Showing papers by "Trinity College, Dublin published in 2012"

Electronics and optoelectronics of two-dimensional transition metal dichalcogenides.

Abstract: Single-layer metal dichalcogenides are two-dimensional semiconductors that present strong potential for electronic and sensing applications complementary to that of graphene.

Guidelines for the use and interpretation of assays for monitoring autophagy

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

The European Sovereign Debt Crisis

Abstract: The origin and propagation of the European sovereign debt crisis can be attributed to the flawed original design of the euro. In particular, there was an incomplete understanding of the fragility of a monetary union under crisis conditions, especially in the absence of banking union and other European-level buffer mechanisms. Moreover, the inherent messiness involved in proposing and implementing incremental multicountry crisis management responses on the fly has been an important destabilizing factor throughout the crisis. After diagnosing the situation, we consider reforms that might improve the resilience of the euro area to future fiscal shocks.

Genetically Distinct Subsets within ANCA-Associated Vasculitis

Abstract: BACKGROUND Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener's granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis. METHODS A genomewide association study was performed in a discovery cohort of 1233 U. K. patients with ANCA-associated vasculitis and 5884 controls and was replicated in 1454 Northern European case patients and 1666 controls. Quality control, population stratification, and statistical analyses were performed according to standard criteria. RESULTS We found both major-histocompatibility-complex (MHC) and non-MHC associations with ANCA-associated vasculitis and also that granulomatosis with polyangiitis and microscopic polyangiitis were genetically distinct. The strongest genetic associations were with the antigenic specificity of ANCA, not with the clinical syndrome. Anti-proteinase 3 ANCA was associated with HLA-DP and the genes encoding alpha(1)-antitrypsin (SERPINA1) and proteinase 3 (PRTN3) (P = 6.2x10(-89), P = 5.6x10(-12), and P = 2.6x10(-7), respectively). Anti-myeloperoxidase ANCA was associated with HLA-DQ (P = 2.1x10(-8)). CONCLUSIONS This study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyangiitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature of proteinase 3 ANCA-associated vasculitis. These data provide preliminary support for the concept that proteinase 3 ANCA-associated vasculitis and myeloperoxidase ANCA-associated vasculitis are distinct autoimmune syndromes. (Funded by the British Heart Foundation and others.)

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

Abstract: Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.

Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity

Abstract: To gain further insight into the genetic architecture of psoriasis, we conducted a meta-analysis of 3 genome-wide association studies (GWAS) and 2 independent data sets genotyped on the Immunochip, including 10,588 cases and 22,806 controls. We identified 15 new susceptibility loci, increasing to 36 the number associated with psoriasis in European individuals. We also identified, using conditional analyses, five independent signals within previously known loci. The newly identified loci shared with other autoimmune diseases include candidate genes with roles in regulating T-cell function (such as RUNX3, TAGAP and STAT3). Notably, they included candidate genes whose products are involved in innate host defense, including interferon-mediated antiviral responses (DDX58), macrophage activation (ZC3H12C) and nuclear factor (NF)-κB signaling (CARD14 and CARM1). These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense.

Translation techniques in cross-language information retrieval

Abstract: Cross-language information retrieval (CLIR) is an active sub-domain of information retrieval (IR). Like IR, CLIR is centered on the search for documents and for information contained within those documents. Unlike IR, CLIR must reconcile queries and documents that are written in different languages. The usual solution to this mismatch involves translating the query and/or the documents before performing the search. Translation is therefore a pivotal activity for CLIR engines. Over the last 15 years, the CLIR community has developed a wide range of techniques and models supporting free text translation. This article presents an overview of those techniques, with a special emphasis on recent developments.

Solvent exfoliation of transition metal dichalcogenides: dispersibility of exfoliated nanosheets varies only weakly between compounds.

Abstract: We have studied the dispersion and exfoliation of four inorganic layered compounds, WS2, MoS2, MoSe2, and MoTe2, in a range of organic solvents. The aim was to explore the relationship between the chemical structure of the exfoliated nanosheets and their dispersibility. Sonication of the layered compounds in solvents generally gave few-layer nanosheets with lateral dimensions of a few hundred nanometers. However, the dispersed concentration varied greatly from solvent to solvent. For all four materials, the concentration peaked for solvents with surface energy close to 70 mJ/m2, implying that all four have surface energy close to this value. Inverse gas chromatography measurements showed MoS2 and MoSe2 to have surface energies of ∼75 mJ/m2, in good agreement with dispersibility measurements. However, this method suggested MoTe2 to have a considerably larger surface energy (∼120 mJ/m2). While surface-energy-based solubility parameters are perhaps more intuitive for two-dimensional materials, Hansen solubil...

Managing patients with multimorbidity: systematic review of interventions in primary care and community settings.

Abstract: Objective To determine the effectiveness of interventions designed to improve outcomes in patients with multimorbidity in primary care and community settings. Design Systematic review. Data sources Medline, Embase, CINAHL, CAB Health, Cochrane central register of controlled trials, the database of abstracts of reviews of effectiveness, and the Cochrane EPOC (effective practice and organisation of care) register (searches updated in April 2011). Eligibility criteria Randomised controlled trials, controlled clinical trials, controlled before and after studies, and interrupted time series analyses reporting on interventions to improve outcomes for people with multimorbidity in primary care and community settings. Multimorbidity was defined as two or more chronic conditions in the same individual. Outcomes included any validated measure of physical or mental health and psychosocial status, including quality of life outcomes, wellbeing, and measures of disability or functional status. Also included were measures of patient and provider behaviour, including drug adherence, utilisation of health services, acceptability of services, and costs. Data selection Two reviewers independently assessed studies for eligibility, extracted data, and assessed study quality. As meta-analysis of results was not possible owing to heterogeneity in participants and interventions, a narrative synthesis of the results from the included studies was carried out. Results 10 studies examining a range of complex interventions totalling 3407 patients with multimorbidity were identified. All were randomised controlled trials with a low risk of bias. Two studies described interventions for patients with specific comorbidities. The remaining eight studies focused on multimorbidity, generally in older patients. Consideration of the impact of socioeconomic deprivation was minimal. All studies involved complex interventions with multiple components. In six of the 10 studies the predominant component was a change to the organisation of care delivery, usually through case management or enhanced multidisciplinary team work. In the remaining four studies, intervention components were predominantly patient oriented. Overall the results were mixed, with a trend towards improved prescribing and drug adherence. The results indicated that it is difficult to improve outcomes in this population but that interventions focusing on particular risk factors in comorbid conditions or functional difficulties in multimorbidity may be more effective. No economic analyses were included, although the improvements in prescribing and risk factor management in some studies could provide potentially important cost savings. Conclusions Evidence on the care of patients with multimorbidity is limited, despite the prevalence of multimorbidity and its impact on patients and healthcare systems. Interventions to date have had mixed effects, although are likely to be more effective if targeted at risk factors or specific functional difficulties. A need exists to clearly identify patients with multimorbidity and to develop cost effective and specifically targeted interventions that can improve health outcomes.

A supramodal accumulation-to-bound signal that determines perceptual decisions in humans.

Abstract: This study uses EEG in humans to isolate and track an evolving, domain-general decision signal, which varies with accumulated evidence, but is independent of overt actions.

VizualAge: A Novel Approach to Laser Ablation ICP‐MS U‐Pb Geochronology Data Reduction

Abstract: VizualAge, a new computer software tool for analysing U-Pb data obtained by laser ablation-inductively coupled plasma-mass spectrometry, was developed. It consists of a data reduction scheme (DRS) for Iolite (a general mass spectrometry data analysis tool) as well as visualisation routines. In addition to the U/Pb and Th/Pb ages calculated by Iolites U-Pb geochronology DRS, VizualAge also calculates 207Pb/206Pb ages and common Pb corrections for each time-slice of raw data. Importantly, VizualAge allows one to display a live concordia diagram for visualising data on such a diagram as an integration interval is being adjusted. This provides instantaneous feedback regarding discordance, uncertainty, error correlation and common Pb. Several zircon data sets were used to illustrate how the live concordia could be used as a powerful inspection tool, revealing a single analysis to consist of zones of concordance, metamict areas, as well as inherited cores or younger overgrowths. VizualAge also constructs histograms, conventional and Tera-Wasserburg type concordia diagrams, as well as 3D U-Th-Pb and total U-Pb concordia diagrams. The precision and accuracy of data reduced with VizualAge are demonstrated with examples of the Plesovice, Temora-2 and Penglai zircon reference materials. Data for zircon from the Long Lake Batholith (Wyoming craton) were used to illustrate how VizualAge calculated common Pb corrections and helped to expose as yet unexplained difficulties with accurately determining 204Pb.

Identification of common variants associated with human hippocampal and intracranial volumes

Abstract: Identifying genetic variants influencing human brain structures may reveal new biological mechanisms underlying cognition and neuropsychiatric illness. The volume of the hippocampus is a biomarker of incipient Alzheimer's disease and is reduced in schizophrenia, major depression and mesial temporal lobe epilepsy. Whereas many brain imaging phenotypes are highly heritable, identifying and replicating genetic influences has been difficult, as small effects and the high costs of magnetic resonance imaging (MRI) have led to underpowered studies. Here we report genome-wide association meta-analyses and replication for mean bilateral hippocampal, total brain and intracranial volumes from a large multinational consortium. The intergenic variant rs7294919 was associated with hippocampal volume (12q24.22; N = 21,151; P = 6.70 × 10(-16)) and the expression levels of the positional candidate gene TESC in brain tissue. Additionally, rs10784502, located within HMGA2, was associated with intracranial volume (12q14.3; N = 15,782; P = 1.12 × 10(-12)). We also identified a suggestive association with total brain volume at rs10494373 within DDR2 (1q23.3; N = 6,500; P = 5.81 × 10(-7)).

Management of precancerous conditions and lesions in the stomach (MAPS): guideline from the European Society of Gastrointestinal Endoscopy (ESGE), European Helicobacter Study Group (EHSG), European Society of Pathology (ESP), and the Sociedade Portuguesa de Endoscopia Digestiva (SPED)

Abstract: Atrophic gastritis, intestinal metaplasia, and epithelial dysplasia of the stomach are common and are associated with an increased risk for gastric cancer. In the absence of guidelines, there is wide disparity in the management of patients with these premalignant conditions. The European Society of Gastrointestinal Endoscopy (ESGE), the European Helicobacter Study Group (EHSG), the European Society of Pathology (ESP) and the Sociedade Portuguesa de Endoscopia Digestiva (SPED) have therefore combined efforts to develop evidence-based guidelines on the management of patients with precancerous conditions and lesions of the stomach (termed MAPS). A multidisciplinary group of 63 experts from 24 countries developed these recommendations by means of repeat online voting and a meeting in June 2011 in Porto, Portugal. The recommendations emphasize the increased cancer risk in patients with gastric atrophy and metaplasia, and the need for adequate staging in the case of high grade dysplasia, and they focus on treatment and surveillance indications and methods.

The syndrome of cognitive impairment in amyotrophic lateral sclerosis: a population-based study

Abstract: Background Despite considerable interest, the population-based frequency, clinical characteristics and natural history of cognitive impairment in amyotrophic lateral sclerosis (ALS) are not known. Methodology The authors undertook a prospective population-based study of cognitive function in 160 incident Irish ALS patients and 110 matched controls. Home-based visits were conducted to collect demographic and neuropsychological data. Patients were classified using the recently published consensus criteria and by a domain-based classification of both executive and non-executive cognitive processes. Results 13.8% of patients fulfilled the Neary criteria for frontotemporal dementia. In addition, 34.1% of ALS patients without evidence of dementia fulfilled the recently published consensus criteria for cognitive impairment. Non-demented ALS patients had a significantly higher frequency of impairment in language and memory domains compared to healthy controls. These deficits occurred primarily in patients with executive dysfunction. 14% of ALS patients had evidence of cognitive impairment without executive dysfunction, and no cognitive abnormality was detected in almost half the cohort (46.9%). Conclusion Co-morbid dementia occurs in approximately 14% of patients with a new diagnosis of ALS. Cognitive impairment, predominantly but not exclusively in the form executive dysfunction, is present in more than 40% of ALS patients who have no evidence of dementia. Cognitive impairment in ALS is not a universal feature, and its manifestations may be more heterogeneous than previously recognised.

Transcription factor RORα is critical for nuocyte development

Abstract: Nuocytes are innate cells with critical roles during infection with parasitic worms. McKenzie and colleagues show that nuocytes differentiate from common lymphoid progenitors and require IL-7, IL-33, Notch and RORα for development.

