick G. , Kreuter Frauke , Mittereder Felicitas
Published: December 2016

Several studies have shown that conversational interviewing (CI) reduces response bias for complex survey questions relative to standardized interviewing. However, no studies have addressed concerns about whether CI increases intra-interviewer correlations (IICs) in the responses collected, which could negatively impact the overall quality of survey estimates. The paper reports the results of an experimental investigation addressing this question in a national face-to-face survey. We find that CI improves response quality, as in previous studies, without substantially or frequently increasing IICs. Furthermore, any slight increases in the IICs do not offset the reduced bias in survey estimates engendered by CI.
Rank-Based Procedures in Factorial Designs: Hypotheses About Non-Parametric Treatment Effects
Authors: Brunner Edgar , Konietschke Frank , Pauly Markus , Puri Madan L.
Published: December 2016

Existing tests for factorial designs in the non-parametric case are based on hypotheses formulated in terms of distribution functions. Typical null hypotheses, however, are formulated in terms of some parameters or effect measures, particularly in heteroscedastic settings. Here this idea is extended to non-parametric models by introducing a novel non-parametric analysis-of-variance type of statistic based on ranks or pseudoranks which is suitable for testing hypotheses formulated in meaningful non-parametric treatment effects in general factorial designs. This is achieved by a careful detailed study of the common distribution of rank-based estimators for the treatment effects. Since the statistic is asymptotically not a pivotal quantity we propose three different approximation techniques, discuss their theoretic properties and compare them in extensive simulations together with two additional Wald-type tests. An extension of the presented idea to general repeated measures designs is briefly outlined. The rank- and pseudorank-based procedures proposed maintain the preassigned type I error rate quite accurately, also in unbalanced and heteroscedastic models.
Association Between TNF‐α Promoter −308 A/G Polymorphism and Systemic Lupus Erythematosus Susceptibility: A Case–Control Study and Meta‐Analysis
Authors: Yang Z.‐C. , Xu F. , Tang M. , Xiong X.
Published: December 2016

The tumour necrosis factor‐α (TNF‐α) promoter −308 A/G polymorphism plays an important role in the aetiology of systemic lupus erythematosus (SLE). Several studies have estimated the association between TNF‐α −308 A/G and SLE risk. However, results were inconsistent. A case–control study was carried out to explore the association between TNF‐α −308 A/G and the SLE risk in a Chinese Han population. Meta‐analysis combining present with previous studies was conducted to further explore the association. Our case–control study included 556 patients with SLE along with 570 matched healthy controls. TNF‐α −308 A allele was significantly increased in patients with SLE compared with controls (OR = 2.184, 95% CI: 1.718–2.778, P < 0.001). Genotypes AA and AG were associated with the susceptibility to SLE as compared with the GG genotype, as well as the dominant model (AA+AG versus GG), respectively. The meta‐analysis included 41 comparative studies involving 4799 patients and 6635 controls. An association between SLE and allele A was found in the overall populations (OR = 1.70, 95% CI: 1.46–1.98, P < 0.001). In addition, we discussed the correlation between this polymorphism and lupus nephritis (LN) risk, showing that allele A was significantly related to LN in the overall populations (OR = 1.80, 95% CI: 1.21–2.68, P = 0.004). The results from our case–control study and the meta‐analysis indicate that the TNF‐α −308 A allele is significantly associated with an increased risk of SLE/LN.
M2000 (β‐D‐Mannuronic Acid) as a Novel Antagonist for Blocking the TLR2 and TLR4 Downstream Signalling Pathway
Authors: Aletaha S. , Haddad L. , Roozbehkia M. , Bigdeli R. , Asgary V. , Mahmoudi M. , Mirshafiey A.
Published: December 2016

