The EMT-activator Zeb1 is a key factor for cell plasticity and promotes metastasis in pancreatic cancer.
Metastasis is the major cause of cancer-associated death. Partial activation of the epithelial-to-mesenchymal transition program (partial EMT) was considered a major driver of tumour progression from initiation to metastasis. However, the role of EMT in promoting metastasis has recently been challenged, in particular concerning effects of the Snail and Twist EMT transcription factors (EMT-TFs) in pancreatic cancer. In contrast, we show here that in the same pancreatic cancer model, driven by Pdx1-cre-mediated activation of mutant Kras and p53 (KPC model), the EMT-TF Zeb1 is a key factor for the formation of precursor lesions, invasion and notably metastasis. Depletion of Zeb1 suppresses stemness, colonization capacity and in particular phenotypic/metabolic plasticity of tumour cells, probably causing the observed in vivo effects. Accordingly, we conclude that different EMT-TFs have complementary subfunctions in driving pancreatic tumour metastasis. Therapeutic strategies should consider these potential specificities of EMT-TFs to target these factors simultaneously.


Deletion in the uridine diphosphate glucuronyltransferase 2B17 gene is associated with delayed pubarche in healthy boys.
Only a few genetic loci are known to be associated with male pubertal events. The ability of excreting testosterone (T) and other steroids in the urine depends on sulfation and glucuronidation. One of several essential glucuronidases is encoded by the UGT2B17 gene. In a preliminary report, we found that homozygous deletion of UGT2B17 in boys was associated with lower urinary excretion of T. We hypothesized that boys with a lower glucuronidation capacity may have altered androgen action and excretion affecting pubarche, as this represents a T-dependent event. 668 healthy boys (cross-sectional) aged 6.1-21.9 years (COPENHAGEN puberty study conducted from 2005 to 2006) were included. 65 of the boys where followed longitudinally every 6 months. Participants were genotyped for UGT2B17 copy number variation (CNV). Clinical pubertal staging including orchidometry, anthropometry and serum reproductive hormone levels. 59 of the 668 boys (8.8%) presented with a homozygous deletion of UGT2B17 (del/del). These boys experienced pubarche at a mean age of 12.73 years (12.00-13.46) vs 12.40 years (12.11-12.68) in boys heterozygous for deletion of UGT2B17 (del/ins) vs 12.06 years (11.79-12.33) in boys with the wild-type genotype (ins/ins) (P = 0.029, corrected for BMI z-score). The effect accounted for 0.34 years delay per allele (95% CI: 0.03-0.64). A comparable trend was observed for onset of testicular enlargement >3 mL but did not reach significance. CNV of UGT2B17 is a factor contributing to the timing of male pubarche.


Positive and negative perceived consequences of first intercourse among middle and high school students in Puebla, Mexico.
Relatively little is known about young people's interpretations of sexual behaviour in Latin America. In this study, we examine the most commonly perceived consequences of first sexual intercourse among Mexican middle and high school students, how perceived consequences differ by gender, and factors that may predict experiencing more positive or negative consequences. Sexually active Mexican students aged 12-19 years (n = 268) reported whether they had experienced each of 19 consequences following first intercourse. Both positive consequences, such as physical satisfaction and closeness to partner, and negative consequences, such as worry about STDs and pregnancy, were common. Sex with a non-relationship partner was associated with fewer positive and more negative consequences, with the effect for positive consequences being stronger for young women. Pressure to have sex was associated with fewer positive consequences of first intercourse, and pressure to remain a virgin was associated with more positive and negative consequences. These findings suggest that young people often report mixed feelings about their first sexual intercourse and that relationship context and sexual socialisation influence their perceptions of the event.


Weighing the benefits of hepatocellular carcinoma surveillance against potential harms.
Hepatocellular carcinoma (HCC) is the most common primary liver cancer and usually occurs in people with liver cirrhosis. Both the incidence and mortality of HCC are increasing worldwide, making it a growing public health issue. HCC diagnosed at an early stage has a far better prognosis than HCC diagnosed at a late stage, mainly because early stage HCC can be treated with potentially curative therapies such as resection and transplantation. This makes surveillance for HCC in patients with liver cirrhosis an important strategy in improving outcomes. Serial measurements of serum alpha fetoprotein (AFP) and abdominal ultrasound (US) are the established methods of surveillance. Surveillance using a combination of these techniques has reasonable sensitivity and specificity and reduces mortality from HCC by varying degrees, depending on the patient population. However, there are potential harms. The main harms result from false-positive and false-negative results. False-positive results commit patients to undergo further, potentially invasive and ultimately unnecessary diagnostic testing - which has both financial and emotional costs. False-negative results can have devastating consequences for patients who later present with more advanced HCC. Obesity is increasingly prevalent and reduces the sensitivity of US in detecting HCC. Obesity-associated non-alcoholic fatty liver disease (NAFLD) presents an additional challenge, where HCC can develop in the absence of cirrhosis. As surveillance with US and AFP is not cost-effective in NAFLD without cirrhosis, it is not advocated. These aspects will be reviewed.


Education and the Relationship Between Supermarket Environment and Diet.
Supermarkets are a major source of food for many families. Knowledge of how educational attainment affects the relationship between in-store environments of supermarkets and diet is needed. This study examined the relationship between maternal dietary quality and overall in-store supermarket environment, and assessed the effect modification of educational attainment. Dietary quality z-scores were calculated for 829 mothers with young children using cross-sectional data collected in 2010-2011 from a 20-item food frequency questionnaire. Information about nine in-store factors (variety, price, quality, promotion, shelf placement, store placement, nutrition information, healthier alternatives, and single fruit sale) on 12 foods known to discriminate between better and poorer dietary quality were collected to create a standardized "healthfulness" z-score for each supermarket where mothers shopped. Multilevel unadjusted linear regression analysis completed in 2014-2015 showed that shopping at more-healthful supermarkets was associated with better dietary quality (β=0.39 SD/SD, p=0.01, 95% CI=0.10, 0.68). However, the relationship differed according to educational attainment (interaction, p=0.006). Among mothers who left school at age 16 years, those who shopped at less healthful supermarkets had poorer dietary quality (β=0.31 SD/SD, 95% CI=0.07, 0.55). Among mothers with degrees, those who shopped at less healthful supermarkets had better dietary quality (β=-0.59 SD/SD, 95% CI=-1.19, 0.00). Mothers with low educational attainment show greater susceptibility to less healthful in-store environments than mothers with higher educational attainment who may be protected by greater psychological and financial resources. Policy initiatives to improve supermarket environments may be necessary to address dietary inequalities.


Obesity and risk of job disability in male firefighters.
Obesity is a major public health problem and a workplace epidemic in Western societies. However, little is known about the association between obesity and job disability in specific occupational groups. To examine the association between obesity and risk of job disability among firefighters. A prospective cohort study design was employed in following 358 Massachusetts firefighters enrolled in a statewide medical surveillance program. We prospectively evaluated time to development of adverse employment outcomes >6 years of follow-up. In multivariable-adjusted Cox proportional hazard models, we found that every one-unit increase in body mass index (BMI) was associated with a 5% increased risk of job disability. Compared to firefighters in the lowest tertile of BMI (BMI < 27.2), those in the highest tertile (BMI >or= 30.2) had a significantly increased risk of an adverse employment event with a multivariable-adjusted hazard ratio (HR) of 1.98 (95% CI 1.06-3.72). There was also a significant dose-response relationship of increasing risk across tertiles, as well as a significant trend: HR 1.39 (95% CI 1.04-1.86). The highest categories of BMI had a 60-90% increased risk of job disability compared to the lowest or normal-weight categories, respectively. Obesity is associated with higher risk of job disability in firefighters. Additional research is needed to further explore our findings. Our study may have economic and public health implications in other occupational settings.


Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries.
Dynamic shifts in transcription factor binding are central to the regulation of biological processes by allowing rapid changes in gene transcription. However, very few genome-wide studies have examined how transcription factor occupancy is coordinated temporally in vivo in higher animals. Here, we quantified the genome-wide binding patterns of two key hepatocyte transcription factors, CEBPA and CEBPB (also known as C/EBPalpha and C/EBPbeta), at multiple time points during the highly dynamic process of liver regeneration elicited by partial hepatectomy in mouse. Combining these profiles with RNA polymerase II binding data, we find three temporal classes of transcription factor binding to be associated with distinct sets of regulated genes involved in the acute phase response, metabolic/homeostatic functions, or cell cycle progression. Moreover, we demonstrate a previously unrecognized early phase of homeostatic gene expression prior to S-phase entry. By analyzing the three classes of CEBP bound regions, we uncovered mutually exclusive sets of sequence motifs, suggesting temporal codes of CEBP recruitment by differential cobinding with other factors. These findings were validated by sequential ChIP experiments involving a panel of central transcription factors and/or by comparison to external ChIP-seq data. Our quantitative investigation not only provides in vivo evidence for the involvement of many new factors in liver regeneration but also points to similarities in the circuitries regulating self-renewal of differentiated cells. Taken together, our work emphasizes the power of global temporal analyses of transcription factor occupancy to elucidate mechanisms regulating dynamic biological processes in complex higher organisms.


Alprazolam in panic disorder and agoraphobia: results from a multicenter trial. III. Discontinuation effects.
Preliminary reports of discontinuation of alprazolam therapy in patients with panic disorder have revealed worsening of symptoms despite gradual withdrawal of medication. In this study, 126 patients with panic disorder and phobic avoidance received either alprazolam or placebo in doses of 2 to 10 mg daily for eight weeks. The medication was tapered over a period of four weeks, and patients were observed for another two weeks after all medication was discontinued. Sixty of the 63 alprazolam-treated patients and 49 of the 63 placebo-treated patients entered the taper and discontinuation study. After improvement in the active treatment period, the alprazolam-treated group had significant relapse between the first and last week of taper. However, during the second postdiscontinuation week, outcome scores were not significantly different from those of the placebo-treated group who did not deteriorate during taper. Twenty-seven percent of the alprazolam-treated group reported a rebound of panic attacks during taper and 13% reported a rebound of anxiety on the Hamilton Anxiety Scale. No serious or life-threatening withdrawal symptoms were reported, but distinct, transient, mild to moderate withdrawal syndrome occurred in 35% of the alprazolam-treated group and in none of the placebo-treated group. The coexistence of symptom rebound and a withdrawal syndrome occurred in 10% of the alprazolam-treated group, but both subsided by the end of the second week without alprazolam. We recommend that patients with panic disorder be treated for a longer period, at least six months, and that medication be tapered over a more prolonged period, at least eight weeks, especially where high doses are employed.


Criteria for Directly Detecting Topological Fermi Arcs in Weyl Semimetals.
The recent discovery of the first Weyl semimetal in TaAs provides the first observation of a Weyl fermion in nature and demonstrates a novel type of anomalous surface state, the Fermi arc. Like topological insulators, the bulk topological invariants of a Weyl semimetal are uniquely fixed by the surface states of a bulk sample. Here we present a set of distinct conditions, accessible by angle-resolved photoemission spectroscopy (ARPES), each of which demonstrates topological Fermi arcs in a surface state band structure, with minimal reliance on calculation. We apply these results to TaAs and NbP. For the first time, we rigorously demonstrate a nonzero Chern number in TaAs by counting chiral edge modes on a closed loop. We further show that it is unreasonable to directly observe Fermi arcs in NbP by ARPES within available experimental resolution and spectral linewidth. Our results are general and apply to any new material to demonstrate a Weyl semimetal.


An experimental study of mummification pertinent to the antiquity of cancer.
The relatively recent description in scientific literature of many types of cancer suggests their infrequency until the relatively recent past, a view supported by the paucity of diagnoses of malignancies in ancient remains. While overall life span was short in antiquity, many individuals did live to the "cancer age," as there is ample evidence of a variety of degenerative disorders. It has been suggested that tumors are not well enough preserved for diagnosis, and tumors experimentally mummified and rehydrated were evaluated as to their preservation. It was found that cancers were actually better preserved than normal tissues. The absence of tumors in ancient tissues must be considered a reflection of a markedly lower incidence than in the modern population of the Lnited States, in which cancer accounts for approximately 17% of all deaths. It is suggested that this increase in cancer is due to factors in the modern industrialized environment.


Brownian Motion at Lipid Membranes: A Comparison of Hydrodynamic Models Describing and Experiments Quantifying Diffusion within Lipid Bilayers.
The capability of lipid bilayers to exhibit fluid-phase behavior is a fascinating property, which enables, for example, membrane-associated components, such as lipids (domains) and transmembrane proteins, to diffuse within the membrane. These diffusion processes are of paramount importance for cells, as they are for example involved in cell signaling processes or the recycling of membrane components, but also for recently developed analytical approaches, which use differences in the mobility for certain analytical purposes, such as in-membrane purification of membrane proteins or the analysis of multivalent interactions. Here, models describing the Brownian motion of membrane inclusions (lipids, peptides, proteins, and complexes thereof) in model bilayers (giant unilamellar vesicles, black lipid membranes, supported lipid bilayers) are summarized and model predictions are compared with the available experimental data, thereby allowing for evaluating the validity of the introduced models. It will be shown that models describing the diffusion in freestanding (Saffman-Delbrück and Hughes-Pailthorpe-White model) and supported bilayers (the Evans-Sackmann model) are well supported by experiments, though only few experimental studies have been published so far for the latter case, calling for additional tests to reach the same level of experimental confirmation that is currently available for the case of freestanding bilayers.


The structure and organization of lamprin genes: multiple-copy genes with alternative splicing and convergent evolution with insect structural proteins.
Lamprin is a unique structural protein which forms the extracellular matrix of several cartilaginous structures found in the lamprey. Lamprin is noncollagenous in nature but shows sequence similarities to elastins and to insect structural proteins. Here, we characterize the structure and organization of lamprin genes, demonstrating the presence of multiple similar but not identical copies of the lamprin gene in the genome of the lamprey. In at least one species of lamprey, Lampetra richardsoni, the multiple gene copies are arranged in tandem in the genome in a head-to-tail orientation. Lamprin genes from Petromyzon marinus contain either seven or eight exons, with exon 4 being alternatively spliced in all genes, resulting in a total of six different lamprin transcripts. All exon junctions are of class 1,1. An unusual feature of the lamprin gene structure is the distribution of the 3' untranslated region sequence among multiple exons. A TATA box and cap sequence have been identified in upstream sequences in close proximity to the transcription start site, but no CAAT box could be identified. Sequence and gene structure comparisons between lamprins, elastins, and insect structural proteins suggest that the regions of sequence similarity are the result of a process of convergent evolution.


Sex determination: lessons from families and embryos.
Genetic studies in familial cases of sex reversal and in human embryos have contributed to the understanding of human sex determination and its disorders. For some heritable disorders of sex reversal, the gonadal phenotype was frequently overlooked until sex reversal was discovered fortuitously by chromosome analysis, often resulting in preventable complications. Within families, the phenotypes are variable and, in some instances, these can be explained by known genetic mechanisms. When a novel molecular marker is shared by family members affected with sex reversal, the level of confidence is higher that this marker may play a role in the development of the phenotype. The identification of pedigrees with sufficient power to generate significant linkage of disorder (lod) scores from genomewide screens can now lead to the identification of novel sex-determining genes. Studies of the gonads of 46,XY human embryos have shown that SOX9 expression follows a pattern similar to that of SRY and, in both instances, stands in contrast to the expression observed in the mouse. Differences between human and mouse embryonic gonads have also been observed for the temporal expression of DAX1, suggesting that the mechanisms of action of SRY, SOX9, and DAX1 may vary between these and other species.


Reasons for delaying or engaging in early sexual initiation among adolescents in Nigeria.
Annually, over 1 million births in Nigeria are to teenage mothers. Many of these pregnancies are unwanted and these mothers are also exposed to the risk of human immunodeficiency virus (HIV) infection. Sexual abstinence is a critical preventative health strategy. Several quantitative studies in Nigeria have identified the correlates and determinants of early sex, yet few have explored in depth the underlying reasons for early sex. This paper explores both the key factors that motivate some unmarried young people to engage in early sex and reasons why some delay. This qualitative study was based on data from 30 focus group discussions held with unmarried 14- to 19-year-olds in four geographically and culturally dispersed Nigerian states. Focus groups were stratified by sexual experience to capture variations among different subgroups. Several reasons for early premarital sex were identified. The "push" factors included situations where parents exposed young female adolescents to street trading. "Pull" factors, particularly for males, included the pervasive viewing of locally produced movies, peer pressure and, for females, transactional sex (where adolescent girls exchange sex for gifts, cash, or other favors). Also noted were overtly coercive factors, including rape. There were also myths and misconceptions that "justified" early sexual initiation. Reasons cited for delay included religious injunction against premarital sex; disease prevention (especially HIV/acquired immunodeficiency syndrome); fear of pregnancy, and linked to this, the fear of dropping out of school; and, for females, the fear of bringing shame to the family, which could lead to their inability to get a "good" husband in the future. The differences observed between sexually active and abstinent adolescents were that the latter were more confident, had greater determination, and, most important, deployed refusal skills to delay first sex. Health promoters need to focus attention on educating adolescents in the skills needed to delay sexual debut.


Towards an affect intensity regulation hypothesis: Systematic review and meta-analyses of the relationship between affective states and alcohol consumption.
While self-medication and positive and negative reinforcement models of alcohol use suggest that there is an association between daily affect and alcohol consumption, findings within the academic literature have been inconsistent. This pre-registered systematic review meta-analytically interrogated the results from studies amongst non-clinical populations that examine the relationship between daily affective states and alcohol consumption volume. PRISMA guided searches of PsychINFO, PsycARTICLES, Science Direct, PubMed, SCOPUS, and JSTOR databases were conducted. When both laboratory and field studies were included, meta-analyses with robust variance estimation yielded 53 eligible studies on negative affect (8355 participants, 127 effect sizes) and 35 studies for positive affect (6384 participants, 50 effect sizes). The significant pooled associations between intra-day affect and alcohol consumption were r = .09, [.03, .14] for negative affect, and r = .17, [.04, .30] for positive affect. A small-to-medium sized effect (d = .275, [.11, .44]) of negative affect on daily alcohol consumption volume was found in laboratory studies (14 studies, 1100 participants). While publication bias was suspected, P-curve analyses suggested that the results were unlikely to be the product of publication bias and p-hacking alone, and selection model analysis revealed no significant differences in results when publication bias was accounted for. For negative affect, using number of drinks as the measure of alcohol consumption was associated with lower effect sizes. For positive affect, the results demonstrated a decline of this observed effect over time. Overall, findings point towards the possibility of developing an affect intensity regulation theory of alcohol use. Conceptualizing the mood-alcohol nexus in terms of affect intensity regulation may afford a more parsimonious explanation of alcohol consumption rather than viewing the behavior as being shaped by either positive or negative affective states.


Immunofluorescence Tomography: High-resolution 3-D reconstruction by serial-sectioning of methacrylate embedded tissues and alignment of 2-D immunofluorescence images.
Immunofluorescence tomography is a high-resolution 3-D reconstruction method based on methacrylate embedding and serial-sectioning, where 2-D images of immuno-stained serial-sections are computationally aligned into image stacks, and the 3-D volume rendered. Butyl-Methyl Methacrylate (BMMA) plastic was adopted as it preserves excellent tissue morphology and can be de-plasticized easily using an organic solvent, which enables immuno-staining of serial-sections without antibody penetration issues over millimeters of 3-D reconstructed tissue (Z-depth). High axial Z-resolution over a large volume was achieved by cutting serial-sections at 2 µm thickness. Stained sections were imaged by multiple modalities, including immunofluorescence, electron microscopy and second harmonic generation (SHG), and there are advantages over confocal microscopy as the tissue does not need to be cleared, while antibody penetration or light scattering issues are minimized. The plastic serial-sections can be re-probed, without a loss in tissue structure, using low pH glycine hydrochloride antibody elution. It is a cost-effective approach as the microscopes needed are significantly cheaper than confocal microscopes and sections can be kept indefinitely. Therefore, immunofluorescence tomography is a powerful new tool to quantify sub-populations of cells in high-resolution 3-D using antibody fluorescence. This article describes the immunofluorescence tomography method for 3-D reconstruction of epithelial tissues such as mammary gland, cornea and the hair follicle.


Can't see the woods for the trees: exploring the range and connection of tobacco industry argumentation in the 2012 UK standardised packaging consultation.
Transnational tobacco company (TTC) submissions to the 2012 UK standardised packaging consultation are studied to examine TTC argumentation in the context of Better Regulation practices. A content analysis was conducted of Philip Morris International and British American Tobacco submissions to the 2012 UK consultation. Industry arguments concerning expected costs and (contested) benefits of the policy were categorised into themes and frames. The inter-relationship between frames through linked arguments was mapped to analyse central arguments using an argumentation network. 173 arguments were identified. Arguments fell into one of five frames: ineffectiveness, negative economic consequences, harm to public health, increased crime or legal ramifications. Arguments highlighted high costs to a wide range of groups, including government, general public and other businesses. Arguments also questioned the public health benefits of standardised packaging and highlighted the potential benefits to undeserving groups. An increase in illicit trade was the most central argument and linked to the greatest variety of arguments. In policy-making systems characterised by mandatory impact assessments and public consultations, the wide range of cost (and contested benefits) based arguments highlights the risk of TTCs overloading policy actors and causing delays in policy adoption. Illicit trade related arguments are central to providing a rationale for these arguments, which include the claim that standardised packaging will increase health risks. The strategic importance of illicit trade arguments to industry argumentation in public consultations underlines the risks of relying on industry data relating to the scale of the illicit trade.


Impact of Intracellular Concentrations on Metabolic Drug-Drug Interaction Studies.
Accurate prediction of drug-drug interactions (DDI) is a challenging task in drug discovery and development. It requires determination of enzyme inhibition in vitro which is highly system-dependent for many compounds. The aim of this study was to investigate whether the determination of intracellular unbound concentrations in primary human hepatocytes can be used to bridge discrepancies between results obtained using human liver microsomes and hepatocytes. Specifically, we investigated if Kpuu could reconcile differences in CYP enzyme inhibition values (Ki or IC50). Firstly, our methodology for determination of Kpuu was optimized for human hepatocytes, using four well-studied reference compounds. Secondly, the methodology was applied to a series of structurally related CYP2C9 inhibitors from a Roche discovery project. Lastly, the Kpuu values of three commonly used CYP3A4 inhibitors-ketoconazole, itraconazole, and posaconazole-were determined and compared to compound-specific hepatic enrichment factors obtained from physiologically based modeling of clinical DDI studies with these three compounds. Kpuu obtained in suspended human hepatocytes gave good predictions of system-dependent differences in vitro. The Kpuu was also in fair agreement with the compound-specific hepatic enrichment factors in DDI models and can therefore be used to improve estimations of enrichment factors in physiologically based pharmacokinetic modeling.


Preparedness for resuscitation at a geographically isolated army troop medical clinic: lessons from Camp Blanding, Florida.
Many Servicemembers rely on nondeployed Role 1 facilities, such as troop medical clinics, as their primary source of healthcare. At geographically isolated military installations, these facilities are the "only game in town" for medical care. Servicemembers may present to these facilities with emergent conditions, regardless of designed intent of the facility or the wishes of staff. The U.S. Army Troop Medical Clinic, Camp Blanding is such a facility. The clinic was reorganized with a 5S approach, streamlining supply, equipment, and workflow processes. This was accomplished to allow the facility to not only improve its general delivery of care but also ensure capability to handle at least one medical or trauma resuscitation. Equipment, disposable supplies, documentation, and staff training were addressed. Results/Discussion/Conclusion: Despite facility intention, lack of supplies/equipment, or staff inexperience with emergency care, an acute ill or injured Servicemember must be stabilized at the nondeployed Role 1 facility while awaiting transport to a higher level of care. This expectation is the same as that of deployed Role 1 facilities. A cost-savings can also be realized when minor "emergencies" are handled in-house.


Roles of ATR1 paralogs YMR279c and YOR378w in boron stress tolerance.
Boron is a necessary nutrient for plants and animals, however excess of it causes toxicity. Previously, Atr1 and Arabidopsis Bor1 homolog were identified as the boron efflux pump in yeast, which lower the cytosolic boron concentration and help cells to survive in the presence of toxic amount of boron. In this study, we analyzed ATR1 paralogs, YMR279c and YOR378w, to understand whether they participate in boron stress tolerance in yeast. Even though these genes share homology with ATR1, neither their deletion rendered cells boron sensitive nor their expression was significantly upregulated by boron treatment. However, expression of YMR279, but not YOR378w, from the constitutive GAPDH promoter on a high copy plasmid provided remarkable boron resistance by decreasing intracellular boron levels. Thus our results suggest the presence of a third boron exporter, YMR279c, which functions similar to ATR1 and provides boron resistance in yeast.


Role of mammalian target of rapamycin signaling in compensatory renal hypertrophy.
Loss of functioning nephrons stimulates the growth of residual kidney tissue to augment work capacity and maintain normal renal function. This growth largely occurs by hypertrophy rather than from hyperplasia of the remaining nephrons. The signaling mechanisms that increase RNA and protein synthesis during compensatory renal hypertrophy are unknown. This study found that the remaining kidney hypertrophied 42% by 16 d after unilateral nephrectomy (UNX) in DBA/2 mice. Immunoblotting analysis revealed increased phosphorylation of the 40S ribosomal protein S6 (rpS6) and the eukaryotic translation initiation factor (eIF) 4E-binding protein 1 (4E-BP1), the two downstream effectors of the mammalian target of rapamycin (mTOR). The highly specific mTOR inhibitor rapamycin blocked UNX-increased phosphorylation of both rpS6 and 4E-BP1. UNX increased the content of not only 40S and 60S ribosomal subunits but also 80S monosomes and polysomes in the remaining kidney. Administration of rapamycin decreased UNX-induced polysome formation and shifted the polysome profile in the direction of monosomes and ribosomal subunits. Pretreatment of the mice with rapamycin inhibited UNX-induced hypertrophy. These studies demonstrate that activation of the mTOR signaling pathway in the remaining kidney after UNX plays an essential role in modulating RNA and protein synthesis during development of compensatory renal hypertrophy.


Factors associated with change in health-related quality of life among individuals treated with long-term mechanical ventilation, a 6-year follow-up study.
To examine changes and explanatory variables for changes in health-related quality of life in patients treated with long-term mechanical ventilation over a 6-year period. Long-term mechanical ventilation is a treatment for individuals with chronic hypercapnic respiratory failure, primarily caused by neuromuscular diseases, obesity hypoventilation syndrome, chronic obstructive pulmonary and restrictive thoracic diseases. Studies on long-term outcome on health-related quality of life and factors influencing it are lacking. Prospective cohort study. Data were collected from the Norwegian Long-Term-Mechanical-Ventilation Registry and from patient-reported questionnaire in 2008 and 2014. Health-related quality of life was measured by the Severe Respiratory Insufficiency questionnaire, containing 49 items and seven subdomains. Linear mixed effects models were used to measure changes and identify factors for changes. After 6 years, 60 patients were still participating, out of 127 at baseline. Health-related quality of life improved significantly in the total score and in four subdomains of the questionnaire. Satisfaction with training in long-term mechanical ventilation was an explanatory variable for improved 'psychological well-being' and follow-up for improvement of 'anxiety'. Side effects of the treatment like facial soreness were associated with the total score. High age and high forced vital capacity were related to lower 'physical function' and improved 'social functioning', respectively. Long-term mechanical ventilation over 6 years improved health-related quality of life in most patients. Patient training, follow-up and reduction of side effects, largely delivered by trained nurses, contribute to achieve the main goal of the treatment-improved health-related quality of life.


Simulating rainbows in their atmospheric environment.
Light and color of geometric optics rainbows are simulated in their atmospheric environment. Sunlight passes through a molecular atmosphere with ozone and an aerosol layer near the ground to strike a cuboidal rain shaft below an overhanging cuboidal cloud. The rainbows are treated as singly scattered sunbeams that are depleted as they pass through the atmosphere and rain shaft. They appear in a setting illuminated by scattered light from behind the observer, from the background beyond the rain shaft, and from the rain shaft. In dark backgrounds the primary and secondary bows first become visible when the optical thickness of rain shafts tau(R) congruent with 0.0003 and tau(R) congruent with 0.003, respectively. The bows are brightest and most colorful for 0.1<or= tau(R) <or= 3, a range that is typical for most showers. The peaks of the scattering phase function for raindrops that correspond to the geometric optics rainbow are so pronounced that rainbows remain bright and colorful for optically thick rain shafts seen against dark backgrounds, but the bows appear washed out or vanish as the background brightens or where the rain shaft is shaded by an overhanging cloud. Rainbows also redden as the Sun approaches the horizon.


Does Mental Fatigue Negatively Affect Outcomes of Functional Performance Tests?
Mental fatigue impairs psychomotor skill performance by affecting visuomotor reaction time, accuracy, and decision-making. Recently, neurocognitive functional performance tests (FPT) that integrate these outcomes have been developed. The aim of this study was to assess the effect of mental fatigue on traditional and neurocognitive FPT in healthy adults. