The T cell response of HLA-DR transgenic mice to human myelin basic protein and other antigens in the presence and absence of human CD4.
Analysis of HLA class II transgenic mice has progressed in recent years from analysis of single chain HLA class II transgenes with expression of mixed mouse/human heterodimers to double transgenic mice expressing normal human heterodimers. Previous studies have used either HLA transgenic mice in which there is a species-matched interaction with CD4 or mice which lack this interaction. Since both systems are reported to generate HLA-restricted responses, the matter of the requirement for species-matched CD4 remains unclear. We have generated triple transgenic mice expressing three human transgenes, DRA, DRB, and CD4, and compared HLA-restricted responses to peptide between human-CD4+ (Hu-CD4+) and Hu-CD4- littermates. We saw no difference between Hu-CD4+ and Hu-CD4- groups, supporting the notion that for some responses at least the requirement for species-matched CD4 may not be absolute. Evidence for positive selection of mouse T cell receptors in HLA-DR transgenic mice came both from the acquisition of new, HLA-restricted responses to various peptides and from an increased frequency of T cells using the TCR V beta 4 gene segment. An important goal with respect to the analysis of function in HLA transgenic mice is the clarification of mechanisms which underpin the recognition of self-antigens in human autoimmune disease. As a first step towards 'humanized' disease models in HLA transgenic mice, we analyzed the responses of HLA-DR transgenic mice to the human MPB 139-154 peptide which has been implicated as an epitope recognized by T cells of multiple sclerosis patients. We obtained T cell responses to this epitope in transgenic mice but not in nontransgenic controls. This study suggests that HLA transgenic mice will be valuable in the analysis of HLA-restricted T cell epitopes implicated in human disease and possibly in the design of new disease models.


Transdermal scopolamine-induced psychosis.
Transdermal scopolamine (Transderm-Scop) is being increasingly used for effective prophylaxis of motion sickness. It is reported to have a lower incidence of CNS side effects than orally administered scopolamine. Although uncommon, such side effects occur more often in the elderly, in those with preexisting psychiatric disease, and in patients concurrently taking other medications with anticholinergic activity. Correct diagnosis may be delayed by the occult location of the delivery system, delayed onset of symptoms, prolonged action, absence of peripheral manifestations, and negative toxicologic screening tests. Treatment is usually supportive. Physostigmine should be reserved for the treatment of severe symptoms.


A germline DNA polymorphism enhances alternative splicing of the KLF6 tumor suppressor gene and is associated with increased prostate cancer risk.
Prostate cancer is a leading and increasingly prevalent cause of cancer death in men. Whereas family history of disease is one of the strongest prostate cancer risk factors and suggests a hereditary component, the predisposing genetic factors remain unknown. We first showed that KLF6 is a tumor suppressor somatically inactivated in prostate cancer and since then, its functional loss has been further established in prostate cancer cell lines and other human cancers. Wild-type KLF6, but not patient-derived mutants, suppresses cell growth through p53-independent transactivation of p21. Here we show that a germline KLF6 single nucleotide polymorphism, confirmed in a tri-institutional study of 3,411 men, is significantly associated with an increased relative risk of prostate cancer in men, regardless of family history of disease. This prostate cancer-associated allele generates a novel functional SRp40 DNA binding site and increases transcription of three alternatively spliced KLF6 isoforms. The KLF6 variant proteins KLF6-SV1 and KLF6-SV2 are mislocalized to the cytoplasm, antagonize wtKLF6 function, leading to decreased p21 expression and increased cell growth, and are up-regulated in tumor versus normal prostatic tissue. Thus, these results are the first to identify a novel mechanism of self-encoded tumor suppressor gene inactivation and link a relatively common single nucleotide polymorphism to both regulation of alternative splicing and an increased risk in a major human cancer.


UBE2S drives elongation of K11-linked ubiquitin chains by the anaphase-promoting complex.
The Anaphase-Promoting Complex (APC) is an E3 ubiquitin ligase that regulates mitosis and G1 by sequentially targeting cell-cycle regulators for ubiquitination and proteasomal degradation. The mechanism of ubiquitin chain formation by APC and the resultant chain topology remains controversial. By using a single-lysine APC substrate to dissect the topology of ubiquitinated substrates, we find that APC-catalyzed ubiquitination has an intrinsic preference for the K11 linkage of ubiquitin that is essential for substrate degradation. K11 specificity is determined by an E2 enzyme, UBE2S/E2-EPF, that elongates ubiquitin chains after the substrates are pre-ubiquitinated by UbcH10 or UbcH5. UBE2S copurifies with APC; dominant-negative Ube2S slows down APC substrate degradation in functional cell-cycle extracts. We propose that Ube2S is a critical, unique component of the APC ubiquitination pathway.


Two-dimensional liquid chromatography of polystyrene-polyethylene oxide block copolymers.
In this study, liquid chromatography at critical conditions of polystyrene (PS) and polyethylene oxide (PEO) is used as the first dimension for the two-dimensional analysis of PS-b-PEO copolymers. Comprehensive two-dimensional liquid chromatography, with size exclusion chromatography as the second dimension, reveals information about the molar mass distributions of all separated fractions from the first dimension. Furthermore, fractions eluting at the critical conditions of one block were collected and subjected to analysis in the second dimension at the critical conditions of the other block. These fractions were analysed by FTIR to determine their chemical compositions. The combination of the above approaches and the calibration of the evaporative light scattering (ELS) detector for the first-dimensional analysis yield deep insights into the molecular heterogeneity of the block copolymer samples. The composition of the samples and the chemical composition of the real block copolymer are also calculated by combining results obtained at both critical conditions.


Systemic inflammatory response syndrome after transcatheter or surgical aortic valve replacement.
An inflammatory response after cardiac surgery is associated with worse clinical outcomes, but recent trials to attenuate it have been neutral. We evaluated the association between systemic inflammatory response syndrome (SIRS) and mortality after transcatheter (TAVR) and surgical aortic valve replacement (SAVR) for aortic stenosis (AS) and evaluated whether diabetes influenced this relationship. Patients (n=747) with severe AS treated with TAVR (n=264) or SAVR (n=483) between January 2008 and December 2013 were included and 37% had diabetes mellitus. SIRS was defined by four criteria 12-48 h after aortic valve replacement (AVR): (1) white blood cell count <4 or >12; (2) heart rate >90; (3) temperature <36 or >38°C; or (4) respiratory rate >20. Severe SIRS was defined as meeting all four criteria. The primary endpoint was 6-month all-cause mortality (60 deaths occurred by 6 months). Inverse probability weighting (IPW) was performed on 44 baseline and procedural variables to minimise confounding. Severe SIRS developed in 6% of TAVR patients and 11% of SAVR patients (p=0.02). Six-month mortality tended to be higher in those with severe SIRS (15.5%) versus those without (7.4%) (p=0.07). After adjustment, severe SIRS was associated with higher 6-month mortality (IPW adjusted HR 2.77, 95% CI 2.04 to 3.76, p<0.001). Moreover, severe SIRS was more strongly associated with increased mortality in diabetic (IPW adjusted HR 4.12, 95% CI 2.69 to 6.31, p<0.001) than non-diabetic patients (IPW adjusted HR 1.74, 95% CI 1.10 to 2.73, p=0.02) (interaction p=0.007). The adverse effect of severe SIRS on mortality was similar after TAVR and SAVR. Severe SIRS was associated with a higher mortality after SAVR or TAVR. It occurred more commonly after SAVR and had a greater effect on mortality in diabetic patients. These findings may have implications for treatment decisions in patients with AS, may help explain differences in outcomes between different AVR approaches and identify diabetic patients as a high-risk subgroup to target in clinical trials with therapies to attenuate SIRS.


Magnesium and Calcium Aluminate Liquids: In Situ High-Temperature 27Al NMR Spectroscopy.
The use of high-temperature nuclear magnetic resonance (NMR) spectroscopy provides a means of investigating the structure of refractory aluminate liquids at temperatures up to 2500 K. Time-averaged structural information indicates that the average aluminum coordination for magnesium aluminate (MgAl(2)O(4)) liquid is slightly greater than for calcium aluminate (CaAl(2)O(4)) liquid and that in both liquids it is close to four. Ion dynamics simulations for these liquids suggest the presence of four-, five-, and six-coordinated aluminate species, in agreement with NMR experiments on fast-quenched glasses. These species undergo rapid chemical exchange in the high-temperature liquids, which is evidenced by a single Lorentzian NMR line.


Providing young women with credible health information about bleeding disorders.
Approximately 1% of U.S. women may have an undiagnosed bleeding disorder, which can diminish quality of life and lead to life-threatening complications during menstruation, childbirth, and surgery. To understand young women's knowledge, attitudes, and perceptions about bleeding disorders and determine the preferred messaging strategy (e.g., gain- versus loss-framed messages) for presenting information. In September 2010, a web-assisted personal interview of women aged 18-25 years was conducted. Preliminary analyses were conducted in 2011 with final analyses in 2013. In total, 1,243 women participated. Knowledge of blood disorders was tabulated for these respondents. Menstrual experiences of women at risk for a bleeding disorder were compared with those not at risk using chi-square analyses. Perceived influence of gain- versus loss-framed messages also was compared. Participants knew that a bleeding disorder is a condition in which bleeding takes a long time to stop (77%) or blood does not clot (66%). Of the women, 57% incorrectly thought that a bleeding disorder is characterized by thin blood; many were unsure if bleeding disorders involve blood types, not getting a period, or mother and fetus having a different blood type. Women at risk for a bleeding disorder were significantly more likely to report that menstruation interfered with daily activities (36% vs 9%); physical or sports activities (46% vs 21%); social activities (29% vs 7%); and school or work activities (20% vs 9%) than women not at risk. Gain-framed messages were significantly more likely to influence women's decisions to seek medical care than parallel loss-framed messages. Findings suggest that the most influential messages focus on knowing effective treatment is available (86% gain-framed vs 77% loss-framed); preventing pregnancy complications (79% gain- vs 71% loss-framed); and maintaining typical daily activities during menstrual periods. Lack of information about bleeding disorders is a serious public health concern. Health communications focused on gain-framed statements might encourage symptomatic young women to seek diagnosis and treatment. These findings and corresponding recommendations align with Healthy People 2020 and with CDC's goal of working to promote the health, safety, and quality of life of women at every life stage.