To date, selective blockade of Toll‐like receptor (TLR) signalling has been developed as a new approach for treatment for many inflammatory diseases. As β‐D‐mannuronic acid (M2000) has been known as an anti‐inflammatory molecule in several experimental models, we investigated the antagonistic effects of M2000 on TLR2 and TLR4 downstream signalling transduction pathway in human embryonic kidney (HEK) 293 cell lines overexpressing TLR2/CD14 and the TLR4/MD2/CD14 complex, respectively. M2000 effectively inhibited mRNA expression of MyD88 and p65, major subunit of nuclear factor‐κB, in HEK293 cells stimulated by lipoteichoic acid (LTA, a TLR2 agonist) and lipopolysaccharide (LPS, a TLR4 agonist) with no evidence of cytotoxicity. In addition, M2000 also suppressed LTA and LPS‐induced production of TNF‐α and IL‐6 inflammatory cytokines in these cells. Furthermore, the results revealed that M2000 had no significant effect on Tollip mRNA expression as a negative regulator of TLR signalling in aforesaid cells. Overall, these data point to M2000 inhibitory effect on Toll‐like receptor (TLR) 2, 4 signalling in HEK293 cells. This information might provide new insights into the possible roles of this small drug in order to introduce it as a TLR signalling pathway inhibitor. However, more studies are needed to confirm β‐D‐mannuronic acid antagonistic effects including the effects of M2000 on peritoneal isolated macrophages and also on blood cells in patients with inflammatory diseases such as ankylosing spondylitis.
Invasive fungal infection after heart transplantation: A 7‐year, single‐center experience
Authors: Echenique Ignacio A. , Angarone Michael P. , Gordon Robert A. , Rich Jonathan , Anderson Allen S. , McGee Edwin C. , Abicht Travis O. , Kang Joseph , Stosor Valentina
Published: December 2016

Background

Invasive fungal infections (IFIs) are an infrequent but major complication of heart transplantation (HT). We sought to describe the epidemiology at our institution.

Methods

A prospective cohort study of 159 heart transplant recipients was performed from June 2005 to December 2012. IFIs were defined by European Organization for Research and Treatment of Cancer/Mycoses Study Group criteria.

Results

By univariate analysis, Hispanic ethnicity was associated with IFI (P=.01, odds ratio [OR] 7.0, 95% confidence interval [CI] 1.7‐27.9). Subsequently, a multivariate logistic regression was performed adjusting for Hispanic ethnicity, age, and gender. Seventeen IFIs were identified, occurring at a median 110 days post HT (interquartile range: 32‐411 days). Five IFIs (29% of IFIs and 3.1% of all HT) occurred during the HT hospitalization, with 13 IFIs during the first year (incidence 8.2%).

Conclusions

The cumulative incidence was 10.7%. IFIs were associated with pre‐ and post‐HT vancomycin‐resistant Enterococcus colonization and/or infection, post‐HT renal replacement therapy, anti‐thymocyte globulin induction, and antibody‐mediated rejection. There were no associations with diabetes mellitus, desensitization, 2R/3R cellular rejection, treatments for rejection, re‐operation, neutropenia, or cytomegalovirus infection. IFIs were associated with death (P=.02, OR 3.9, 95% CI 1.3‐12.1) and 1‐year mortality (P<.001, OR 9.0, 95% CI 2.3‐35.7), but not 3‐year mortality. Associations with Hispanic ethnicity must be validated. Optimal strategies for risk reduction and prophylaxis remain undefined.
Color Processing in Synesthesia: What Synesthesia Can and Cannot Tell Us About Mechanisms of Color Processing
Authors: Janik McErlean Agnieszka B. , Banissy Michael J.
Published: December 2016

Synesthetic experiences of color have been traditionally conceptualized as a perceptual phenomenon. However, recent evidence suggests a role of higher order cognition in the formation of synesthetic experiences. Here, we discuss how synesthetic experiences of color differ from and influence veridical color processing, and how non‐perceptual processes such as imagery and color memory might play a role in eliciting synesthetic color experience.
Microscale magnetic microparticle‐based immunopurification of cytokinins from Arabidopsis root apex
Authors: Plačková Lenka , Oklestkova Jana , Pospíšková Kristýna , Poláková Kateřina , Buček Jan , Stýskala Jakub , Zatloukal Marek , Šafařík Ivo , Zbořil Radek , Strnad Miroslav , Doležal Karel , Novák Ondřej
Published: December 2016

