bluuebunny/crossref_metadata_2025 huggingface dataset:
DYNAMIC LINEAR PANEL REGRESSION MODELS WITH INTERACTIVE FIXED EFFECTS
Authors: Moon Hyungsik Roger , Weidner Martin
Published: December 2015

We analyze linear panel regression models with interactive fixed effects and predetermined regressors, for example lagged-dependent variables. The first-order asymptotic theory of the least squares (LS) estimator of the regression coefficients is worked out in the limit where both the cross-sectional dimension and the number of time periods become large. We find two sources of asymptotic bias of the LS estimator: bias due to correlation or heteroscedasticity of the idiosyncratic error term, and bias due to predetermined (as opposed to strictly exogenous) regressors. We provide a bias-corrected LS estimator. We also present bias-corrected versions of the three classical test statistics (Wald, LR, and LM test) and show their asymptotic distribution is a χ2-distribution. Monte Carlo simulations show the bias correction of the LS estimator and of the test statistics also work well for finite sample sizes.
Acceptability and feasibility of the ‘DASH for Asthma’ intervention in a randomized controlled trial pilot study
Authors: Blonstein Andrea C , Lv Nan , Camargo Carlos A , Wilson Sandra R , Buist A Sonia , Rosas Lisa G , Strub Peg , Ma Jun
Published: December 2015

Objective

‘DASH for Asthma’ (n90) was a 6-month randomized controlled trial that demonstrated potential benefits of a DASH (Dietary Approaches to Stop Hypertension) behavioural intervention for improving diet quality and asthma control by comparing intervention to usual care in adults with uncontrolled asthma. The present study examined acceptability and feasibility of the intervention from the perspective of intervention participants and lifestyle coaches.

Design

Grounded in Social Cognitive Theory, the 3-month intensive stage, including three individual and eight group sessions, focused on diet modifications and behavioural self-regulation. The 3-month maintenance stage contained telephone consultations. Participants and lifestyle coaches completed surveys including 5-point Likert scales and open-ended questions. We analysed data using descriptive and inductive content analyses.

Subjects

Forty-six intervention participants (survey response rate was 65–72 %) and two lifestyle coaches.

Results

Participants and lifestyle coaches were highly satisfied (all mean ratings >4) with individual and group sessions. Participants identified mastery of knowledge and skills (awareness, goal setting, self-monitoring, problem solving), social learning (class members sharing experiences and ideas) and good coaching skills (reflective listening, empathy, motivational counselling) as important contributors to self-efficacy and programme satisfaction. Participants also valued personalized feedback received in individual sessions. Lifestyle coaches viewed participant engagement as a facilitator to effective sessions. Finally, participants and lifestyle coaches identified food tasting as beneficial for observational learning and facilitation of participant engagement. High class attendance and self-monitoring rate also reflected the high engagement among participants.

Conclusions

The DASH behavioural intervention was feasible and highly acceptable to participants with uncontrolled asthma and lifestyle coaches.
BERTRAND RUSSELL'S TRIUMPH AND FAILURE
Authors: Reinhardt Lloyd
Published: December 2015

Bertrand Russell was, along with G.E. Moore, deserving of accolade as a founder of analytic philosophy, and of its close companion, the linguistic turn. Here I explain how his ‘Theory of Descriptions’ relocates philosophy's concern with appearance and reality as a concern with grammatical surface and logical depth. I then on remark the irony of Russell's unhappiness with views to the effect that an ethical judgment is not, despite linguistic appearances, really something that can be true or false. A further irony lies in Russell's error of assigning metaphysical grandeur to logical truths, an error he could have avoided by more fully appreciating how logically misleading linguistic appearances can be.
Evolutionary roots of the conodonts with increased number of elements in the apparatus
Authors: Dzik Jerzy
Published: December 2015

Four kinds of robust elements have been recognised inAmorphognathus quinquiradiatusMoskalenko, 1977 (inKanyginet al. 1977) from the early Late Ordovician of Siberia, indicating that at least 17 elements were present in the apparatus, one of them similar to the P1element of the Early SilurianDistomodus. The new generic nameMoskalenkodusis proposed for these conodonts with a pterospathodontid-like S series element morphology. This implies that the relatedDistomodus,PterospathodusandGamachignathuslineages had a long cryptic evolutionary history, probably ranging back to the early Ordovician, when they split from the lineage ofIcriodella, having a duplicated M location in common. The balognathidPromissum, with a 19-element apparatus, may have shared ancestry withIcriodellain Ordovician high latitudes, withSagittodontina,Lenodus,TrapezognathusandPhragmodusas possible connecting links. The pattern of the unbalanced contribution ofBaltonioduselement types to samples suggests that duplication of M and P2series elements may have been an early event in the evolution of balognathids. The proposed scenario implies a profound transformation of the mouth region in the evolution of conodonts. The probable original state was a chaetognath-like arrangement of coniform elements; all paired and of relatively uniform morphology. This was modified at the origin of protopanderodontids by the introduction of a medial S0element, which resulted in the separation of the exposed unit of M and S series elements from the P series elements hidden in the throat. A rotation of the S series elements to an almost horizontal position in early prioniodontids may have promoted duplication of the M element pair. InGamachignathus,IcriodellaandPterospathoduslineages, these elements are differentiated morphologically. Subsequent anteriorward bending of the P element series caused duplication of the balognathid P2element pair, but they remained undifferentiated, even in the otherwise elaboratePromissum. The whole clade of conodonts with supernumerary element pairs in the apparatus has its roots in high latitudes of the Ordovician.
Early growth and changes in blood pressure during adult life
Authors: Sandboge S. , Osmond C. , Kajantie E. , Eriksson J. G
Published: December 2015

Previous studies suggest that the inverse association between birth weight and adult blood pressure amplifies with age. Rapid childhood growth has also been linked to hypertension. The objective of this study was to determine whether the association between childhood growth and adult blood pressure amplifies with age. The study comprised 574 women and 462 men from the Helsinki Birth Cohort Study who attended a clinical study in 2001–2004 and a follow-up in 2006–2008. Mean age at the clinic visits was 61.5 and 66.4 years, respectively. Blood pressure was measured at both occasions. Conditional growth models were used to assess relative weight gain and linear growth. We studied the associations between conditional growth and blood pressure as well as the presence of hypertension. Relative weight gain and linear growth between ages 2 and 11 years were inversely associated with systolic blood pressure at mean age 66.4 years, after adjustment for sex, blood pressure at mean age 61.5 years, as well as other covariates. A one s.d. increase in linear growth between 2 and 11 years was associated with an OR of 0.61 for hypertension at mean age 66.4 years. Contrary to previous studies, we have shown an inverse association between childhood growth and adult blood pressure. There were, however, no associations between childhood growth and systolic blood pressure at mean age 61.5 years indicating that the beneficial effects of a more rapid than expected childhood growth might become more apparent with increasing age.
When Death Is Compelling
Authors: Schindler Simon , Reinhard Marc-André
Published: December 2015

Abstract. Research on terror management theory has found evidence that people under mortality salience strive to live up to activated social norms and values. Recently, research has shown that mortality salience also increases adherence to the norm of reciprocity. Based on this, in the current paper we investigated the idea that mortality salience influences persuasion strategies that are based on the norm of reciprocity. We therefore assume that mortality salience should enhance compliance for a request when using the door-in-the-face technique – a persuasion strategy grounded in the norm of reciprocity. In a hypothetical scenario (Study 1), and in a field experiment (Study 2), applying the door-in-the-face technique enhanced compliance in the mortality salience condition compared to a control group.
Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM
Authors: Hesketh Emma L. , Meshcheriakova Yulia , Dent Kyle C. , Saxena Pooja , Thompson Rebecca F. , Cockburn Joseph J. , Lomonossoff George P. , Ranson Neil A.
Published: December 2015

Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly.
Cellobiohydrolase 1 from Trichoderma reesei degrades cellulose in single cellobiose steps
Authors: Brady Sonia K. , Sreelatha Sarangapani , Feng Yinnian , Chundawat Shishir P. S. , Lang Matthew J
Published: December 2015

Cellobiohydrolase 1 from Trichoderma reesei (TrCel7A) processively hydrolyses cellulose into cellobiose. Although enzymatic techniques have been established as promising tools in biofuel production, a clear understanding of the motor’s mechanistic action has yet to be revealed. Here, we develop an optical tweezers-based single-molecule (SM) motility assay for precision tracking of TrCel7A. Direct observation of motility during degradation reveals processive runs and distinct steps on the scale of 1 nm. Our studies suggest TrCel7A is not mechanically limited, can work against 20 pN loads and speeds up when assisted. Temperature-dependent kinetic studies establish the energy requirements for the fundamental stepping cycle, which likely includes energy from glycosidic bonds and other sources. Through SM measurements of isolated TrCel7A domains, we determine that the catalytic domain alone is sufficient for processive motion, providing insight into TrCel7A’s molecular motility mechanism.
Chronic acidosis in the tumour microenvironment selects for overexpression of LAMP2 in the plasma membrane
Authors: Damaghi Mehdi , Tafreshi Narges K. , Lloyd Mark C. , Sprung Robert , Estrella Veronica , Wojtkowiak Jonathan W. , Morse David L. , Koomen John M. , Bui Marilyn M. , Gatenby Robert A , Gillies Robert J
Published: December 2015

Early cancers are avascular and hence, profoundly acidic. Pre-malignant cells must adapt to acidosis to thrive in this hostile microenvironment. Here, we investigate MCF-7 cells that are adapted to grow in acidic conditions using SILAC proteomics and we reveal a significant upregulation of lysosomal proteins. Prominent among these is LAMP2 that functions to protect lysosomal membranes from acid proteolysis. LAMP2 upregulation by acidosis is confirmed both in vitro and in vivo. Furthermore, we show that the depletion of LAMP2 is sufficient to increase acidosis-mediated toxicity. In breast cancer patient samples, there is a high correlation of LAMP2 mRNA and protein expression with progression. We also observe that LAMP2 is located at the plasma membrane in clinical samples and this redistribution is acid-induced in vitro. Our findings suggest a potential adaptive mechanism, wherein cells chronically exposed to an acidic environment translocate lysosomal proteins to their surface, thus protecting the plasmalemma from acid-induced hydrolysis.
Corresponding morphological and molecular indicators of crude oil toxicity to the developing hearts of mahi mahi
Authors: Edmunds Richard C. , Gill J. A. , Baldwin David H. , Linbo Tiffany L. , French Barbara L. , Brown Tanya L. , Esbaugh Andrew J. , Mager Edward M. , Stieglitz John , Hoenig Ron , Benetti Daniel , Grosell Martin , Scholz Nathaniel L. , Incardona John P.
Published: December 2015

Crude oils from distinct geological sources worldwide are toxic to developing fish hearts. When oil spills occur in fish spawning habitats, natural resource injury assessments often rely on conventional morphometric analyses of heart form and function. The extent to which visible indicators correspond to molecular markers for cardiovascular stress is unknown for pelagic predators from the Gulf of Mexico. Here we exposed mahi (Coryphaena hippurus) embryos to field-collected crude oil samples from the 2010 Deepwater Horizon disaster. We compared visible heart defects (edema, abnormal looping, reduced contractility) to changes in expression of cardiac-specific genes that are diagnostic of heart failure in humans or associated with loss-of-function zebrafish cardiac mutants. Mahi exposed to crude oil during embryogenesis displayed typical symptoms of cardiogenic syndrome as larvae. Contractility, looping and circulatory defects were evident, but larval mahi did not exhibit downstream craniofacial and body axis abnormalities. A gradation of oil exposures yielded concentration-responsive changes in morphometric and molecular responses, with relative sensitivity being influenced by age. Our findings suggest that 1) morphometric analyses of cardiac function are more sensitive to proximal effects of crude oil-derived chemicals on the developing heart and 2) molecular indicators reveal a longer-term adverse shift in cardiogenesis trajectory.
Successful treatment of biofilm infections using shock waves combined with antibiotic therapy
Authors: Gnanadhas Divya Prakash , Elango Monalisha , Janardhanraj S. , Srinandan C. S. , Datey Akshay , Strugnell Richard A. , Gopalan Jagadeesh , Chakravortty Dipshikha
Published: December 2015

Many bacteria secrete a highly hydrated framework of extracellular polymer matrix on suitable substrates and embed within the matrix to form a biofilm. Bacterial biofilms are observed on many medical devices, endocarditis, periodontitis and lung infections in cystic fibrosis patients. Bacteria in biofilm are protected from antibiotics and >1,000 times of the minimum inhibitory concentration may be required to treat biofilm infections. Here, we demonstrated that shock waves could be used to remove Salmonella, Pseudomonas and Staphylococcus biofilms in urinary catheters. The studies were extended to a Pseudomonas chronic pneumonia lung infection and Staphylococcus skin suture infection model in mice. The biofilm infections in mice, treated with shock waves became susceptible to antibiotics, unlike untreated biofilms. Mice exposed to shock waves responded to ciprofloxacin treatment, while ciprofloxacin alone was ineffective in treating the infection. These results demonstrate for the first time that, shock waves, combined with antibiotic treatment can be used to treat biofilm infection on medical devices as well as in situ infections.
A behavioral defect of temporal association memory in mice that partly lack dopamine reuptake transporter
Authors: Deng Shining , Zhang Lingli , Zhu Tailin , Liu Yan-Mei , Zhang Hailong , Shen Yiping , Li Wei-Guang , Li Fei
Published: December 2015

Temporal association memory, like working memory, is a type of episodic memory in which temporally discontinuous elements are associated. However, the mechanisms that govern this association remain incompletely understood. Here, we identify a crucial role of dopaminergic action in temporal association memory. We used hemizygote hyperdopaminergic mutant mice with reduced dopamine transporter (DAT) expression, referred to as DAT+/− mice. We found that mice with this modest dopamine imbalance exhibited significantly impaired trace fear conditioning, which necessitates the association of temporally discontinuous elements and intact delay auditory fear conditioning, which does not. Moreover, the DAT+/− mice displayed substantial impairments in non-matching-to-place spatial working-memory tasks. Interestingly, these temporal association and working memory deficits could be mimicked by a low dose of the dopamine D2 receptor antagonist haloperidol. The shared phenotypes resulting from either the genetic reduction of DAT or the pharmacological inhibition of the D2 receptor collectively indicate that temporal association memory necessitates precise regulation of dopaminergic signaling. The particular defect in temporal association memory due to partial lack of DAT provides mechanistic insights on the understanding of cognitive impairments in multiple neurodevelopmental disorders.
Context-dependent dynamic UV signaling in female threespine sticklebacks
Authors: Hiermes Meike , Bakker Theo C. M. , Mehlis Marion , Rick Ingolf P.
Published: December 2015

Color signals, including ultraviolet (UV) signals, are widespread throughout the animal kingdom and color changes can be influenced by reproductive and motivational state. However, studies on dynamic changes of UV signals are scarce. Threespine sticklebacks (Gasterosteus aculeatus) that show intraspecific UV communication were used to study dynamic UV signaling in females. Reflectance measurements were taken from the distended abdomen, which serves as signal of female fecundity and readiness to spawn for courting males and the melanized dorsal region. Scans were taken during egg maturation as well as before and after stimulation with a male to investigate context-dependent color changes. We used a physiological model of vision to determine how females might be perceived by conspecifics and quantified chromatic contrasts among both body regions and between body regions and the background for all stages. Females showed a significant increase in abdominal UV intensity during egg maturation and in response to a courting male. Measures of chromatic contrast among body regions (abdomen vs. dorsal region) and against the background (abdomen vs. background) were also increased during egg maturation and in response to the male stimulus (abdomen vs. background). Our results provide evidence for dynamic UV signaling in females in a reproductive context.
Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM)
Authors: Coghlan Megan L. , Maker Garth , Crighton Elly , Haile James , Murray Dáithí C. , White Nicole E. , Byard Roger W. , Bellgard Matthew I. , Mullaney Ian , Trengove Robert , Allcock Richard J. N. , Nash Christine , Hoban Claire , Jarrett Kevin , Edwards Ross , Musgrave Ian F. , Bunce Michael
Published: December 2015

Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds. Here, for the first time, a multidisciplinary approach to assessing the molecular content of 26 TCMs is described. Next generation DNA sequencing is combined with toxicological and heavy metal screening by separation techniques and mass spectrometry (MS) to provide a comprehensive audit. Genetic analysis revealed that 50% of samples contained DNA of undeclared plant or animal taxa, including an endangered species of Panthera (snow leopard). In 50% of the TCMs, an undeclared pharmaceutical agent was detected including warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass spectrometry revealed heavy metals including arsenic, lead and cadmium, one with a level of arsenic >10 times the acceptable limit. The study showed 92% of the TCMs examined were found to have some form of contamination and/or substitution. This study demonstrates that a combination of molecular methodologies can provide an effective means by which to audit complementary and alternative medicines.
Influence of ionic liquid and ionic salt on protein against the reactive species generated using dielectric barrier discharge plasma
Authors: Attri Pankaj , Sarinont Thapanut , Kim Minsup , Amano Takaaki , Koga Kazunori , Cho Art E. , Ha Choi Eun , Shiratani Masaharu
Published: December 2015

The presence of salts in biological solution can affect the activity of the reactive species (RS) generated by plasma and so they can also have an influence on the plasma-induced sterilization. In this work, we assess the influence that diethylammonium dihydrogen phosphate (DEAP), an ionic liquid (IL) and sodium chloride (NaCl), an ionic salt (IS), have on the structural changes in hemoglobin (Hb) in the presence of RS generated using dielectric barrier discharge (DBD) plasma in the presence of various gases [O2, N2, Ar, He, NO (10%) + N2 and Air]. We carry out fluorescence spectroscopy to verify the generation of •OH with or without the presence of DEAP IL and IS and we use electron spin resonance (ESR) to check the generation of H• and •OH. In addition, we verified the structural changes in the Hb structure after treatment with DBD in presence and absence of IL and IS. We then assessed the structural stability of the Hb in the presence of IL and IS by using molecular dynamic (MD) simulations. Our results indicate that the IL has a strong effect on the conservation of the Hb structure relative to that of IS against RS generated by plasma.
Thermodynamic consequences of the kinetic nature of the glass transition
Authors: Koperwas Kajetan , Grzybowski Andrzej , Tripathy Satya N. , Masiewicz Elzbieta , Paluch Marian
Published: December 2015

In this paper, we consider the glass transition as a kinetic process and establish one universal equation for the pressure coefficient of the glass transition temperature, dTg/dp, which is a thermodynamic characteristic of this process. Our findings challenge the common previous expectations concerning key characteristics of the transformation from the liquid to the glassy state, because it suggests that without employing an additional condition, met in the glass transition, derivation of the two independent equations for dTg/dp is not possible. Hence, the relation among the thermodynamic coefficients, which could be equivalent to the well-known Prigogine-Defay ratio for the process under consideration, cannot be obtained. Besides, by comparing the predictions of our universal equation for dTg/dp and Ehrenfest equations, we find the aforementioned supplementary restriction, which must be met to use the Prigogine-Defay ratio for the glass transition.
Reactivity of Metal-Free and Metal-Associated Amyloid-β with Glycosylated Polyphenols and Their Esterified Derivatives
Authors: Korshavn Kyle J. , Jang Milim , Kwak Yeon Ju , Kochi Akiko , Vertuani Silvia , Bhunia Anirban , Manfredini Stefano , Ramamoorthy Ayyalusamy , Lim Mi Hee
Published: December 2015

Both amyloid-β (Aβ) and transition metal ions are shown to be involved in the pathogenesis of Alzheimer’s disease (AD), though the importance of their interactions remains unclear. Multifunctional molecules, which can target metal-free and metal-bound Aβ and modulate their reactivity (e.g., Aβ aggregation), have been developed as chemical tools to investigate their function in AD pathology; however, these compounds generally lack specificity or have undesirable chemical and biological properties, reducing their functionality. We have evaluated whether multiple polyphenolic glycosides and their esterified derivatives can serve as specific, multifunctional probes to better understand AD. The ability of these compounds to interact with metal ions and metal-free/-associated Aβ and further control both metal-free and metal-induced Aβ aggregation was investigated through gel electrophoresis with Western blotting, transmission electron microscopy, UV-Vis spectroscopy, fluorescence spectroscopy and NMR spectroscopy. We also examined the cytotoxicity of the compounds and their ability to mitigate the toxicity induced by both metal-free and metal-bound Aβ. Of the polyphenols investigated, the natural product (Verbascoside) and its esterified derivative (VPP) regulate the aggregation and cytotoxicity of metal-free and/or metal-associated Aβ to different extents. Our studies indicate Verbascoside represents a promising structure for further multifunctional tool development against both metal-free Aβ and metal-Aβ.
Upregulation of Phosphodiesterase type 5 in the Hyperplastic Prostate
Authors: Zhang Wenhao , Zang Ning , Jiang Yaoming , Chen Ping , Wang Xinghuan , Zhang Xinhua
Published: December 2015

Both erectile dysfunction (ED) and lower urinary tract symptoms (LUTS)/benign prostatic hyperplasia (BPH) are common in the aging male. Numerous clinical trials have demonstrated the efficacy and safety of phosphodiesterase type 5 inhibitors (PDE5-Is) for treating LUTS/BPH with/without ED. However, the influence of BPH on prostatic PDE5 expression has never been studied. A testosterone-induced rat model of BPH was developed and human hyperplastic prostate specimens were harvested during cystoprostatectomy. PDE5, nNOS, eNOS and α1-adrenoreceptor subtypes (α1aARs, α1bARs and α1dARs) were determined with real-time RT-PCR for rat tissues whilst PDE5 and α1-adrenoreceptor subtypes were determined in human samples. PDE5 was further analyzed with Western-blot and histological examination. Serum testosterone was measured with ELISA. The rat BPH model was validated as having a significantly enlarged prostate. PDE5 localized mainly in fibromuscular stroma in prostate. Our data showed a significant and previously undocumented upregulation of PDE5 in both rat and human BPH, along with increased expression of nNOS and α1dARs for rat tissues and α1aARs for human BPH. The upregulation of PDE5 in the hyperplastic prostate could explain the mechanism and contribute to the high effectiveness of PDE5-Is for treating LUTS/BPH. Fibromuscular stroma could be the main target for PDE5-Is within prostate.
Climate Change and the Evolution and Fate of the Tangier Islands of Chesapeake Bay, USA
Authors: Schulte David M. , Dridge Karin M. , Hudgins Mark H.
Published: December 2015

Climate change and associated sea level rise (SLR) are already impacting low-lying coastal areas, including islands, throughout the world. Many of these areas are inhabited, many will need to be abandoned in coming decades as SLR continues. We examine the evolution (1850-2013) of the last inhabited offshore island in Virginia waters of Chesapeake Bay USA, the Tangier Islands. Three SLR scenarios, a low, mid and high, were considered. Since 1850, 66.75% of the islands landmass has been lost. Under the mid-range SLR scenario, much of the remaining landmass is expected to be lost in the next 50 years and the Town will likely need to be abandoned. The high SLR scenario will accelerate the land loss and subsidence, such that the Town may need to be abandoned in as few as 25 years. We propose a conceptual plan that would significantly extend the lifespan of the islands and Town.
GaN Haeckelite Single-Layered Nanostructures: Monolayer and Nanotubes
Authors: Camacho-Mojica Dulce C. , López-Urías Florentino
Published: December 2015

Nowadays, III-V semiconductors are interesting candidate materials for the tailoring of two dimensional (2D) graphene-like structures. These new 2D materials have attracted profound interest opening the possibility to find semiconductor materials with unexplored properties. First-principles density functional theory calculations are performed in order to investigate the electronic properties of GaN planar and nanotube morphologies based on Haeckelite structures (containing octagonal and square membered rings). Optimized geometries, band-structures, phonon dispersion, binding energies, transmission electron microscopy images simulations, x-ray diffraction patterns, charge densities and electronic band gaps are calculated. We demonstrated that GaN Haeckelite structures are stable exhibiting a semiconducting behavior with an indirect band gap. Furthermore, it was found that GaN Haeckelite nanotubes are semiconductor with a band gap nature (direct or indirect) that depends of the nanotube´s chirality and diameter. In addition, it was demonstrated that surface passivation and the interaction with hydrazine, water, ammonia and carbon monoxide molecules can change the band-gap nature. Our results are compared with the corresponding GaN hexagonal honeycomb structures.
The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)
Authors: Carrique-Mas Juan J. , Tue Ngo T. , Bryant Juliet E. , Saylors Karen , Cuong Nguyen V. , Hoa Ngo T. , An Nguyen N. , Hien Vo B. , Lao Pham V. , Tu Nguyen C. , Chuyen Nguyen K. , Chuc Nguyen T.K. , Tan Dinh V. , Duong Hoang Van V. , Toan Tran K. , Chi Nguyen T.Y. , Campbell James , Rabaa Maia A. , Nadjm Behzad , Woolhouse Mark , Wertheim Heiman , Thwaites Guy , Baker Stephen
Published: December 2015