Hybrid Graphene and Graphitic Carbon Nitride Nanocomposite: Gap Opening, Electron–Hole Puddle, Interfacial Charge Transfer, and Enhanced Visible Light Response

Abstract: Opening up a band gap and finding a suitable substrate material are two big challenges for building graphene-based nanodevices. Using state-of-the-art hybrid density functional theory incorporating long-range dispersion corrections, we investigate the interface between optically active graphitic carbon nitride (g-C(3)N(4)) and electronically active graphene. We find an inhomogeneous planar substrate (g-C(3)N(4)) promotes electron-rich and hole-rich regions, i.e., forming a well-defined electron-hole puddle, on the supported graphene layer. The composite displays significant charge transfer from graphene to the g-C(3)N(4) substrate, which alters the electronic properties of both components. In particular, the strong electronic coupling at the graphene/g-C(3)N(4) interface opens a 70 meV gap in g-C(3)N(4)-supported graphene, a feature that can potentially allow overcoming the graphene's band gap hurdle in constructing field effect transistors. Additionally, the 2-D planar structure of g-C(3)N(4) is free of dangling bonds, providing an ideal substrate for graphene to sit on. Furthermore, when compared to a pure g-C(3)N(4) monolayer, the hybrid graphene/g-C(3)N(4) complex displays an enhanced optical absorption in the visible region, a promising feature for novel photovoltaic and photocatalytic applications.

Lag Phase Is a Distinct Growth Phase That Prepares Bacteria for Exponential Growth and Involves Transient Metal Accumulation

Abstract: Lag phase represents the earliest and most poorly understood stage of the bacterial growth cycle. We developed a reproducible experimental system and conducted functional genomic and physiological analyses of a 2-h lag phase in Salmonella enterica serovar Typhimurium. Adaptation began within 4 min of inoculation into fresh LB medium with the transient expression of genes involved in phosphate uptake. The main lag-phase transcriptional program initiated at 20 min with the upregulation of 945 genes encoding processes such as transcription, translation, iron-sulfur protein assembly, nucleotide metabolism, LPS biosynthesis, and aerobic respiration. ChIP-chip revealed that RNA polymerase was not "poised" upstream of the bacterial genes that are rapidly induced at the beginning of lag phase, suggesting a mechanism that involves de novo partitioning of RNA polymerase to transcribe 522 bacterial genes within 4 min of leaving stationary phase. We used inductively coupled plasma mass spectrometry (ICP-MS) to discover that iron, calcium, and manganese are accumulated by S. Typhimurium during lag phase, while levels of cobalt, nickel, and sodium showed distinct growth-phase-specific patterns. The high concentration of iron during lag phase was associated with transient sensitivity to oxidative stress. The study of lag phase promises to identify the physiological and regulatory processes responsible for adaptation to new environments.

Preparation of High Concentration Dispersions of Exfoliated MoS2 with Increased Flake Size

Abstract: Solvent exfoliation of inorganic layered compounds is likely to be important for a range of applications. However, this method generally gives dispersions of small nanosheets at low concentrations. Here we describe methods, based on sonication of powdered MoS2 in the solvent N-methyl-pyrrolidone, to prepare dispersions with significantly increased lateral nanosheet size and dispersed concentration. We find the concentration to scale linearly with starting MoS2 mass allowing the definition of a yield. This yield can be increased to ∼40% by controlling the sonication time, resulting in concentrations as high as 40 mg/mL. We find the nanosheet size to increase initially with sonication time reaching ∼700 nm (for a concentration of ∼7.5 mg/mL). At longer sonication times the nanosheets size falls off due to sonication induced scission. The nanosheets produced by such methods are relatively thin and have no observable defects. We can separate the dispersed nanosheets by size using controlled centrifugation. Th...

Designing electrical contacts to MoS2 monolayers: a computational study.

Abstract: Studying the reason why single-layer molybdenum disulfide (MoS2) appears to fall short of its promising potential in flexible nanoelectronics, we find that the nature of contacts plays a more important role than the semiconductor itself In order to understand the nature of MoS2/metal contacts, we perform ab initio density functional theory calculations for the geometry, bonding, and electronic structure of the contact region We find that the most common contact metal (Au) is rather inefficient for electron injection into single-layer MoS2 and propose Ti as a representative example of suitable alternative electrode materials