Cytokinins (CKs) are pivotal plant hormones that have crucial roles in plant growth and development. However, their isolation and quantification are usually challenging because of their extremely low levels in plant tissues (pmol g−1 fresh weight). We have developed a simple microscale magnetic immunoaffinity‐based method for selective one‐step isolation of CKs from very small amounts of plant tissue (less than 0.1 mg fresh weight). The capacity of the immunosorbent and the effect of the complex plant matrix on the yield of the rapid one‐step purification were tested using a wide range of CK concentrations. The total recovery range of the new microscale isolation procedure was found to be 30–80% depending on individual CKs. Immunoaffinity extraction using group‐specific monoclonal CK antibodies immobilized onto magnetic microparticles was combined with a highly sensitive ultrafast mass spectrometry‐based method with a detection limit close to one attomole. This combined approach allowed metabolic profiling of a wide range of naturally occurring CKs (bases, ribosides and N9‐glucosides) in 1.0‐mm sections of the Arabidopsis thaliana root meristematic zone. The magnetic immunoaffinity separation method was shown to be a simple and extremely fast procedure requiring minimal amounts of plant tissue.
The impact of Arabidopsis thaliana SNF1‐related‐kinase 1 (SnRK1)‐activating kinase 1 (SnAK1) and SnAK2 on SnRK1 phosphorylation status: characterization of a SnAK double mutant
Authors: Glab Nathalie , Oury Céline , Guérinier Thomas , Domenichini Séverine , Crozet Pierre , Thomas Martine , Vidal Jean , Hodges Michael
Published: December 2016

Arabidopsis thaliana SNF1‐related‐kinase 1 (SnRK1)‐activating kinase 1 (AtSnAK1) and AtSnAK2 have been shown to phosphorylate in vitro and activate the energy signalling integrator, SnRK1. To clarify this signalling cascade in planta, a genetic‐ and molecular‐based approach was developed. Homozygous single AtSnAK1 and AtSnAK2 T‐DNA insertional mutants did not display an apparent phenotype. Crossing of the single mutants did not allow the isolation of double‐mutant plants, whereas self‐pollinating the S1−/− S2+/− sesquimutant specifically gave approximatively 22% individuals in their offspring that, when rescued on sugar‐supplemented media in vitro, were shown to be AtSnAK1 AtSnAK2 double mutants. Interestingly, this was not obtained in the case of the other sesquimutant, S1+/− S2−/−. Although reduced in size, the double mutant had the capacity to produce flowers, but not seeds. Immunological characterization established the T‐loop of the SnRK1 catalytic subunit to be non‐phosphorylated in the absence of both SnAKs. When the double mutant was complemented with a DNA construct containing an AtSnAK2 open reading frame driven by its own promoter, a normal phenotype was restored. Therefore, wild‐type plant growth and development is dependent on the presence of SnAK in vivo, and this is correlated with SnRK1 phosphorylation. These data show that both SnAKs are kinases phosphorylating SnRK1, and thereby they contribute to energy signalling in planta.
Identification of core subunits of photosystem II as action sites of HSP21, which is activated by the GUN5‐mediated retrograde pathway in Arabidopsis
Authors: Chen Si‐Ting , He Ning‐Yu , Chen Juan‐Hua , Guo Fang‐Qing
Published: December 2016