Safety of pleurodesis with talc poudrage in malignant pleural effusion: a prospective cohort study.
Talc is the most effective chemical pleurodesis agent for patients with malignant pleural effusion. However, concerns have arisen about the safety of intrapleural application of talc, after reports of development of acute respiratory distress syndrome in 1-9% of treated patients. Our aim was to establish whether use of large-particle-size talc is safe in patients with malignant pleural effusion. We did a multicentre, open-label, prospective cohort study of 558 patients with malignant pleural effusion who underwent thoracoscopy and talc poudrage with 4 g of calibrated French large-particle talc in 13 European hospitals, and one in South Africa. The primary endpoint was the occurrence of acute respiratory distress syndrome after talc pleurodesis. No patients developed acute respiratory distress syndrome (frequency 0%, one-sided 95% CI 0-0.54%). 11 (2%) patients died within 30 days. Additionally, seven patients had non-fatal post-thoracoscopy complications (1.2%), including one case of respiratory failure due to unexplained bilateral pneumothorax. Use of large-particle talc for pleurodesis in malignant pleural effusion is safe, and not associated with the development of acute respiratory distress syndrome.


Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates.
POTE (prostate, ovary, testis, and placenta expressed) genes belong to a primate-specific gene family expressed in prostate, ovary, and testis as well as in several cancers including breast, prostate, and lung cancers. Due to their tumor-specific expression, POTEs are potential oncogenes, therapeutic targets, and biomarkers for these malignancies. This gene family maps within human and primate segmental duplications with a copy number ranging from two to 14 in different species. Due to the high sequence identity among the gene copies, specific efforts are needed to assemble these loci in order to correctly define the organization and evolution of the gene family. Using single-molecule, real-time (SMRT) sequencing, in silico analyses, and molecular cytogenetics, we characterized the structure, copy number, and chromosomal distribution of the POTE genes, as well as their expression in normal and disease tissues, and provided a comparative analysis of the POTE organization and gene structure in primate genomes. We were able, for the first time, to de novo sequence and assemble a POTE tandem duplication in marmoset that is misassembled and collapsed in the reference genome, thus revealing the presence of a second POTE copy. Taken together, our findings provide comprehensive insights into the evolutionary dynamics of the primate-specific POTE gene family, involving gene duplications, deletions, and long interspersed nuclear element (LINE) transpositions to explain the actual repertoire of these genes in human and primate genomes.


Localization of white matter volume increase in autism and developmental language disorder.
Increased brain volume in autism appears to be driven mainly by an unexplained white matter enlargement, and we have reported a similar phenomenon in developmental language disorder (DLD). Localization of this enlargement would strongly guide research into its cause, tissue basis, and functional implications. We utilized a white matter parcellation technique that divides cerebral white matter into an outer zone containing the radiate compartment and an inner zone containing sagittal and bridging system compartments. In both high-functioning autism and DLD, enlargement localized to the radiate white matter (all lobes in autism, all but parietal in DLD), whereas inner zone white matter compartments showed no volume differences from controls. Furthermore, in both autism and DLD, later or longer-myelinating regions showed greater volume increases over controls. Neither group showed cerebral cortex, corpus callosum, or internal capsule volume differences from control. Radiate white matter myelinates later than deep white matter; this pattern of enlargement thus is consistent with striking postnatal head circumference percentile increases reported in autism. These findings suggest an ongoing postnatal process in both autism and DLD that is probably intrinsic to white matter, that primarily affects intrahemispheric and corticocortical connections, and that places these two disorders on the same spectrum.


Promoting Patient Utilization of Outpatient Cardiac Rehabilitation: A JOINT INTERNATIONAL COUNCIL AND CANADIAN ASSOCIATION OF CARDIOVASCULAR PREVENTION AND REHABILITATION POSITION STATEMENT.
Cardiac rehabilitation (CR) is a recommendation in international clinical practice guidelines given its benefits; however, use is suboptimal. The purpose of this position statement was to translate evidence on interventions that increase CR enrollment and adherence into implementable recommendations. The writing panel was constituted by representatives of societies internationally concerned with preventive cardiology and included disciplines that would be implementing the recommendations. Patient partners served, as well as policy makers. The statement was developed in accordance with AGREE II, among other guideline checklists. Recommendations were based on our update of the Cochrane review on interventions to promote patients' utilization of CR. These were circulated to panel members, who were asked to rate each on a 7-point Likert scale in terms of scientific acceptability, actionability, and feasibility of assessment. A Web call was convened to achieve consensus and confirm strength of the recommendations (based on Grading of Recommendations Assessment, Development, and Evaluation [GRADE]). The draft underwent external review and public comment. The 3 drafted recommendations were that to increase enrollment, health care providers, particularly nurses (strong), should promote CR to patients face-to-face (strong), and that to increase adherence, part of CR could be delivered remotely (weak). Ratings (mean ± SD) for the 3 recommendations were 5.95 ± 0.69, 5.33 ± 1.12, and 5.64 ± 1.08, respectively. Interventions can significantly increase utilization of CR and hence should be widely applied. We call upon cardiac care institutions to implement these strategies to augment CR utilization and to ensure that CR programs are adequately resourced to serve enrolling patients and support them to complete programs.


Tumor Response and Symptom Palliation from RAINBOW, a Phase III Trial of Ramucirumab Plus Paclitaxel in Previously Treated Advanced Gastric Cancer.
In the intent-to-treat (ITT) population of the RAINBOW study, objective response rate (ORR) was 28% and 16% in the ramucirumab and control arms, respectively. To further characterize tumor response, we present details on timing and extent of tumor shrinkage, as well as associations with symptom palliation. Tumor response was assessed with RECIST v1.1, and quality of life (QoL) was assessed with the European Organization for Research and Treatment of Cancer Quality-of-Life Questionnaire-Core 30 (EORTC QLQ-C30) v3.0. Prespecified and post hoc analyses were conducted in the ITT population, patients with measurable disease, or responders, and included best overall response (BOR), ORR, disease control rate (DCR), duration of response, time to response (TtR), change in tumor size, and associations of QoL with tumor shrinkage and BOR. In both treatment arms, median TtR was 1.5 months. Responses were more durable in the ramucirumab versus control arm (median 4.4 vs. 2.8 months). In patients with measurable disease (78% of ITT), ORR was 36% versus 20%; DCR was 81% versus 61% in the ramucirumab versus control arms. Waterfall plots demonstrated more tumor shrinkage in the ramucirumab versus control arm. Regardless of treatment, tumor response and stable disease were associated with improved or stable QoL, with more tumor shrinkage associated with greater symptom palliation. Treatment with ramucirumab plus paclitaxel yielded the highest ORR reported to date for patients with previously treated advanced gastric or gastroesophageal junction adenocarcinoma. Additional details demonstrate robustness of tumor response results. The extent of tumor shrinkage is directly associated with symptom palliation and should be considered when evaluating patient needs and treatment selection. Clinical trial identification number. NCT01170663. Ramucirumab plus paclitaxel is a recognized standard of care as it improves survival for patients with advanced gastric or gastroesophageal junction adenocarcinoma who have been previously treated with recommended first-line therapy. These additional data on tumor response demonstrate a positive association between tumor shrinkage and symptom palliation in a patient population that is often symptomatic. These observations included patients with nonmeasurable disease, a group of patients often underrepresented in clinical trials. This knowledge can inform treatment decisions, which align individual patient characteristics and needs with demonstrated benefits.


Extracapsular cataract surgery compared with manual small incision cataract surgery in community eye care setting in western India: a randomised controlled trial.
To study "manual small incision cataract surgery (MSICS)" for the rehabilitation of cataract visually impaired and blind patients in community based, high volume, eye hospital setting; to compare the safety and effectiveness of MSICS with conventional extracapsular cataract surgery (ECCE). In a single masked randomised controlled clinical trial, 741 patients, aged 40-90 years, with operable cataract were randomly assigned to receive either MSICS or ECCE and operated upon by one of eight participating surgeons. Intraoperative and postoperative complications were graded and scored according to the Oxford Cataract Treatment and Evaluation Team recommendations. The patients were followed up at 1 week, 6 weeks, and 1 year after surgery and their visual acuity recorded. This paper reports outcomes at 1 and 6 weeks. 706 of the 741(95.3%) patients completed the 6 week follow up. 135 of 362 (37.3%) of ECCE group and 165 of 344 (47.9%) of MSICS group had uncorrected visual acuity of 6/18 or better after 6 weeks of follow up. 314 of 362 (86.7%) of ECCE group and 309 of 344 (89.8%) of MSICS group had corrected postoperative vision of 6/18 or better. Four of 362 (1.1%) of ECCE group and six of 344 (1.7%) of MSICS group had corrected postoperative visual acuity less than 6/60. There were no significant differences between the two groups for intraoperative and severe postoperative complications. MSICS and ECCE are both safe and effective techniques for treatment of cataract patients in community eye care settings. MSICS needs similar equipment to ECCE, but gives better uncorrected vision.