The Vietnam Initiative for Zoonotic Infections (VIZIONS) includes community-based ‘high-risk sentinel cohort’ (HRSC) studies investigating individuals at risk of zoonotic infection due to occupational or residential exposure to animals. A total of 852 HRSC members were recruited between March 2013 and August 2014 from three provinces (Ha Noi, Dak Lak and Dong Thap). The most numerous group (72.8%) corresponded to individuals living on farms, followed by slaughterers (16.3%) and animal health workers (8.5%). Nasal/pharyngeal and rectal swabs were collected from HRSC members at recruitment and after notifying illness. Exposure to exotic animals (including wild pigs, porcupine, monkey, civet, bamboo rat and bat) was highest for the Dak Lak cohort (53.7%), followed by Ha Noi (13.7%) and Dong Thap (4.0%). A total of 26.8% of individuals reported consumption of raw blood over the previous year; 33.6% slaughterers reported no use of protective equipment at work. Over 686 person-years of observation, 213 episodes of suspect infectious disease were notified, equivalent of 0.35 reports per person-year. Responsive samples were collected from animals in the farm cohort. There was noticeable time and space clustering of disease episodes suggesting that the VIZIONS set up is also suitable for the formal epidemiological investigation of disease outbreaks.
Strain induced topological phase transitions in monolayer honeycomb structures of group-V binary compounds
Authors: Nie Yaozhuang , Rahman Mavlanjan , Wang Daowei , Wang Can , Guo Guanghua
Published: December 2015

We present first-principles calculations of electronic structures of a class of two-dimensional (2D) honeycomb structures of group-V binary compounds. Our results show these new 2D materials are stable semiconductors with direct or indirect band gaps. The band gap can be tuned by applying lattice strain. During their stretchable regime, they all exhibit metal-indirect gap semiconductor-direct gap semiconductor-topological insulator (TI) transitions with increasing strain from negative (compressive) to positive (tensile) values. The topological phase transition results from the band inversion at the Γ point which is due to the evolution of bonding and anti-bonding states under lattice strain.
Cartilage development requires the function of Estrogen-related receptor alpha that directly regulates sox9 expression in zebrafish
Authors: Kim Yong-Il , No Lee Joon , Bhandari Sushil , Nam In-Koo , Yoo Kyeong-Won , Kim Se-Jin , Oh Gi-Su , Kim Hyung-Jin , So Hong-Seob , Choe Seong-Kyu , Park Raekil
Published: December 2015

Estrogen-related receptor alpha (ESRRa) regulates a number of cellular processes including development of bone and muscles. However, direct evidence regarding its involvement in cartilage development remains elusive. In this report, we establish an in vivo role of Esrra in cartilage development during embryogenesis in zebrafish. Gene expression analysis indicates that esrra is expressed in developing pharyngeal arches where genes necessary for cartilage development are also expressed. Loss of function analysis shows that knockdown of esrra impairs expression of genes including sox9, col2a1, sox5, sox6, runx2 and col10a1 thus induces abnormally formed cartilage in pharyngeal arches. Importantly, we identify putative ESRRa binding elements in upstream regions of sox9 to which ESRRa can directly bind, indicating that Esrra may directly regulate sox9 expression. Accordingly, ectopic expression of sox9 rescues defective formation of cartilage induced by the knockdown of esrra. Taken together, our results indicate for the first time that ESRRa is essential for cartilage development by regulating sox9 expression during vertebrate development.
Correlative cryo-fluorescence and cryo-scanning electron microscopy as a straightforward tool to study host-pathogen interactions
Authors: Strnad Martin , Elsterová Jana , Schrenková Jana , Vancová Marie , Rego Ryan O. M. , Grubhoffer Libor , Nebesářová Jana
Published: December 2015

Correlative light and electron microscopy is an imaging technique that enables identification and targeting of fluorescently tagged structures with subsequent imaging at near-to-nanometer resolution. We established a novel correlative cryo-fluorescence microscopy and cryo-scanning electron microscopy workflow, which enables imaging of the studied object of interest very close to its natural state, devoid of artifacts caused for instance by slow chemical fixation. This system was tested by investigating the interaction of the zoonotic bacterium Borrelia burgdorferi with two mammalian cell lines of neural origin in order to broaden our knowledge about the cell-association mechanisms that precedes the entry of the bacteria into the cell. This method appears to be an unprecedentedly fast (<3 hours), straightforward and reliable solution to study the finer details of pathogen-host cell interactions and provides important insights into the complex and dynamic relationship between a pathogen and a host.
Proteome Analysis of Renoprotection Mediated by a Novel Cyclic Helix B Peptide in Acute Kidney Injury
Authors: Yang Cheng , Liu Junjun , Li Long , Hu Meiyu , Long Yaqiu , Liu Xiaohui , Zhu Tongyu , Huang Xiao , Zhao Shouliang , Liu Shangfeng , Rong Ruiming
Published: December 2015

We developed a novel, erythropoietin-derived, non-erythropoiesis, cyclic helix B peptide (CHBP) that displays potent renoprotection against acute kidney injury (AKI). To determine the mechanism of CHBP-mediated protection, we investigated the proteomic profile of mice treated with CHBP in a kidney ischemia-reperfusion (IR) injury model. The isobaric tags for relative and absolute quantitation (iTRAQ)-labeled samples were analyzed using a QSTAR XL LC/MS system. In total, 38 differentially expressed proteins (DEPs) were shared by all experimental groups, while 3 DEPs were detected specifically in the IR + CHBP group. Eight significant pathways were identified and oxidative phosphorylation was shown to be the most important pathway in CHBP-mediated renoprotection. The significant DEPs in the oxidative phosphorylation pathway elicited by CHBP are NADH-ubiquinone oxidoreductase Fe-S protein 6 (NDUFS6), alpha-aminoadipic semialdehyde synthase (AASS) and ATP-binding cassette sub-family D member 3 (ABCD3). The DEPs mentioned above were verified by RT-qPCR and immunostaining in mouse kidneys. We tested 6 DEPs in human biopsy samples from kidney transplant recipients. The trend of differential expression was consistent with that in the murine model. In conclusion, this study helps to elucidate the pharmacological mechanisms of CHBP before clinical translation.
Is overexpression of TWIST, a transcriptional factor, a prognostic biomarker of head and neck carcinoma? Evidence from fifteen studies
Authors: Zhuo Xianlu , Luo Huanli , Chang Aoshuang , Li Dairong , Zhao Houyu , Zhou Qi
Published: December 2015