Photosystem II (PSII) is the most thermolabile photosynthetic complex. Physiological evidence suggests that the small chloroplast heat‐shock protein 21 (HSP21) is involved in plant thermotolerance, but the molecular mechanism of its action remains largely unknown. Here, we have provided genetic and biochemical evidence that HSP21 is activated by the GUN5‐dependent retrograde signaling pathway, and stabilizes PSII by directly binding to its core subunits such as D1 and D2 proteins under heat stress. We further demonstrate that the constitutive expression of HSP21 sufficiently rescues the thermosensitive stability of PSII and survival defects of the gun5 mutant with dramatically improving granal stacking under heat stress, indicating that HSP21 is a key chaperone protein in maintaining the integrity of the thylakoid membrane system under heat stress. In line with our interpretation based on several lines of in vitro and in vivo protein‐interaction evidence that HSP21 interacts with core subunits of PSII, the kinetics of HSP21 binding to the D1 and D2 proteins was determined by performing an analysis of microscale thermophoresis. Considering the major role of HSP21 in protecting the core subunits of PSII from thermal damage, its heat‐responsive activation via the heat‐shock transcription factor HsfA2 is critical for the survival of plants under heat stress. Our findings reveal an auto‐adaptation loop pathway that plant cells optimize particular needs of chloroplasts in stabilizing photosynthetic complexes by relaying the GUN5‐dependent plastid signal(s) to activate the heat‐responsive expression of HSP21 in the nucleus during adaptation to heat stress in plants.
A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip
Authors: Roselli Sandro , Olry Alexandre , Vautrin Sonia , Coriton Olivier , Ritchie Dave , Galati Gianni , Navrot Nicolas , Krieger Célia , Vialart Guilhem , Bergès Hélène , Bourgaud Frédéric , Hehn Alain
Published: December 2016

Furanocoumarins are specialized metabolites that are involved in the defense of plants against phytophagous insects. The molecular and functional characterization of the genes involved in their biosynthetic pathway is only partially complete. Many recent reports have described gene clusters responsible for the biosynthesis of specialized metabolites in plants. To investigate possible co‐localization of the genes involved in the furanocoumarin pathway, we sequenced parsnip BAC clones spanning two different gene loci. We found that two genes previously identified in this pathway, CYP71AJ3 and CYP71AJ4, were located on the same BAC, whereas a third gene, PsPT1, belonged to a different BAC clone. Chromosome mapping using fluorescence in situ hybridization (FISH) indicated that PsPT1 and the CYP71AJ3‐CYP71AJ4 clusters are located on two different chromosomes. Sequencing the BAC clone harboring PsPT1 led to the identification of a gene encoding an Fe(II) α‐ketoglutarate‐dependent dioxygenase (PsDIOX) situated in the neighborhood of PsPT1 and confirmed the occurrence of a second gene cluster involved in the furanocoumarin pathway. This enzyme metabolizes p‐coumaroyl CoA, leading exclusively to the synthesis of umbelliferone, an important intermediate compound in furanocoumarin synthesis. This work provides an insight into the genomic organization of genes from the furanocoumarin biosynthesis pathway organized in more than one gene cluster. It also confirms that the screening of a genomic library and the sequencing of BAC clones represent a valuable tool to identify genes involved in biosynthetic pathways dedicated to specialized metabolite synthesis.
Development of an Attitude Scale towards High School Physics Lessons
Authors: Yavaş Pervin Ünlü , Çağan Sultan
Published: December 2016

The aim of this study was to develop a Likert type attitude scale for high school students with regard to high school physics lessons. The research was carried out with high school students who were studying in Ankara. First, the opinions of 105 high school students about physics lessons were obtained and then 55 scale items were determined from these opinions. Expert opinions were sought for the language and content validity of these items. In line with the expert opinions some items were corrected and some were taken out of the scale. The draft scale, which had 44 items, was tested on 698 high school students. The factor structure of the scale was ascertained by carrying out exploratory factor analysis from the data that were gathered. The variance of the scale, which consists of 28 items and 4 factors (interest, anxiety, importance, and self-efficacy), was 60%. The consistent between the model and the scale data was observed by carrying out confirmatory factor analysis. Since the fit indices of the scale ensure the acceptability criteria, it was observed that the factor model is appropriate. The Cronbach-alpha reliability coefficients of the factors of the scale developed were calculated and it was decided that the scale is reliable.
Lowering coefficient of friction in Cu alloys with stable gradient nanostructures
Authors: Chen Xiang , Han Zhong , Li Xiuyan , Lu K.
Published: December 2016