Regulation of the micromechanical properties of pulmonary endothelium by S1P and thrombin: role of cortactin.
Disruption of pulmonary endothelial cell (EC) barrier function is a critical pathophysiologic event in highly morbid inflammatory conditions such as sepsis and acute respiratory disease stress syndrome. Actin cytoskeleton, an essential regulator of endothelial permeability, is a dynamic structure whose stimuli-induced rearrangement is linked to barrier modulation. Here, we used atomic force microscopy to characterize structural and mechanical changes in the F-actin cytoskeleton of cultured human pulmonary artery EC in response to both barrier-enhancing (induced by sphingosine 1-phosphate (S1P)) and barrier-disrupting (induced by thrombin) conditions. Atomic force microscopy elasticity measurements show differential effects: for the barrier protecting molecule S1P, the elastic modulus was elevated significantly on the periphery; for the barrier-disrupting molecule thrombin, on the other hand, it was elevated significantly in the central region of the cell. The force and elasticity maps correlate with F-actin rearrangements as identified by immunofluorescence analysis. Significantly, reduced expression (via siRNA) of cortactin, an actin-binding protein essential to EC barrier regulation, resulted in a shift in the S1P-mediated elasticity pattern to more closely resemble control, unstimulated endothelium.


Clinical reactivity to ingestion challenge with mixed mold extract may be enhanced in subjects sensitized to molds.
Manifestations of mold allergy are classically associated with inhalation of mold spores leading to symptoms of asthma and other respiratory illnesses. It is largely unknown, however, whether ingestion of aeroallergenic molds, mold spores, or other fungi found in food can also elicit hypersensitivity reactions in mold-sensitive individuals. The aim of this study was to evaluate the association between exposure to molds by oral challenge and elicitation of symptoms in mold- versus nonmold-sensitive individuals. Thirty-four adult atopic subjects were randomized into mold-sensitive groups based on skin test reactivity by skin percutaneous testing (SPT) and/or intradermal (ID) testing to a mixed mold (MM) extract preparation. All subjects underwent a single-blinded, placebo-controlled food challenge to the MM preparation. A modified scoring system was used to grade the clinical severity of symptoms elicited by challenge. All subjects tolerated challenges to the maximal oral mold dose concentration. However, higher symptom scores after challenge were found in mold-sensitive subjects compared with nonmold-sensitive subjects (p = 0.01). When mold-sensitive subjects were compared based on SPT and/or ID reactivity, higher symptom scores and lower symptom-eliciting concentrations of mold were associated with the SPT reactive subgroup compared with the subgroup with ID reactivity alone. In summary, based on our challenge results and scoring model, mold-sensitive subjects compared with nonmold-sensitive subjects experienced cumulatively higher symptom scores after oral challenge to an MM extract preparation. Future studies are warranted to confirm whether ingestion of aeroallergenic molds in food may be another contributor to symptoms in mold-sensitive individuals.


On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin.
Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(α) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.


Profile of bacteria and fungi on money coins.
To determine the quantity and quality of bacterial and fungi on money coins and to identify those that could pose a public health risk. Random sampling of coins from subjects within predetermined categories. Westlands division of Nairobi Metropolitan province. Twenty-shilling coin samples were collected from matatu (a common commuter vehicle in Kenya) taxi conductors, greengrocers, shoe shiners, butchers, food kiosk/restaurant attendants, grocery shops attendants, roast maize vendors and school children. Forty coin samples were analysed for both the total viable content and the types of bacterial and fungal organisms. Average bacterial content on the coins ranged from 2.3 x 10(3) to 25.5 x 10(3) and fungi content from 11 to 377 colony forming units. The following potentially pathogenic bacteria were among those isolated: Escherichia coli, Klebsiella, Serratia, Enterobacter, Salmonella, Acinetobacter, Enterococci, Staphylococcus and Bacillus cereus. In addition, this is the first report of potentially pathogenic fungal isolation from money coins. Penicillium spp, Aspergillus niger, Fusarium, Rhizopus, Altenaria spp, Candida spp and Cryptococcus were isolated. Money coins harbour potentially pathogenic bacteria and fungi that may pose a public health risk. Hand hygiene is therefore strongly recommended, especially for those who simultaneously handle food and money.


α-Rank: Multi-Agent Evaluation by Evolution.
We introduce α-Rank, a principled evolutionary dynamics methodology, for the evaluation and ranking of agents in large-scale multi-agent interactions, grounded in a novel dynamical game-theoretic solution concept called Markov-Conley chains (MCCs). The approach leverages continuous-time and discrete-time evolutionary dynamical systems applied to empirical games, and scales tractably in the number of agents, in the type of interactions (beyond dyadic), and the type of empirical games (symmetric and asymmetric). Current models are fundamentally limited in one or more of these dimensions, and are not guaranteed to converge to the desired game-theoretic solution concept (typically the Nash equilibrium). α-Rank automatically provides a ranking over the set of agents under evaluation and provides insights into their strengths, weaknesses, and long-term dynamics in terms of basins of attraction and sink components. This is a direct consequence of the correspondence we establish to the dynamical MCC solution concept when the underlying evolutionary model's ranking-intensity parameter, α, is chosen to be large, which exactly forms the basis of α-Rank. In contrast to the Nash equilibrium, which is a static solution concept based solely on fixed points, MCCs are a dynamical solution concept based on the Markov chain formalism, Conley's Fundamental Theorem of Dynamical Systems, and the core ingredients of dynamical systems: fixed points, recurrent sets, periodic orbits, and limit cycles. Our α-Rank method runs in polynomial time with respect to the total number of pure strategy profiles, whereas computing a Nash equilibrium for a general-sum game is known to be intractable. We introduce mathematical proofs that not only provide an overarching and unifying perspective of existing continuous- and discrete-time evolutionary evaluation models, but also reveal the formal underpinnings of the α-Rank methodology. We illustrate the method in canonical games and empirically validate it in several domains, including AlphaGo, AlphaZero, MuJoCo Soccer, and Poker.


Cultural and linguistic diversity of people living with chronic hepatitis B in 2011-2016: changing migration, shifting epidemiology.
To estimate the cultural and linguistic diversity in Australians currently living with chronic hepatitis B (CHB), the majority of whom were born overseas, and to identify trends in this diversity over time. Estimates were generated by combining Australian census country of birth information with seroprevalence data generated from antenatal serology linked with surveillance notifications. The number of people living with CHB was assessed according to country of birth using the 2011 and 2016 censuses. The total number of Australian residents living with CHB increased by 20% between 2011 and 2016, substantially outpacing population growth. The most common country of birth continued to be China, with the number of Chinese-born Australians living with CHB increasing by 60% in the 5-year period. Decreased numbers were observed for people born in European countries. The epidemiology of chronic hepatitis B in Australia has shifted over time due to changing migration patterns, with increases in many countries in the Asia-Pacific, African and Middle Eastern regions. Implications for public health: Interventions to improve the health of people living with CHB are imperative, and these up-to-date estimates identify priority groups and communities, which are constantly changing.


Intussusception risk after rotavirus vaccination in U.S. infants.
International postlicensure studies have identified an increased risk of intussusception after vaccination with the second-generation rotavirus vaccines RotaTeq (RV5, a pentavalent vaccine) and Rotarix (RV1, a monovalent vaccine). We studied this association among infants in the United States. The study included data from infants 5.0 to 36.9 weeks of age who were enrolled in three U.S. health plans that participate in the Mini-Sentinel program sponsored by the Food and Drug Administration. Potential cases of intussusception and vaccine exposures from 2004 through mid-2011 were identified through procedural and diagnostic codes. Medical records were reviewed to confirm the occurrence of intussusception and the status with respect to rotavirus vaccination. The primary analysis used a self-controlled risk-interval design that included only vaccinated children. The secondary analysis used a cohort design that included exposed and unexposed person-time. The analyses included 507,874 first doses and 1,277,556 total doses of RV5 and 53,638 first doses and 103,098 total doses of RV1. The statistical power for the analysis of RV1 was lower than that for the analysis of RV5. The number of excess cases of intussusception per 100,000 recipients of the first dose of RV5 was significantly elevated, both in the primary analysis (attributable risk, 1.1 [95% confidence interval, 0.3 to 2.7] for the 7-day risk window and 1.5 [95% CI, 0.2 to 3.2] for the 21-day risk window) and in the secondary analysis (attributable risk, 1.2 [95% CI, 0.2 to 3.2] for the 21-day risk window). No significant increase in risk was seen after dose 2 or 3. The results with respect to the primary analysis of RV1 were not significant, but the secondary analysis showed a significant risk after dose 2. RV5 was associated with approximately 1.5 (95% CI, 0.2 to 3.2) excess cases of intussusception per 100,000 recipients of the first dose. The secondary analysis of RV1 suggested a potential risk, although the study of RV1 was underpowered. These risks must be considered in light of the demonstrated benefits of rotavirus vaccination. (Funded by the Food and Drug Administration.).


Management of anal squamous intraepithelial lesions.
Anal squamous intraepithelial lesions include both low-grade squamous intraepithelial lesions (LSIL) and high-grade squamous intraepithelial lesions (HSIL) and are caused by chronic infection with the human papillomavirus (HPV). The disease is increasing in both incidence and prevalence, especially among patients with the following risk factors: homosexual men, acquired or iatrogenic immunosuppression, and presence of other HPV-related diseases. Although the natural history of the disease is unknown, there is significant evidence that untreated HSIL progresses to squamous cell carcinoma in 11% of patients and in up to 50% of patients with extensive disease and immunosuppression. Anal cytology and reflex HPV DNA testing are used to screen for disease, particularly among patients with the aforementioned risk factors. Evaluation of the patient should include physical examination and high-resolution anoscopy (HRA) to evaluate for disease above and below the dentate line. Intervention is warranted and this can be achieved in many ways. The treatment option associated with the best outcomes is ablation directed with HRA, which can be performed in the office or in the operating room with minimal morbidity. This strategy is effective in patients with both low-volume and high-volume disease and is associated with a malignant progression rate of 0.4% in patients with treated HSIL.