TWIST, a basic helix-loop-helix transcription factor, has been indicated to play a critical role in the progression of numerous malignant disorders. Published data on the significance of TWIST expression in head and neck carcinoma (HNC) risk have yielded conflicting results. Thus, we conducted a quantitative meta-analysis to obtain a precise estimate of this subject. After systematic searching and screening, a total of fifteen studies using immunohistochemistry for TWIST detection were included. The results showed that TWIST positive expression rate in HNC tissues was higher than that in normal tissues. TWIST expression might have a correlation with clinical features such as low differentiation, advanced clinical stage, presence of lymph node metastasis, distant metastasis and local recurrence (P < 0.05) , but not with age, gender, T stage and smoking as well as drinking (P > 0.05). In addition, over-expression of TWIST was a prognostic factor for HNC (HR = 1.92, 95% CI = 1.13–3.25). The data suggested that TWIST might play critical roles in cancer progression and act as a prognostic factor for HNC patients.
Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure
Authors: Nimusiima Jean , Köberl Martina , Tumuhairwe John Baptist , Kubiriba Jerome , Staver Charles , Berg Gabriele
Published: December 2015

Africa is among the continents where the battle over genetically modified crops is currently being played out. The impact of GM in Africa could potentially be very positive. In Uganda, researchers have developed transgenic banana lines resistant to bananaXanthomonaswilt. The transgenic lines expressinghrapandpflpcan provide a timely solution to the pandemic. However, the impact of the transgenes expression on non-target microorganisms has not yet been investigated. To study this effect, transgenic and control lines were grown under field conditions and their associated microbiome was investigated by 16S rRNA gene profiling combining amplicon sequencing and molecular fingerprinting. Three years after sucker planting, no statistically significant differences between transgenic lines and their non-modified predecessors were detected for their associated bacterial communities. The overall gammaproteobacterial rhizosphere microbiome was highly dominated byXanthomonadales, whilePseudomonadalesandEnterobacterialeswere accumulated in the pseudostem. Shannon indices revealed much higher diversity in the rhizosphere than in the pseudostem endosphere. However, the expression of the transgenes did not result in changes in the diversity ofGammaproteobacteria, the closest relatives of the target pathogen. In this field experiment, the expression of the resistance genes appears to have no consequences for non-target rhizobacteria and endophytes.
A single-nucleotide exon found in Arabidopsis
Authors: Guo Lei , Liu Chun-Ming
Published: December 2015

The presence of introns in gene-coding regions is one of the most mysterious evolutionary inventions in eukaryotic organisms. It has been proposed that, although sequences involved in intron recognition and splicing are mainly located in introns, exonic sequences also contribute to intron splicing. The smallest constitutively spliced exon known so far has 6 nucleotides and the smallest alternatively spliced exon has 3 nucleotides. Here we report that the Anaphase Promoting Complex subunit 11 (APC11) gene in Arabidopsis thaliana carries a constitutive single-nucleotide exon. In vivo transcription and translation assays performed using APC11-Green Fluorescence Protein (GFP) fusion constructs revealed that intron splicing surrounding the single-nucleotide exon is effective in both Arabidopsis and rice. This discovery warrants attention to genome annotations in the future.
Effective Energy Transfer via Plasmon-Activated High-Energy Water Promotes Its Fundamental Activities of Solubility, Ionic Conductivity and Extraction at Room Temperature
Authors: Yang Chih-Ping , Chen Hsiao-Chien , Wang Ching-Chiung , Tsai Po-Wei , Ho Chia-Wen , Liu Yu-Chuan
Published: December 2015

Water is a ubiquitous solvent in biological, physical and chemical processes. Unique properties of water result from water’s tetrahedral hydrogen-bonded (HB) network (THBN). The original THBN is destroyed when water is confined in a nanosized environment or localized at interfaces, resulting in corresponding changes in HB-dependent properties. In this work, we present an innovative idea to validate the reserve energy of high-energy water and applications of high-energy water to promote water’s fundamental activities of solubility, ionic conductivity and extraction at room temperature. High-energy water with reduced HBs was created by utilizing hot electrons with energies from the decay of surface plasmon excited at gold (Au) nanoparticles (NPs). Compared to conventional deionized (DI) water, solubilities of alkali metal-chloride salts in high-energy water were significantly increased, especially for salts that release heat when dissolved. The ionic conductivity of NaCl in high-energy water was also markedly higher, especially when the electrolyte’s concentration was extremely low. In addition, antioxidative components, such as polyphenols and 2,3,5,4’-tetrahydroxystilbene-2-O-beta-d-glucoside (THSG) from teas and Polygonum multiflorum (PM), could more effectively be extracted using high-energy water. These results demonstrate that high-energy water has emerged as a promising innovative solvent for promoting water’s fundamental activities via effective energy transfer.
Cdk5-mediated inhibition of APC/C-Cdh1 switches on the cyclin D1-Cdk4-pRb pathway causing aberrant S-phase entry of postmitotic neurons
Authors: Veas-Pérez de Tudela Miguel , Maestre Carolina , Delgado-Esteban María , Bolaños Juan P. , Almeida Angeles
Published: December 2015

The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that regulates cell cycle progression in proliferating cells. To enter the S-phase, APC/C must be inactivated by phosphorylation of its cofactor, Cdh1. In post-mitotic cells such as neurons APC/C-Cdh1 complex is highly active and responsible for the continuous degradation of mitotic cyclins. However, the specific molecular pathway that determines neuronal cell cycle blockade in post-mitotic neurons is unknown. Here, we show that activation of glutamatergic receptors in rat cortical primary neurons endogenously triggers cyclin-dependent kinase-5 (Cdk5)-mediated phosphorylation of Cdh1 leading to its cytoplasmic accumulation and disassembly from the APC3 core protein, causing APC/C inactivation. Conversely, pharmacological or genetic inhibition of Cdk5 promotes Cdh1 ubiquitination and proteasomal degradation. Furthermore, we show that Cdk5-mediated phosphorylation and inactivation of Cdh1 leads to p27 depletion, which switches on the cyclin D1-cyclin-dependent kinase-4 (Cdk4)-retinoblastoma protein (pRb) pathway to allow the S-phase entry of neurons. However, neurons do not proceed through the cell cycle and die by apoptosis. These results indicate that APC/C-Cdh1 actively suppresses an aberrant cell cycle entry and death of neurons, highlighting its critical function in neuroprotection.
Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae)
Authors: Yang Chunxiao , Pan Huipeng , Noland Jeffrey Edward , Zhang Deyong , Zhang Zhanhong , Liu Yong , Zhou Xuguo
Published: December 2015

Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for quantifying gene expression across various biological processes, of which requires a set of suited reference genes to normalize the expression data. Coleomegilla maculata (Coleoptera: Coccinellidae), is one of the most extensively used biological control agents in the field to manage arthropod pest species. In this study, expression profiles of 16 housekeeping genes selected from C. maculata were cloned and investigated. The performance of these candidates as endogenous controls under specific experimental conditions was evaluated by dedicated algorithms, including geNorm, Normfinder, BestKeeper and ΔCt method. In addition, RefFinder, a comprehensive platform integrating all the above-mentioned algorithms, ranked the overall stability of these candidate genes. As a result, various sets of suitable reference genes were recommended specifically for experiments involving different tissues, developmental stages, sex and C. maculate larvae treated with dietary double stranded RNA. This study represents the critical first step to establish a standardized RT-qPCR protocol for the functional genomics research in a ladybeetle C. maculate. Furthermore, it lays the foundation for conducting ecological risk assessment of RNAi-based gene silencing biotechnologies on non-target organisms; in this case, a key predatory biological control agent.
Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago
Authors: Shinzato Chuya , Mungpakdee Sutada , Arakaki Nana , Satoh Noriyuki
Published: December 2015

Following a global coral bleaching event in 1998, Acropora corals surrounding most of Okinawa island (OI) were devastated, although they are now gradually recovering. In contrast, the Kerama Islands (KIs) only 30 km west of OI, have continuously hosted a great variety of healthy corals. Taking advantage of the decoded Acropora digitifera genome and using genome-wide SNP analyses, we clarified Acropora population structure in the southern Ryukyu Archipelago (sRA). Despite small genetic distances, we identified distinct clusters corresponding to specific island groups, suggesting infrequent long-distance dispersal within the sRA. Although the KIs were believed to supply coral larvae to OI, admixture analyses showed that such dispersal is much more limited than previously realized, indicating independent recovery of OI coral populations and the necessity of local conservation efforts for each region. We detected strong historical migration from the Yaeyama Islands (YIs) to OI and suggest that the YIs are the original source of OI corals. In addition, migration edges to the KIs suggest that they are a historical sink population in the sRA, resulting in high diversity. This population genomics study provides the highest resolution data to date regarding coral population structure and history.
Plasmonic Hot Hole Generation by Interband Transition in Gold-Polyaniline
Authors: Barman Tapan , Hussain Amreen A. , Sharma Bikash , Pal Arup R.
Published: December 2015

Studies on hot carrier science and technology associated with various types of nanostructures are dominating today’s nanotechnology research. Here we report a novel synthesis of polyaniline-gold (PAni-Au) nanocomposite thin films with gold nanostructures (AuNs) of desired shape and size uniformly incorporated in the polymer matrix. According to shape as well as size variation of AuNs, two tunable plasmonic UV-Visible absorption bands are observed in each of the nanocomposites. Plasmonic devices are fabricated using PAni-Au nanocomposite having different UV-Visible plasmon absorption bands. However, all the devices show strong photoelectrical responses in the blue region (400–500 nm) of the visible spectrum. The d-band to sp-band (d-sp) transition of electrons in AuNs produces hot holes that are the only carriers in the material responsible for photocurrent generation in the device. This work provides an experimental evidence of novel plasmonic hot hole generation process that was still a prediction.