Submillimeter-thick stable gradient nanograined surface layer greatly reduces dry-sliding coefficient of friction in Cu alloys.
Influences of pH and Iron Concentration on the Salivary Microbiome in Individual Humans with and without Caries
Authors: Zhou Jianye , Jiang Nan , Wang Zhenzhen , Li Longqing , Zhang Jumei , Ma Rui , Nie Hongbing , Li Zhiqiang
Published: December 2016

This study aimed to identify the differences in the oral microbial communities in saliva from patients with and without caries by performing sequencing with the Illumina MiSeq platform, as well as to further assess their relationships with environmental factors (salivary pH and iron concentration). Forty-three volunteers were selected, including 21 subjects with and 22 without caries, from one village in Gansu, China. Based on 966,255 trimmed sequences and clustering at the 97% similarity level, 1,303 species-level operational taxonomic units were generated. The sequencing data for the two groups revealed that (i) particular distribution patterns (synergistic effects or competition) existed in the subjects with and without caries at both the genus and species levels and (ii) both the salivary pH and iron concentration had significant influences on the microbial community structure.

IMPORTANCE
The significant influences of the oral environment observed in this study increase the current understanding of the salivary microbiome in caries. These results will be useful for expanding research directions and for improving disease diagnosis, prognosis, and therapy.
Contribution of Pentose Catabolism to Molecular Hydrogen Formation by Targeted Disruption of Arabinose Isomerase (
araA
) in the Hyperthermophilic Bacterium Thermotoga maritima
Authors: White Derrick , Singh Raghuveer , Rudrappa Deepak , Mateo Jackie , Kramer Levi , Freese Laura , Blum Paul
Published: December 2016

Thermotoga maritima
ferments a broad range of sugars to form acetate, carbon dioxide, traces of lactate, and near theoretic yields of molecular hydrogen (H
2
). In this organism, the catabolism of pentose sugars such as arabinose depends on the interaction of the pentose phosphate pathway with the Embden-Myerhoff and Entner-Doudoroff pathways. Although the values for H
2
yield have been determined using pentose-supplemented complex medium and predicted by metabolic pathway reconstruction, the actual effect of pathway elimination on hydrogen production has not been reported due to the lack of a genetic method for the creation of targeted mutations. Here, a spontaneous and genetically stable
pyrE
deletion mutant was isolated and used as a recipient to refine transformation methods for its repair by homologous recombination. To verify the occurrence of recombination and to assess the frequency of crossover events flanking the deleted region, a synthetic
pyrE
allele, encoding synonymous nucleotide substitutions, was used. Targeted inactivation of
araA
(encoding arabinose isomerase) in the
pyrE
mutant was accomplished using a divergent, codon-optimized
Thermosipho africanus pyrE
allele fused to the
T. maritima groES
promoter as a genetic marker. Mutants lacking
araA
were unable to catabolize arabinose in a defined medium. The
araA
mutation was then repaired using targeted recombination. Levels of synthesis of H
2
using arabinose-supplemented complex medium by wild-type and
araA
mutant cell lines were compared. The difference between strains provided a direct measurement of H
2
production that was dependent on arabinose consumption. Development of a targeted recombination system for genetic manipulation of
T. maritima
provides a new strategy to explore H
2
formation and life at an extremely high temperature in the bacterial domain.