Altered gene expression in human placentas after IVF/ICSI.
Is gene expression in placental tissue of IVF/ICSI patients altered when compared with a spontaneously conceived group, and are these alterations due to loss of imprinting (LOI) in the case of imprinted genes? An altered imprinted gene expression of H19 and Pleckstrin homology-like domain family A member 2 (PHLDA2), which was not due to LOI, was observed in human placentas after IVF/ICSI and several biological pathways were significantly overrepresented and mostly up-regulated. Genomic imprinting plays an important role in placental biology and in placental adaptive responses triggered by external stimuli. Changes in placental development and function can have dramatic effects on the fetus and its ability to cope with the intrauterine environment. An increased frequency of placenta-related problems as well as an adverse perinatal outcome is seen in IVF/ICSI derived pregnancies, but the role of placental epigenetic deregulation is not clear yet. In this prospective cohort study, a total of 115 IVF/ICSI and 138 control couples were included during pregnancy. After applying several exclusion criteria (i.e. preterm birth or stillbirth, no placental samples, pregnancy complications or birth defects), respectively, 81 and 105 placentas from IVF/ICSI and control pregnancies remained for analysis. Saliva samples were collected from both parents. We quantitatively analysed the mRNA expression of several growth-related imprinted genes [H19, insulin-like growth factor 2 (IGF2), PHLDA2, cyclin-dependent kinase inhibitor 1C (CDKN1C), mesoderm-specific transcript homolog (MEST) isoform α and β by quantitative PCR] after standardization against three housekeeping genes [Succinate dehydrogenase A (SDHA), YWHAZ and TATA-binding protein (TBP)]. A quantitative allele-specific expression analysis of the differentially expressed imprinted genes was performed to investigate LOI, independent of the mechanism of imprinting. Furthermore, a microarray analysis was carried out (n = 10 in each group) to investigate the expression of non-imprinted genes as well. Both H19 and PHLDA2 showed a significant change, respectively, a 1.3-fold (P = 0.033) and 1.5-fold (P = 0.002) increase in mRNA expression in the IVF/ICSI versus control group. However, we found no indication that there is an increased frequency of LOI in IVF/ICSI placental samples. Genome-wide mRNA expression revealed 13 significantly overrepresented biological pathways involved in metabolism, immune response, transmembrane signalling and cell cycle control, which were mostly up-regulated in the IVF/ICSI placental samples. Only a subset of samples was found to be fully informative, which unavoidably led to lower sample numbers for our LOI analysis. Our study cannot distinguish whether the reported differences in the IVF/ICSI group are exclusively attributable to the IVF/ICSI technique itself or to the underlying subfertility of the patients. Whether these placental adaptations observed in pregnancies conceived by IVF/ICSI might be connected to an adverse perinatal outcome after IVF remains unknown. However, it is possible that these differences affect fetal development and long-term patterns of gene expression, as well as maternal gestational physiology. Partly funded by an unrestricted research grant by Organon BV (now MSD BV) and GROW School for Oncology and Developmental Biology without any role in study design, data collection and analysis or preparation of the manuscript. No conflict of interests to declare. Dutch Trial Registry (NTR) number 1298.


[Dietary fiber in the dietetic therapy of diabetes mellitus. Experimental data with purified glucomannans].
In the last years the use of alimentary fibres in dietetic management of diabetic patients increased. The aim of this work was to evaluate, in type 2 diabetic subjects, the glycaemic and insulinemic increments after a standard breakfast with glucomannanos enriched biscuits and with common slices of toast containing the same amounts of carbohydrates and calories. The basal serum values of glucose and C-peptide were similar in the two days of the test. The mean increments of glucose and C-peptide were significantly higher (p < 0.001) after slices of toast than after glucomannanos enriched biscuits. In conclusion our results show a reduction in glycaemic increments after breakfast with glucomannanos-biscuits. The decreased insulin secretion and the reduction of insulin need can longer preserve the functional reserve of beta-cells.


Carbon X-ray absorption spectra of fluoroethenes and acetone: a study at the coupled cluster, density functional, and static-exchange levels of theory.
Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π∗-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π∗-peak separations due to spectral compressions, a characteristic which is inherent to this method.


Parallels between experimental and natural evolution of legume symbionts.
The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. Here we compare the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time span, environment, genetic background, and phenotypic achievement, both processes resulted in rapid genetic diversification dominated by purifying selection. We observe no adaptation in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation was associated with positive selection in a set of genes that led to the co-option of the same quorum-sensing system in both processes. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis.


Elevated TRIB2 with NOTCH1 activation in paediatric/adult T-ALL.
TRIB2 is a potent oncogene, elevated in a subset of human acute myeloid leukaemias (AML) with a mixed myeloid/lymphoid phenotype and NOTCH1 mutations. Although rare in AML, activating NOTCH1 mutations occur in 50% of all T cell acute lymphoblastic leukaemias (T-ALL). TRIB2 is a NOTCH1 target gene that functions in the degradation of key proteins and modulation of MAPK signalling pathways, implicated in haematopoietic cell survival and proliferation. This study showed that TRIB2 expression level is highest in the lymphoid compartment of normal haematopoietic cells, specifically in T cells. Analysis of TRIB2 expression across 16 different subtypes of human leukaemia demonstrated that TRIB2 expression was higher in ALL phenotypes versus all other phenotypes including AML, chronic lymphocytic leukaemia (CLL), myelodysplastic syndrome (MDS) and chronic myeloid leukaemia (CML). A T cell profile was distinguished by high TRIB2 expression in normal and malignant haematopoiesis. High TRIB2 expression was seen in T-ALL with normal karyotype and correlated with NOTCH signalling pathways. High TRIB2 expression correlated with NOTCH1/FBXW7 mutations in a paediatric T-ALL cohort, strongly linking NOTCH1 activation and high TRIB2 expression in paediatric T-ALL. The relationship between TRIB2 and T cell signalling pathways uniquely identifies leukaemia subtypes and will be useful in the advancement of our understanding of T cell and ALL biology.


Safeguarding Our Genetic Resources with Libraries of Doubled-Haploid Lines.
Thousands of landraces are stored in seed banks as "gold reserves" for future use in plant breeding. In many crops, their utilization is hampered because they represent heterogeneous populations of heterozygous genotypes, which harbor a high genetic load. We show, with high-density genotyping in five landraces of maize, that libraries of doubled-haploid (DH) lines capture the allelic diversity of genetic resources in an unbiased way. By comparing allelic differentiation between heterozygous plants from the original landraces and 266 derived DH lines, we find conclusive evidence that, in the DH production process, sampling of alleles is random across the entire allele frequency spectrum, and purging of landraces from their genetic load does not act on specific genomic regions. Based on overall process efficiency, we show that generating DH lines is feasible for genetic material that has never been selected for inbreeding tolerance. We conclude that libraries of DH lines will make genetic resources accessible to crop improvement by linking molecular inventories of seed banks with meaningful phenotypes.


Curvature Corrections Remove the Inconsistencies of Binary Classical Nucleation Theory.
The study of nucleation in fluid mixtures exposes challenges beyond those of pure systems. A striking example is homogeneous condensation in highly surface-active water-alcohol mixtures, where classical nucleation theory yields an unphysical, negative number of water molecules in the critical embryo. This flaw has rendered multicomponent nucleation theory useless for many industrial and scientific applications. Here, we show that this inconsistency is removed by properly incorporating the curvature dependence of the surface tension of the mixture into classical nucleation theory for multicomponent systems. The Gibbs adsorption equation is used to explain the origin of the inconsistency by linking the molecules adsorbed at the interface to the curvature corrections of the surface tension. The Tolman length and rigidity constant are determined for several water-alcohol mixtures and used to show that the corrected theory is free of physical inconsistencies and provides accurate predictions of the nucleation rates. In particular, for the ethanol-water and propanol-water mixtures, the average error in the predicted nucleation rates is reduced from 11-15 orders of magnitude to below 1.5. The curvature-corrected nucleation theory opens the door to reliable predictions of nucleation rates in multicomponent systems, which are crucial for applications ranging from atmospheric science to research on volcanos.


False biomarker discovery due to reactivity of a commercial ELISA for CUZD1 with cancer antigen CA125.
By using proteomics and bioinformatics, we have previously identified a group of highly pancreas-specific proteins as candidate pancreatic ductal adenocarcinoma (PDAC) biomarkers. With the use of commercially available ELISAs, the performance of some of these candidates was initially evaluated in a relatively small serum cohort (n = 100 samples). This phase revealed that CUB and zona pellucida-like domains protein 1 (CUZD1) may represent a new, promising PDAC biomarker. We performed detailed experiments to investigate the specificity of the commercial CUZD1 ELISA assay. CUZD1 was expressed in house in both bacteria and yeast expression systems. Recombinant CUZD1 and biological samples containing CUZD1, as well as commercial CUZD1 ELISA standards, were analyzed by Western blot, size exclusion HPLC, and mass spectrometry (LC-MS Orbitrap). We confirmed that instead of CUZD1, the commercial assay is recognizing a nonhomologous, known cancer antigen [cancer antigen 125 (CA125)]. We conclude that poor characterization of commercial ELISA assays is a factor that could lead to false biomarker discovery. To our knowledge, this is the first report documenting that a commercial ELISA marketed for one analyte (CUZD1) may, in fact, recognize a different, nonhomologous antigen (CA125).