An agronomic assessment of greenhouse gas emissions from major cereal crops

Abstract: Agricultural greenhouse gas (GHG) emissions contribute approximately 12% to total global anthropogenic GHG emissions. Cereals (rice, wheat, and maize) are the largest source of human calories, and it is estimated that world cereal production must increase by 1.3% annually to 2025 to meet growing demand. Sustainable intensification of cereal production systems will require maintaining high yields while reducing environmental costs. We conducted a meta-analysis (57 published studies consisting of 62 study sites and 328 observations) to test the hypothesis that the global warming potential (GWP) of CH4 and N2O emissions from rice, wheat, and maize, when expressed per ton of grain (yield-scaled GWP), is similar, and that the lowest value for each cereal is achieved at near optimal yields. Results show that the GWP of CH4 and N2O emissions from rice (3757 kg CO2 eq ha � 1 season � 1 ) was higher than wheat (662 kg CO2 eq ha � 1 season � 1 ) and maize (1399 kg CO2 eq ha � 1 season � 1 ). The yield-scaled GWP of rice was about four times higher (657 kg CO2 eq Mg � 1 ) than wheat (166 kg CO2 eq Mg � 1 ) and maize (185 kg CO2 eq Mg � 1 ). Across cereals, the lowest yield-scaled GWP values were achieved at 92% of maximal yield and were about twice as high for rice (279 kg CO2 eq Mg � 1 ) than wheat (102 kg CO2 eq Mg � 1 ) or maize (140 kg CO2 eq Mg � 1 ), suggesting greater mitigation opportunities for rice systems. In rice, wheat and maize, 0.68%, 1.21%, and 1.06% of N applied was emitted as N2O, respectively. In rice systems, there was no correlation between CH4 emissions and N rate. In addition, when evaluating issues related to food security and environmental sustainability, other factors including cultural significance, the provisioning of ecosystem services, and human health and well-being must also be considered.

PDK1 regulation of mTOR and hypoxia-inducible factor 1 integrate metabolism and migration of CD8+ T cells

Abstract: mTORC1 (mammalian target of rapamycin complex 1) controls transcriptional programs that determine CD8 + cytolytic T cell (CTL) fate. In some cell systems, mTORC1 couples phosphatidylinositol-3 kinase (PI3K) and Akt to the control of glucose uptake and glycolysis. However, PI3K–Akt-independent mechanisms control glucose metabolism in CD8 + T cells, and the role of mTORC1 has not been explored. The present study now demonstrates that mTORC1 activity in CD8 + T cells is not dependent on PI3K or Akt but is critical to sustain glucose uptake and glycolysis in CD8 + T cells. We also show that PI3K- and Akt-independent pathways mediated by mTORC1 regulate the expression of HIF1 (hypoxia-inducible factor 1) transcription factor complex. This mTORC1–HIF1 pathway is required to sustain glucose metabolism and glycolysis in effector CTLs and strikingly functions to couple mTORC1 to a diverse transcriptional program that controls expression of glucose transporters, multiple rate-limiting glycolytic enzymes, cytolytic effector molecules, and essential chemokine and adhesion receptors that regulate T cell trafficking. These data reveal a fundamental mechanism linking nutrient and oxygen sensing to transcriptional control of CD8 + T cell differentiation.

Meta‐analysis of structural MRI studies in children and adults with attention deficit hyperactivity disorder indicates treatment effects

Abstract: Frodl T, Skokauskas N. Meta-analysis of structural MRI studies in children and adults with attention deficit hyperactivity disorder indicates treatment effects. Objective: About 50–80% of ADHD cases have been found to persist into adulthood, but ADHD symptoms change with age. The aim of this study was to perform a meta-analysis of MRI voxel-based morphometry (VBM) and manual tracing studies to identify the differences between adults and children with ADHD as well as between treated and untreated individuals. Method: Several databases were searched using keywords ‘attention-deficit and MRI’, ‘ADHD and MRI’. Gray matter volumes from VBM studies and caudate volumes from tracing studies of patients and controls were analyzed using signed differential mapping. Results: Meta-analyses detected reduced right globus pallidus and putamen volumes in VBM studies as well as decreased caudate volumes in manual tracing studies in children with ADHD. Adult patients with ADHD showed volume reduction in the anterior cingulate cortex (ACC). A higher percentage of treated participants were associated with less changes. Conclusion: Basal ganglia regions like the right globus pallidus, the right putamen, and the nucleus caudatus are structurally affected in children with ADHD. These changes and alterations in limbic regions like ACC and amygdala are more pronounced in non-treated populations and seem to diminish over time from child to adulthood. Treatment seems to have positive effects on brain structure.

Oxygen radical functionalization of boron nitride nanosheets.

Abstract: The covalent chemical functionalization of exfoliated hexagonal boron–nitride nanosheets (BNNSs) is achieved by the solution-phase oxygen radical functionalization of boron atoms in the h-BN lattice. This involves a two-step procedure to initially covalently graft alkoxy groups to boron atoms and the subsequent hydrolytic defunctionalization of the groups to yield hydroxyl-functionalized BNNSs (OH-BNNSs). Characterization of the functionalized-BNNSs using HR-TEM, Raman, UV–vis, FTIR, NMR, and TGA was performed to investigate both the structure of the BNNSs and the covalent functionalization methodology. OH-BNNSs were used to prepare polymer nanocomposites and their mechanical properties analyzed. The influence of the functional groups grafted to the surface of the BNNSs is investigated by demonstrating the impact on mechanical properties of both noncovalent and covalent bonding at the interface between the nanofiller and polymer matrixes.

Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis

Abstract: The strong restriction barrier present in Staphylococcus aureus and Staphylococcus epidermidis has limited functional genomic analysis to a small subset of strains that are amenable to genetic manipulation. Recently, a conserved type IV restriction system termed SauUSI (which specifically recognizes cytosine methylated DNA) was identified as the major barrier to transformation with foreign DNA. Here we have independently corroborated these findings in a widely used laboratory strain of S. aureus. Additionally, we have constructed a DNA cytosine methyltransferase mutant in the high-efficiency Escherichia coli cloning strain DH10B (called DC10B). Plasmids isolated from DC10B can be directly transformed into clinical isolates of S. aureus and S. epidermidis. We also show that the loss of restriction (both type I and IV) in an S. aureus USA300 strain does not have an impact on virulence. Circumventing the SauUSI restriction barrier, combined with an improved deletion and transformation protocol, has allowed the genetic manipulation of previously untransformable strains of these important opportunistic pathogens. IMPORTANCE Staphylococcal infections place a huge burden on the health care sector due both to their severity and also to the economic impact of treating the infections because of prolonged hospitalization. To improve the understanding of Staphylococcus aureus and Staphylococcus epidermidis infections, we have developed a series of improved techniques that allow the genetic manipulation of strains that were previously refractory to transformation. These developments will speed up the process of mutant construction and increase our understanding of these species as a whole, rather than just a small subset of strains that could previously be manipulated.

Cognitive and clinical characteristics of patients with amyotrophic lateral sclerosis carrying a C9orf72 repeat expansion: a population-based cohort study

Abstract: Summary Background Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease of upper and lower motor neurons, associated with frontotemporal dementia (FTD) in about 14% of incident cases. We assessed the frequency of the recently identified C9orf72 repeat expansion in familial and apparently sporadic cases of ALS and characterised the cognitive and clinical phenotype of patients with this expansion. Methods A population-based register of patients with ALS has been in operation in Ireland since 1995, and an associated DNA bank has been in place since 1999. 435 representative DNA samples from the bank were screened using repeat-primed PCR for the presence of a GGGGCC repeat expansion in C9orf72 . We assessed clinical, cognitive, behavioural, MRI, and survival data from 191 (44%) of these patients, who comprised a population-based incident group and had previously participated in a longitudinal study of cognitive and behavioural changes in ALS. Findings Samples from the DNA bank included 49 cases of known familial ALS and 386 apparently sporadic cases. Of these samples, 20 (41%) cases of familial ALS and 19 (5%) cases of apparently sporadic ALS had the C9orf72 repeat expansion. Of the 191 patients for whom phenotype data were available, 21 (11%) had the repeat expansion. Age at disease onset was lower in patients with the repeat expansion (mean 56·3 [SD 8·3] years) than in those without (61·3 [10·6] years; p=0·043). A family history of ALS or FTD was present in 18 (86%) of those with the repeat expansion. Patients with the repeat expansion had significantly more co-morbid FTD than patients without the repeat (50% vs 12%), and a distinct pattern of non-motor cortex changes on high-resolution 3 T magnetic resonance structural neuroimaging. Age-matched univariate analysis showed shorter survival (20 months vs 26 months) in patients with the repeat expansion. Multivariable analysis showed an increased hazard rate of 1·9 (95% 1·1–3·7; p=0·035) in those patients with the repeat expansion compared with patients without the expansion Interpretation Patients with ALS and the C9orf72 repeat expansion seem to present a recognisable phenotype characterised by earlier disease onset, the presence of cognitive and behavioural impairment, specific neuroimaging changes, a family history of neurodegeneration with autosomal dominant inheritance, and reduced survival. Recognition of patients with ALS who carry an expanded repeat is likely to be important in the context of appropriate disease management, stratification in clinical trials, and in recognition of other related phenotypes in family members. Funding Health Seventh Framework Programme, Health Research Board, Research Motor Neuron, Irish Motor Neuron Disease Association, The Motor Neurone Disease Association of Great Britain and Northern Ireland, ALS Association.