IMPORTANCE
We describe here the development of a genetic system for manipulation of
Thermotoga maritima
.
T. maritima
is a hyperthermophilic anaerobic bacterium that is well known for its efficient synthesis of molecular hydrogen (H
2
) from the fermentation of sugars. Despite considerable efforts to advance compatible genetic methods, chromosome manipulation has remained elusive and hindered use of
T. maritima
or its close relatives as model hyperthermophiles. Lack of a genetic method also prevented efforts to manipulate specific metabolic pathways to measure their contributions to H
2
yield. To overcome this barrier, a homologous chromosomal recombination method was developed and used to characterize the contribution of arabinose catabolism to H
2
formation. We report here a stable genetic method for a hyperthermophilic bacterium that will advance studies on the basic and synthetic biology of
Thermotogales
.
Arsenic Detoxification by Geobacter Species
Authors: Dang Yan , Walker David J. F. , Vautour Kaitlin E. , Dixon Steven , Holmes Dawn E.
Published: December 2016

Insight into the mechanisms for arsenic detoxification by
Geobacter
species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different
Geobacter
genomes showed that all of these species have genes coding for an arsenic detoxification system (
ars
operon), and several have genes required for arsenic respiration (
arr
operon) and methylation (
arsM
). Genes encoding four arsenic repressor-like proteins were detected in the genome of
G. sulfurreducens
; however, only one (ArsR1) regulated transcription of the
ars
operon. Elimination of
arsR1
from the
G. sulfurreducens
chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while
arsC
deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how
Geobacter
influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface.

IMPORTANCE
This study examines arsenic transformation mechanisms utilized by
Geobacter
, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments.
Geobacter
species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of
Geobacter
should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different
Geobacter
genomes and found that all of these species possess genes coding for an arsenic detoxification system (
ars
operon), and some also have genes required for arsenic respiration (
arr
operon) and arsenic methylation (
arsM
).
Insecticidal Specificity of Cry1Ah to Helicoverpa armigera Is Determined by Binding of APN1 via Domain II Loops 2 and 3
Authors: Zhou Zishan , Liu Yuxiao , Liang Gemei , Huang Yongping , Bravo Alejandra , Soberón Mario , Song Fuping , Zhou Xueping , Zhang Jie
Published: December 2016

Bacillus thuringiensis
Cry1Ah protein is highly toxic against
Helicoverpa armigera
but shows no toxicity against
Bombyx mori
larvae. In contrast, the closely related Cry1Ai toxin showed the opposite phenotype: high activity against
B. mori
but no toxicity against
H. armigera.
Analysis of binding of Cry1Ah to brush border membrane vesicle (BBMV) proteins from
H. armigera
and
B. mori
by surface plasmon resonance revealed association of toxin binding with insect specificity. Pulldown experiments identified aminopeptidase N1 (APN1) as a Cry1Ah binding protein that was not observed in the assays using
B. mori
BBMV proteins. The APN1 Cry1Ah binding region was narrowed to the region from
A
548 to
S
798 (fragment H3) by expressing four different APN1 fragments in
Escherichia coli
and analyzing Cry1Ah binding by ligand blot. Binding competition experiments of Cry1Ah to APN1 fragment H3 using synthetic peptides corresponding to four predicted domain II loop regions showed that loop 2 and loop 3 have additive effects on binding to APN1 fragment H3. Moreover, switching of loop 2 and loop 3 regions from Cry1Ah to Cry1Ai toxins showed that loop 2 and loop 3 are both involved in specificity and toxicity against
H. armigera
.

IMPORTANCE
Domain II loop regions have been shown to be involved in binding to larval gut proteins mediating insect specificity. The modification of loop regions is a direct and effective method to construct new Cry toxin variants to increase toxicity or modify specificity. Our results show that the exchange of loop regions from one toxin into another is a successful scheme for modification of
B. thuringiensis
Cry toxin specificity.
BspK, a Serine Protease from the Predatory Bacterium Bdellovibrio bacteriovorus with Utility for Analysis of Therapeutic Antibodies
Authors: Bratanis Eleni , Molina Henrik , Naegeli Andreas , Collin Mattias , Lood Rolf
Published: December 2016

The development of therapeutic and diagnostic antibodies is a rapidly growing field of research, being the fastest expanding group of products on the pharmaceutical market, and appropriate quality controls are crucial for their application. We have identified and characterized the serine protease termed BspK (Bdellovibrioserine protease K) fromBdellovibrio bacteriovorusand here show its activity on antibodies. Mutation of the serine residue at position 230 rendered the protease inactive. Further investigations of BspK enzymatic characteristics revealed autoproteolytic activity, resulting in numerous cleavage products. Two of the autoproteolytic cleavage sites in the BspK fusion protein were investigated in more detail and corresponded to cleavage after K28and K210in the N- and C-terminal parts of BspK, respectively. Further, BspK displayed stable enzymatic activity on IgG within the pH range of 6.0 to 9.5 and was inhibited in the presence of ZnCl2. BspK demonstrated preferential hydrolysis of human IgG1 compared to other immunoglobulins and isotypes, with hydrolysis of the heavy chain at position K226generating two separate Fab fragments and an intact IgG Fc domain. Finally, we show that BspK preferentially cleaves its substrates C-terminally to lysines similar to the protease LysC. However, BspK displays a unique cleavage profile compared to several currently used proteases on the market.

IMPORTANCEThe rapid development of novel therapeutic antibodies is partly hindered by difficulties in assessing their quality and safety. The lack of tools and methods facilitating such quality controls obstructs and delays the process of product approval, eventually affecting the patients in need of treatment. These difficulties in product evaluations indicate a need for new and comprehensive tools for such analysis. Additionally, recent concerns raised regarding the limitations of established products on the market (e.g., trypsin) further highlight a general need for a larger array of proteases with novel cleavage profiles to meet current and future needs, within both the life science industry and the academic research community.
Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers
Authors: Lachapelle Virginie , Letellier Ann , Fravalo Philippe , Brassard Julie , L'Homme Yvan
Published: December 2016

Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively.

IMPORTANCE
Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.
Anti-adalimumab antibodies in psoriasis: lack of clinical utility and laboratory evidence
Authors: Lombardi G , Perego S , Sansoni V , Diani M , Banfi G , Altomare G
Published: December 2016

Objective

Adalimumab has proven effective in psoriasis; however, secondary failure may result from the drug's immunogenicity. Prevalence data on the immunogenicity of biologicals, and of adalimumab in particular, are highly variable. We investigated the prevalence of anti-adalimumab antibodies and the association with clinical indexes and tumour necrosis factor α (TNFα) serum levels in psoriatic patients.

Design

Case–control, longitudinal.

Setting

Single centre.

Participants

Patient groups: I (n=20) receiving biological therapies after switching from adalimumab; II (n=30) ongoing adalimumab therapy; III (n=30) novel adalimumab therapy; IV (n=15) biological therapies other than adalimumab.

Healthy subjects: (group V; n=15) never treated with immunosuppressants or biologicals.

Interventions

All groups were tested at enrolment. Group II was also tested at 12 months, and group III at 1, 3, and 6 months.

Primary and secondary outcome measures

Standard clinical evaluations (Psoriasis Area Severity Index (PASI)), blood samples and two-site ELISA-based measurement of serum adalimumab trough levels, anti-adalimumab antibodies and TNFα.

Results

The false-positive rate was 23% for adalimumab detection and 22% for anti-adalimumab antibodies in patients naïve to adalimumab. Spurious positivity for anti-adalimumab antibodies (one-time-point positivity in group III during follow-up) accounted for 33% of the total. The prevalence of anti-drug antibodies was highest (87%) in group I patients. No correlations were found between the presence of anti-adalimumab antibodies or adalimumab levels and changes in PASI scores.

Conclusions

High variability of results, high prevalence of false-positives and lack of association between anti-adalimumab antibodies and TNFα level/PASI score limit this assay's usefulness. Accurate clinical evaluation is key to early identification of treatment failures.