Transient neurologic symptoms after spinal anesthesia with lidocaine in obstetric patients.
We investigated the relationship between intrathecal lidocaine and transient neurologic symptoms in the obstetric population because lidocaine spinal anesthetics are commonly used for various obstetric procedures, and little has been reported in this regard from within this population. In this study, 58 ASA physical status I patients presenting for postpartum bilateral tubal ligation under spinal anesthesia were randomized to receive either hyperbaric 5% lidocaine or 0.75% bupivacaine in a double-blinded manner. All patients were in the supine position for their surgery. Postoperatively, all patients were followed by a blinded investigator using a standardized symptom checklist. The incidence of transient neurologic symptoms with lidocaine was 3% (95% confidence interval = 0.1%--17.8%) and that with bupivacaine was 7% (95% confidence interval = 0.9%--23.5%), (P = not significant). Symptoms consistent with this syndrome occurred within 24 h without any associated sensory or motor deficits or functional impairment, and resolved within 48 h without any intervention.


Comparison of two different S-1 plus cisplatin dosing schedules as first-line chemotherapy for metastatic and/or recurrent gastric cancer: a multicenter, randomized phase III trial (SOS).
Five-weekly S-1 plus cisplatin (SP5) is one of the standard first-line regimens for advanced gastric cancer (GC), proven in a Japanese phase III study. To enhance the dose intensity of cisplatin, 3-weekly S-1 plus cisplatin (SP3) was developed. This multicenter, randomized, open-label, phase III study evaluated whether SP3 (S-1 80 mg/m(2)/day on days 1-14 and cisplatin 60 mg/m(2) on day 1) was noninferior/superior to SP5 (S-1 80-120 mg/day on days 1-21 and cisplatin 60 mg/m(2) on day 1 or 8) in terms of progression-free survival (PFS). Chemotherapy-naive patients with metastatic, recurrent gastric or gastroesophageal junction adenocarcinoma were randomized 1 : 1 to receive either SP3 or SP5. The trial is registered at ClinicalTrials.gov (NCT00915382). Between February 2009 and January 2012, 625 patients were randomized at 42 sites in Korea and Japan. With a median follow-up duration of 32.4 months (range, 13.3-48.6 months) in surviving patients, SP3 was not only noninferior but also superior to SP5 in terms of PFS [median 5.5 versus 4.9 months; hazard ratio (HR) = 0.82; 95% confidence interval (CI) 0.68-0.99; P = 0.0418 for superiority). There was no difference in overall survival (OS) between the groups (median 14.1 versus 13.9 months; HR = 0.99; 95% CI 0.81-1.21; P = 0.9068). In patients with measurable disease, the response rates were 60% in the SP3 arm and 50% in the SP5 arm (P = 0.065). Both regimens were generally well tolerated, but grade 3 or higher anemia (19% versus 9%) and neutropenia (39% versus 9%) were more frequent in SP3. SP3 is superior to SP5 in terms of PFS. However, since the improvement in PFS was only slight and there was no difference in OS, both SP3 and SP5 can be recommended as first-line treatments for patients with advanced GC.


Variation for N Uptake System in Maize: Genotypic Response to N Supply.
An understanding of the adaptations made by plants in their nitrogen (N) uptake systems in response to reduced N supply is important to the development of cereals with enhanced N uptake efficiency (NUpE). Twenty seven diverse genotypes of maize (Zea mays, L.) were grown in hydroponics for 3 weeks with limiting or adequate N supply. Genotypic response to N was assessed on the basis of biomass characteristics and the activities of the nitrate ([Formula: see text]) and ammonium ([Formula: see text]) high-affinity transport systems. Genotypes differed greatly for the ability to maintain biomass with reduced N. Although, the N response in underlying biomass and N transport related characteristics was less than that for biomass, there were clear relationships, most importantly, lines that maintained biomass at reduced N maintained net N uptake with no change in size of the root relative to the shoot. The root uptake capacity for both [Formula: see text] and [Formula: see text] increased with reduced N. Transcript levels of putative [Formula: see text] and [Formula: see text] transporter genes in the root tissue of a subset of the genotypes revealed that predominately ZmNRT2 transcript levels responded to N treatments. The correlation between the ratio of transcripts of ZmNRT2.2 between the two N levels and a genotype's ability to maintain biomass with reduced N suggests a role for these transporters in enhancing NUpE. The observed variation in the ability to capture N at low N provides scope for both improving NUpE in maize and also to better understand the N uptake system in cereals.


Organ donation: what can we learn from North America?
The aim of this qualitative case study was to investigate how organ donation is promoted and managed in North America aimed specifically at patients and relatives. A 4-week study to Boston and Baltimore in America was undertaken to observe and learn how organ donation is promoted and managed within a critical care environment. The study tour was undertaken specifically to examine the policy and procedures that enhance the procurement of organ donation in specific centres in the USA. The study tour wanted to examine and gain a better understanding of the issues, policies and procedures used by these centres when seeking permission for organ donation. Data were collected by a variety of methods involving observation, unstructured informal interviews, examinations of policies and procedures and a daily diary was maintained. A thematic analysis method was used to analyse the qualitative data collected. Four areas were identified as potential areas for learning. Approaching relatives of potential donors for consent, at a time of intense emotional crisis, is a challenge that involves all nurses working in critical areas. Nurses are identified as a key component in the process of organ donation; research highlights that approaching relatives can be problematic and stressful for nursing staff. The British government should consider required request legislation that ensures all hospitals refer potential donors to the Regional Transplant Center. In-house coordinators could be appointed and protocols developed for referrals of potential donors. It is also suggested that the approach for consent is decoupled and designated requesters approach relatives.


GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.
Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally-determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-à-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods.


Structural and biochemical characterization of the Cop9 signalosome CSN5/CSN6 heterodimer.
The Cop9 signalosome complex (CSN) regulates the functional cycle of the major E3 ubiquitin ligase family, the cullin RING E3 ubiquitin ligases (CRLs). Activated CRLs are covalently modified by the ubiquitin-like protein Nedd8 (neural precursor cell expressed developmentally down-regulated protein 8). CSN serves an essential role in myriad cellular processes by reversing this modification through the isopeptidase activity of its CSN5 subunit. CSN5 alone is inactive due to an auto-inhibited conformation of its catalytic domain. Here we report the molecular basis of CSN5 catalytic domain activation and unravel a molecular hierarchy in CSN deneddylation activity. The association of CSN5 and CSN6 MPN (for Mpr1/Pad1 N-terminal) domains activates its isopeptidase activity. The CSN5/CSN6 module, however, is inefficient in CRL deneddylation, indicating a requirement of further elements in this reaction such as other CSN subunits. A hybrid molecular model of CSN5/CSN6 provides a structural framework to explain these functional observations. Docking this model into a published CSN electron density map and using distance constraints obtained from cross-linking coupled to mass-spectrometry, we find that the C-termini of the CSN subunits could form a helical bundle in the centre of the structure. They likely play a key scaffolding role in the spatial organization of CSN and precise positioning of the dimeric MPN catalytic core.


Transfer of functional thermoresponsive poly(glycidyl ether) coatings for cell sheet fabrication from gold to glass surfaces.
Thermoresponsive polymer coatings can facilitate cell sheet fabrication under mild conditions by promoting cell adhesion and proliferation at 37 °C. At lower temperatures the detachment of confluent cell sheets is triggered without enzymatic treatment. Thus, confluent cell sheets with intact extracellular matrix for regenerative medicine or tissue engineering applications become available. Herein, we applied the previously identified structural design parameters of functional, thermoresponsive poly(glycidyl ether) brushes on gold to the more application-relevant substrate glass via the self-assembly of a corresponding block copolymer (PGE-AA) with a short surface-reactive, amine-presenting anchor block. Both, physical and covalent immobilization on glass via either multivalent ionic interactions of the anchor block with bare glass or the coupling of the anchor block to a polydopamine (PDA) adhesion layer on glass resulted in stable coatings. Atomic force microscopy revealed a high degree of roughness of covalently attached coatings on the PDA adhesion layer, while physically attached coatings on bare glass were smooth and in the brush-like regime. Cell sheets of primary human dermal fibroblasts detached reliably (86%) and within 20 ± 10 min from physically tethered PGE-AA coatings on glass when prepared under cloud point grafting conditions. The presence of the laterally inhomogeneous PDA adhesion layer, however, hindered the spontaneous temperature-triggered cell detachment from covalently grafted PGE-AA, decreasing both detachment rate and reliability. Despite being only physically attached, self-assembled monolayer brushes of PGE-AA block copolymers on glass are functional and stable thermoresponsive coatings for application in cell sheet fabrication of human fibroblasts as determined by X-ray photoelectron spectroscopy.


Gestational route to healthy birth (GaRBH): protocol for an Indian prospective cohort study.
Pregnancy is characterised by a high rate of metabolic shifts from early to late phases of gestation in order to meet the raised physiological and metabolic needs. This change in levels of metabolites is influenced by gestational weight gain (GWG), which is an important characteristic of healthy pregnancy. Inadequate/excessive GWG has short-term and long-term implications on maternal and child health. Exploration of gestational metabolism is required for understanding the quantitative changes in metabolite levels during the course of pregnancy. Therefore, our aim is to study trimester-specific variation in levels of metabolites in relation to GWG and its influence on fetal growth and newborn anthropometric traits at birth. A prospective longitudinal study is planned (start date: February 2018; end date: March 2023) on pregnant women that are being recruited in the first trimester and followed in subsequent trimesters and at the time of delivery (total 3 follow-ups). The study is being conducted in a hospital located in Bikaner district (66% rural population), Rajasthan, India. The estimated sample size is of 1000 mother-offspring pairs. Information on gynaecological and obstetric history, socioeconomic position, diet, physical activity, tobacco and alcohol consumption, depression, anthropometric measurements and blood samples is being collected for metabolic assays in each trimester using standardised methods. Mixed effects regression models will be used to assess the role of gestational weight in influencing metabolite levels in each trimester. The association of maternal levels of metabolites with fetal growth, offspring's weight and body composition at birth will be investigated using regression modelling. The study has been approved by the ethics committees of the Department of Anthropology, University of Delhi and Sardar Patel Medical College, Rajasthan. We are taking written informed consent after discussing the various aspects of the study with the participants in the local language.


Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.


Comparability of Mayo-Portland Adaptability Inventory ratings by staff, significant others and people with acquired brain injury.
To determine the internal consistency, reliability and comparability of the Mayo-Portland Adaptability Inventory (MPAI-4) and sub-scales completed by people with acquired brain injury (ABI), family and significant others (SO) and rehabilitation staff. 134 people with ABI consecutively seen for outpatient rehabilitation evaluation. MPAI-4 protocols based on independent ratings by the people with ABI undergoing evaluation, SO and rehabilitation staff were submitted to Rasch Facets analysis to determine the internal consistency of the overall measure and sub-scales (Ability, Adjustment and Participation indices) for each rater group and for a composite measure based on all rater groups. Rater agreement for individual items was also examined. Rasch indicators of internal consistency were entirely within acceptable limits for 3-rater composite full scale and sub-scale measures; these indicators were generally within acceptable limits for measures based on a single rater group. Item agreement was generally acceptable; disagreements suggested various sources of bias for specific rater groups. The MPAI-4 possesses satisfactory internal consistency regardless of rating source. A composite measure based on ratings made independently by people with ABI, SO and staff may serve as a 'gold standard' for research purposes. In the clinical setting, assessment of varying perspectives and biases may not only best represent outcome as evaluated by all parties involved but be essential to developing effective rehabilitation plans.


Peptide surfactants for cell-free production of functional G protein-coupled receptors.
Two major bottlenecks in elucidating the structure and function of membrane proteins are the difficulty of producing large quantities of functional receptors, and stabilizing them for a sufficient period of time. Selecting the right surfactant is thus crucial. Here we report using peptide surfactants in commercial Escherichia coli cell-free systems to rapidly produce milligram quantities of soluble G protein-coupled receptors (GPCRs). These include the human formyl peptide receptor, human trace amine-associated receptor, and two olfactory receptors. The GPCRs expressed in the presence of the peptide surfactants were soluble and had α-helical secondary structures, suggesting that they were properly folded. Microscale thermophoresis measurements showed that one olfactory receptor expressed using peptide surfactants bound its known ligand heptanal (molecular weight 114.18). These short and simple peptide surfactants may be able to facilitate the rapid production of GPCRs, or even other membrane proteins, for structure and function studies.


Effects of 900 MHz GSM wireless communication signals on DMBA-induced mammary tumors in rats.
The purpose of the study was to investigate whether exposure to 900 MHz GSM wireless communication signals enhances mammary tumor development and growth induced by low-dose DMBA. Five hundred female Sprague-Dawley rats were treated with a single dose of 35 mg/kg DMBA and then divided into five groups in a blinded fashion: one cage control group and four exposure groups, including three microwave exposure groups and one sham exposure with specific absorption rates (SARs) of 4.0, 1.33, 0.44 and 0 W/kg, respectively. Exposure started on the day after DMBA administration and lasted 4 h/day, 5 days/week for 26 weeks. Rats were weighed and palpated weekly for the presence of tumors and were killed humanely at the end of the 26-week exposure period. All mammary glands were examined histologically. There were no statistically significant differences in body weight between sham- and GSM microwave-exposed groups. No significant differences in overall mammary tumor incidence, latency to tumor onset, tumor multiplicity, or tumor size were observed between microwave- and sham-exposed groups. There was a tendency for reduction of mammary adenocarcinoma incidence in the lowest microwave exposure group (0.44 W/ kg) compared with the sham-exposed group (P = 0.058). Additionally, a higher incidence of adenocarcinoma was noticed in the 4.0 W/kg group from the 15th to 26th weeks, especially in the 19th week (P = 0.358 compared to sham). However, neither tendency was statistically significant; thus this study does not provide evidence that GSM microwave exposure promotes mammary tumor development in rats. In the present study there were significant differences between the cage controls and the experimental groups (sham and exposure). Body weight and mammary tumor (malignant plus benign) incidence in the cage control group were significantly higher than in the sham- and GSM microwave-exposed groups. The latency to the mammary tumor onset was significantly shorter in the cage control group than in the other groups.


Removal of organic micro-pollutants (phenol, aniline and nitrobenzene) via forward osmosis (FO) process: Evaluation of FO as an alternative method to reverse osmosis (RO).
In this study, we have explored and compared the effectiveness of using (1) lab-fabricated forward osmosis (FO) membranes under both FO and reverse osmosis (RO) modes and (2) commercially available RO membranes under the RO mode for the removal of organic micro-pollutants. The lab-fabricated FO membranes are thin film composite (TFC) membranes consisting of a polyamide layer and a porous substrate cast from three different materials; namely, Matrimid, polyethersulfone (PESU) and sulfonated polyphenylene sulfone (sPPSU). The results show that the FO mode is superior to the RO mode in the removal of phenol, aniline and nitrobenzene from wastewater. The rejections of all three TFC membranes to all the three organic micro-pollutants under the FO processes are higher than 72% and can be even higher than 90% for aniline when a 1000 ppm aromatic aqueous solution and 1 M NaCl are employed as feeds. These performances outperform the results obtained from themselves and commercially available RO membranes under the RO mode. In addition, the rejection can be maintained even when treating a more concentrated feed solution (2000 ppm). The removal performance can be further enhanced by using a more concentrated draw solution (2 M). The water flux is almost doubled, and the rejection increment can reach up to 17%. Moreover, it was observed that annealing as a post-treatment would help compact the membrane selective layer and further enhance the separating efficiency. The obtained organic micro-pollutant rejections and water fluxes under various feasible operating conditions indicate that the FO process has potential to be a viable treatment for wastewater containing organic micro-pollutants.


Identifying clinically relevant prognostic subgroups of postmenopausal women with node-positive hormone receptor-positive early-stage breast cancer treated with endocrine therapy: a combined analysis of ABCSG-8 and ATAC using the PAM50 risk of recurrence score and intrinsic subtype.
In the adjuvant treatment of hormone receptor-positive (HR+) breast cancer, variables like tumour size, grade and nodal status have great impact on therapy decisions. As most node-positive patients with HR+ breast cancer currently receive adjuvant chemotherapy improved methods for characterization of individuals' metastasis risk are needed to reduce overtreatment. Tissue specimens from node-positive patients of the ABCSG-8 and ATAC trials who received adjuvant tamoxifen and/or anastrozole were included in this study. Analysing RNA from paraffin blocks using the PAM50 test, the primary objective was to evaluate the prognostic information of the risk of recurrence (ROR) score added to combined clinical standard variables in patients with one positive node (1N+) and in patients with two or three positive nodes (2-3N+), using log-likelihood ratio tests. At a median follow-up of 9.6 years, distant metastases occurred in 97 (18%) of 543 node-positive patients. In a multivariate analysis, the PAM50-derived ROR score provided reliable prognostic information in addition to and beyond established clinical factors for 1N+ (P < 0.0001) and 2-3N+ patients (P = 0.0002). Ten-year distant recurrence risk was significantly increased in the high-risk compared with the low-risk group derived from ROR score for 1N+ [25.5%, 95% confidence interval (CI) 17.5% to 36.1%versus 6.6%, 95% CI 3.3% to 12.8%] and compared with the combined low/intermediate risk group for 2-3N+ patients (33.7%, 95% CI 25.5% to 43.8% versus 12.5%, 95% CI 6.6% to 22.8%). Additionally, the luminal A intrinsic subtype (IS) exhibited significantly lower risk of distant recurrence compared with the luminal B subtype in 1N+ and 2-3N+ patients. PAM50 ROR score and IS can identify node-positive patient subgroups with limited risk of metastasis after endocrine therapy, for whom adjuvant chemotherapy can be spared. The PAM50 test is a valuable tool in determining treatment of node-positive early-stage breast cancer patients.


Characterization of secondary care for COPD in Sweden.
Introduction: Only a selected proportion of chronic obstructive pulmonary disease (COPD) patients are managed in secondary care. The aim of this study was to characterize disease severity, treatment and structure of secondary care for COPD in Sweden. Methods: Information was collected from 29 of 33 existing secondary care units of respiratory medicine in Sweden, using both individual data from 373 consecutively enrolled COPD patients with Global initiative on Obstructive Lung Disease (GOLD) stage III-IV and a structural questionnaire about available resources at the units. Patient data included exacerbations, health status assessed by COPD Assessment Test (CAT), lung function, comorbid conditions, pharmacological treatment and vaccinations. Structural data included available smoking cessation support, multidisciplinary rehabilitation, physical training, patient education and routine follow-up after exacerbations at the respective unit. All patients were reclassified according to the GOLD 2014 group A-D classification. Multiple linear regression investigated associations of available resources with number of exacerbations and CAT score. Results: According to GOLD 2014, 87% of the population were GOLD D and 13% were GOLD C. Triple inhaled therapy were prescribed in 88% of the patients. Over 75% of the units had resources for smoking cessation, multidisciplinary rehabilitation, physical training and patient education. Routine follow-up after exacerbations was available in 35% of the units. Being managed at units with access to structured patient education was associated with statistically significantly fewer exacerbations (adjusted regression coefficient (95% confidence interval) -0.79 (-1.39 to -0.19), p = 0.010). Conclusion: Most stage III-IV COPD patients managed at secondary care respiratory units in Sweden have maximized inhaled therapy and high risk disease even when reclassified according to GOLD 2014. Most units have access to smoking cessation, rehabilitation and patient education. Patients managed at units with structured patient education have a lower exacerbation risk.


Risk factors for autism: translating genomic discoveries into diagnostics.
Autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in communication and reciprocal social interaction, and the presence of restricted and repetitive behaviors. The spectrum of autistic features is variable, with severity of symptoms ranging from mild to severe, sometimes with poor clinical outcomes. Twin and family studies indicate a strong genetic basis for ASD susceptibility. Recent progress in defining rare highly penetrant mutations and copy number variations as ASD risk factors has prompted early uptake of these research findings into clinical diagnostics, with microarrays becoming a 'standard of care' test for any ASD diagnostic work-up. The ever-changing landscape of the generation of genomic data coupled with the vast heterogeneity in cause and expression of ASDs (further influenced by issues of penetrance, variable expressivity, multigenic inheritance and ascertainment) creates complexity that demands careful consideration of how to apply this knowledge. Here, we discuss the scientific, ethical, policy and communication aspects of translating the new discoveries into clinical and diagnostic tools for promoting the well-being of individuals and families with ASDs.


Divergent immunometabolic changes in adipose tissue and skeletal muscle with ageing in healthy humans.
Ageing is associated with increased systemic inflammation and metabolic dysfunction that contributes to the development of age-associated diseases. The role of adipose tissue in immunometabolic alterations that take place with ageing is unknown in humans. We show, in healthy, active and lean older adults, that adipose tissue, but not skeletal muscle, displays considerable pro-inflammatory transcriptomic, cellular and secretory changes, as well as a reduction in insulin signalling proteins compared to younger adults. These findings indicate that adipose tissue undergoes substantial immunometabolic alterations with ageing, and that these changes are tissue-specific and more profound than those observed in skeletal muscle or in the circulation. These results identify adipose tissue as an important tissue in the biological ageing process in humans, which may exhibit signs of immunometabolic dysfunction prior to systemic manifestation. Ageing and obesity are both characterized by inflammation and a deterioration in metabolic health. It is now clear that adipose tissue plays a major role in inflammation and metabolic control in obesity, although little is known about the role of adipose tissue in human ageing. To understand how ageing impacts adipose tissue, we characterized subcutaneous adipose tissue and skeletal muscle samples from twelve younger (27 ± 4 years [Young]) and twelve older (66 ± 5 years [Old]) active/non-obese males. We performed a wide-range of whole-body and tissue measures, including RNA-sequencing and multicolour flow cytometry. We also measured a range of inflammatory and metabolic proteins in the circulation and their release by adipose tissue, ex vivo. Both adipose tissue and muscle had ∼2-fold more immune cells per gram of tissue with ageing. In adipose tissue, this immune cell infiltration was driven by increased memory/effector T-cells, whereas, in muscle, the accumulation was driven by memory/effector T-cells and macrophages. Transcriptomic analysis revealed that, with ageing, adipose tissue, but not muscle, was enriched for inflammatory transcripts/pathways related to acquired and innate immunity. Ageing also increased the adipose tissue pro-inflammatory secretory profile. Insulin signalling protein content was reduced in adipose tissue, but not muscle. Our findings indicate that adipose tissue undergoes substantial immunometabolic changes with ageing in humans, and that these changes are tissue-specific and more profound than those observed in the circulation and skeletal muscle.


Alpha thalassaemia in Zambian newborn.
The umbilical cord blood from 109 consecutive Zambian neonates (excluding those found to be anti-HIV positive) were analysed for haemoglobin (Hb) Bart's and for alpha thalassaemia by restriction endonuclease analysis. This showed that 52.3% had the genotype alpha alpha/alpha alpha, 38.5% had -alpha 3.7/alpha alpha, 7.3% had -alpha 3.7/-alpha 3.7 and 1.8% had alpha alpha alpha/alpha alpha. The alpha thalassaemia gene (-alpha) frequency was 0.27. There were no apparent differences in gene frequency between six major Zambian ethnic groups. Detection of Hb Bart's identified all alpha-thalassaemia homozygotes (-alpha/-alpha), but fewer than 10% of heterozygotes (-alpha/alpha alpha). alpha-thalassaemia was associated with slight but significant anaemia and microcytosis.


Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment.
Although dragonflies are excellent environmental indicators for monitoring terrestrial water ecosystems, automatic monitoring techniques using digital tools are limited. We designed a novel camera trapping system with an original dragonfly detector based on the hypothesis that perching dragonflies can be automatically detected using inexpensive and energy-saving photosensors built in a perch-like structure. A trial version of the camera trap was developed and evaluated in a case study targeting red dragonflies (Sympetrum spp.) in Japan. During an approximately 2-month period, the detector successfully detected Sympetrum dragonflies while using extremely low power consumption (less than 5 mW). Furthermore, a short-term field experiment using time-lapse cameras for validation at three locations indicated that the detection accuracy was sufficient for practical applications. The frequency of false positive detection ranged from 17 to 51 over an approximately 2-day period. The detection sensitivities were 0.67 and 1.0 at two locations, where a time-lapse camera confirmed that Sympetrum dragonflies perched on the trap more than once. However, the correspondence between the detection frequency by the camera trap and the abundance of Sympetrum dragonflies determined by field observations conducted in parallel was low when the dragonfly density was relatively high. Despite the potential for improvements in our camera trap and its application to the quantitative monitoring of dragonflies, the low cost and low power consumption of the detector make it a promising tool.


The VACS index accurately predicts mortality and treatment response among multi-drug resistant HIV infected patients participating in the options in management with antiretrovirals (OPTIMA) study.
The VACS Index is highly predictive of all-cause mortality among HIV infected individuals within the first few years of combination antiretroviral therapy (cART). However, its accuracy among highly treatment experienced individuals and its responsiveness to treatment interventions have yet to be evaluated. We compared the accuracy and responsiveness of the VACS Index with a Restricted Index of age and traditional HIV biomarkers among patients enrolled in the OPTIMA study. Using data from 324/339 (96%) patients in OPTIMA, we evaluated associations between indices and mortality using Kaplan-Meier estimates, proportional hazards models, Harrel's C-statistic and net reclassification improvement (NRI). We also determined the association between study interventions and risk scores over time, and change in score and mortality. Both the Restricted Index (c = 0.70) and VACS Index (c = 0.74) predicted mortality from baseline, but discrimination was improved with the VACS Index (NRI = 23%). Change in score from baseline to 48 weeks was more strongly associated with survival for the VACS Index than the Restricted Index with respective hazard ratios of 0.26 (95% CI 0.14-0.49) and 0.39(95% CI 0.22-0.70) among the 25% most improved scores, and 2.08 (95% CI 1.27-3.38) and 1.51 (95%CI 0.90-2.53) for the 25% least improved scores. The VACS Index predicts all-cause mortality more accurately among multi-drug resistant, treatment experienced individuals and is more responsive to changes in risk associated with treatment intervention than an index restricted to age and HIV biomarkers. The VACS Index holds promise as an intermediate outcome for intervention research.


Synthesis and cytotoxic activity of MOM-ether analogs of isosteviol.
Lung cancer is one of the most common malignancies worldwide. In this Letter, novel MOM-ether analogs of isosteviol were designed and synthesized to be tested for anticancer activities against H1299 lung cancer cell lines. The effects of these derivatives were studied in H1299 human large cell lung carcinoma cells that are null for p53 and compared to normal counterparts NL-20 normal lung epithelial cells. The initial screening of twelve MOM-ether analogs of isosteviol derivatives on H1299 lung cancer cells by MTT assay revealed that two derivatives (an ester and a carbamate) were the most potent in reducing cell viability. The IC50 values for these derivatives were determined to be 14 and 21 μM respectively. We compared the cytotoxicity of the best derivatives in H1299 lung cancer cells and NL-20 normal lung epithelial cells. Both derivatives showed lower cytotoxic effects on NL-20 normal lung epithelial cells. Moreover, both derivatives induced apoptosis in H1299 lung cancer cells more than NL-20 normal lung epithelial cells.


Generation of human hepatic progenitor cells with regenerative and metabolic capacities from primary hepatocytes.
Hepatocytes are regarded as the only effective cell source for cell transplantation to treat liver diseases; however, their availability is limited due to a donor shortage. Thus, a novel cell source must be developed. We recently reported that mature rodent hepatocytes can be reprogrammed into progenitor-like cells with a repopulative capacity using small molecule inhibitors. Here, we demonstrate that hepatic progenitor cells can be obtained from human infant hepatocytes using the same strategy. These cells, named human chemically induced liver progenitors (hCLiPs), had a significant repopulative capacity in injured mouse livers following transplantation. hCLiPs redifferentiated into mature hepatocytes in vitro upon treatment with hepatic maturation-inducing factors. These redifferentiated cells exhibited cytochrome P450 (CYP) enzymatic activities in response to CYP-inducing molecules and these activities were comparable with those in primary human hepatocytes. These findings will facilitate liver cell transplantation therapy and drug discovery studies.


Notch1 targeting siRNA delivery nanoparticles for rheumatoid arthritis therapy.
Notch pathway plays a pivotal role in synoviocytes involved in progression of rheumatoid arthritis (RA). Herein, we designed the Notch1 targeting siRNA delivery nanoparticles (siRNA-NPs) in order to confirm the anti-inflammatory effect in collagen-induced arthritis (CIA) model. The siRNA-NPs were successfully produced by encapsulating polymerized siRNA (poly-siRNA) into thiolated glycol chitosan (tGC) nanoparticles in aqueous condition. The in vitro Notch1 inhibition of siRNA-NPs in murine macrophage cell (RAW 264.7) was confirmed using confocal microscopy and real time PCR. Fluorescently labeled siRNA-NPs were successfully transfected in RAW 264.7 and modulated the expression of Notch1 in mRNA level. For in vivo study, siRNA-NPs exhibited the higher targeting efficiency in the arthritic joins of CIA mice, confirmed by the near-infrared fluorescence (NIRF) imaging. Furthermore, inhibition of Notch1 with siRNA-NPs resulted in retarded progression of inflammation, bone erosion, and cartilage damage in CIA mice. Novel Notch1 targeting siRNA delivery system of siRNA-NPs showed effective RA treatment by suppressing Notch1 signaling pathway without undesirable severe toxicity. Thus, Notch1 inhibiting siRNA-NPs demonstrated the great potential in RA therapeutics that was hard to be achieved using conventional drugs.


Duration of treatment in pulmonary tuberculosis: are international guidelines on the management of tuberculosis missing something?
Despite evidence of an association between tuberculosis (TB) treatment outcomes and the performance of national tuberculosis programmes (NTP), no study to date has rigorously documented the duration of treatment among TB patients. As such, this study was conducted to report the durations of the intensive and continuation phases of TB treatment and their predictors among new smear-positive pulmonary tuberculosis (PTB) patients in Malaysia. Descriptive, non-experimental, follow-up cohort study. This study was conducted at the Chest Clinic of Penang General Hospital between March 2010 and February 2011. The medical records and TB notification forms of all new smear-positive PTB patients, diagnosed during the study period, were reviewed to obtain sociodemographic and clinical data. Based on standard guidelines, the normal benchmarks for the durations of the intensive and continuation phases of PTB treatment were taken as two and four months, respectively. A patient in whom the clinicians decided to extend the intensive phase of treatment by ≥2 weeks was categorized as a case with a prolonged intensive phase. The same criterion applied for the continuation phase. Multiple logistic regression analysis was performed to find independent factors associated with the duration of TB treatment. Data were analyzed using Predictive Analysis Software Version 19.0. Of the 336 patients included in this study, 261 completed the intensive phase of treatment, and 226 completed the continuation phase of treatment. The mean duration of TB treatment (n = 226) was 8.19 (standard deviation 1.65) months. Half (49.4%, 129/261) of the patients completed the intensive phase of treatment in two months, whereas only 37.6% (85/226) of the patients completed the continuation phase of treatment in four months. On multiple logistic regression analysis, being a smoker, being underweight and having a history of cough for ≥4 weeks at TB diagnosis were found to be predictive of a prolonged intensive phase of treatment. Diabetes mellitus and the presence of lung cavities at the start of treatment were the only predictors found for a prolonged continuation phase of treatment. The average durations of the intensive and continuation phases of treatment among PTB patients were longer than the targets recommended by the World Health Organization. As there are no internationally agreed criteria, it was not possible to judge how well the Malaysian NTP performed in terms of managing treatment duration among PTB patients.


Real-Time Temporal Dynamics of Bicistronic Expression Mediated by Internal Ribosome Entry Site and 2A Cleaving Sequence.
Multicistronic elements, such as the internal ribosome entry site (IRES) and 2A-like cleavage sequence, serve crucial roles in the eukaryotic ectopic expression of exogenous genes. For utilization of multicistronic elements, the cleavage efficiency and order of elements in multicistronic vectors have been investigated; however, the dynamics of multicistronic element-mediated expression remains unclear. Here, we investigated the dynamics of encephalomyocarditis virus (EMCV) IRES- and porcine teschovirus-1 2A (p2A)-mediated expression. By utilizing real-time fluorescent imaging at a minute-level resolution, we monitored the expression of fluorescent reporters bridged by either EMCV IRES or p2A in two independent cultured cell lines, HEK293 and Neuro2a. We observed significant correlations for the two fluorescent reporters in both multicistronic elements, with a higher correlation coefficient for p2A in HEK293 but similar coefficients for IRES-mediated expression and p2A-mediated expression in Neuro2a. We further analyzed the causal relationship of multicistronic elements by convergent cross mapping (CCM). CCM revealed that in all four conditions examined, the expression of the preceding gene causally affected the dynamics of the subsequent gene. As with the cross correlation, the predictive skill of p2A was higher than that of IRES in HEK293, while the predictive skills of the two multicistronic elements were indistinguishable in Neuro2a. To summarize, we report a significant temporal correlation in both EMCV IRES- and p2A-mediated expression based on the simple bicistronic vector and real-time fluorescent monitoring. The current system also provides a valuable platform to examine the dynamic aspects of expression mediated by diverse multicistronic elements under various physiological conditions.


Isolation and characterization of two human transcription factor IIH (TFIIH)-related complexes: ERCC2/CAK and TFIIH.
Transcription factor IIH (TFIIH) is a multisubunit protein complex essential for both the initiation of RNA polymerase class II (pol II)-catalyzed transcription and nucleotide excision repair of DNA. Recent studies have shown that TFIIH copurifies with the cyclin-dependent kinase (cdk)-activating kinase complex (CAK) that includes cdk7, cyclin H, and p36/MAT1. Here we report the isolation of two TFIIH-related complexes: TFIIH* and ERCC2/CAK. TFIIH* consists of a subset of the TFIIH complex proteins including ERCC3 (XPB), p62, p44, p41, and p34 but is devoid of detectable levels of ERCC2 (XPD) and CAK. ERCC2/CAK was isolated as a complex that exhibits CAK activity that cosediments with the three CAK components (cdk7, cyclin H, and p36/MAT1) as well as the ERCC2 (XPD) protein. TFIIH* can support pol II-catalyzed transcription in vitro with lower efficiency compared with TFIIH. This TFIIH*-dependent transcription reaction was stimulated by ERCC2/CAK. The ERCC2/CAK and TFIIH* complexes are each active in DNA repair as shown by their ability to complement extracts prepared from ERCC2 (XPD)- and ERCC3 (XPB)-deficient cells, respectively, in supporting the excision of DNA containing a cholesterol lesion. These data suggest that TFIIH* and ERCC2/CAK interact to form the TFIIH holoenzyme capable of efficiently assembling the pol II transcription initiation complex and directly participating in excision repair reactions.


The Lister AirSeal® port closure technique - Initial patient outcomes.
The 12-mm AirSeal® port is widely used in robotically assisted laparoscopic prostatectomy due to its ability to maintain stable pneumoperitoneal pressures and smoke evacuation. However, it creates a potential risk of port site hernia. We have traditionally used EndoClose™ to perform full thickness closure of this port, but noted that patients experienced increased pain related to this procedure, which sometimes persisted for several months. Using the Da Vinci Si we performed peritoneal closure with 2-0 vicryl by switching the fourth arm to the right master controller. The external oblique sheath was closed outside with 1 Ethibond. We performed this closure in 20 consecutive patients (group 1). Postoperative day 1, 2 and post-discharge telephone consultation pain scores (1-10) were recorded and compared with the previous 20 consecutive patients who had the EndoClose closure (group 2). We recorded an instructional video to enable reproduction of the new technique. The mean length of stay was 1.5 days for patients in group 1 and 1.9 days for those in group 2 (P = 0.04). There was no difference in operating time or average day 1 pain scores. Post-discharge follow-up call revealed 1 of 20 patients who had AirSeal port site pain in group 1 and 5 of 17 in group 2 (P = 0.04). Pain scores also tended to be higher for group 2. Our preliminary analysis of this novel technique to close the AirSeal port in two separate layers improves postoperative pain related to this port site.


Supervised Phenotype Discovery From Multimodal Brain Imaging.
Data-driven discovery of image-derived phenotypes (IDPs) from large-scale multimodal brain imaging data has enormous potential for neuroscientific and clinical research by linking IDPs to subjects' demographic, behavioural, clinical and cognitive measures (i.e., non-imaging derived phenotypes or nIDPs). However, current approaches are primarily based on unsupervised approaches, without the use of information in nIDPs. In this paper, we proposed a semi-supervised, multimodal, and multi-task fusion approach, termed SuperBigFLICA, for IDP discovery, which simultaneously integrates information from multiple imaging modalities as well as multiple nIDPs. SuperBigFLICA is computationally efficient and largely avoids the need for parameter tuning. Using the UK Biobank brain imaging dataset with around 40,000 subjects and 47 modalities, along with more than 17,000 nIDPs, we showed that SuperBigFLICA enhances the prediction power of nIDPs, benchmarked against IDPs derived by conventional expert-knowledge and unsupervised-learning approaches (with average nIDP prediction accuracy improvements of up to 46%). It also enables the learning of generic imaging features that can predict new nIDPs. Further empirical analysis of the SuperBigFLICA algorithm demonstrates its robustness in different prediction tasks and the ability to derive biologically meaningful IDPs in predicting health outcomes and cognitive nIDPs, such as fluid intelligence and hypertension.


Stochastic epidemic models: a survey.
This paper is a survey paper on stochastic epidemic models. A simple stochastic epidemic model is defined and exact and asymptotic (relying on a large community) properties are presented. The purpose of modelling is illustrated by studying effects of vaccination and also in terms of inference procedures for important parameters, such as the basic reproduction number and the critical vaccination coverage. Several generalizations towards realism, e.g. multitype and household epidemic models, are also presented, as is a model for endemic diseases.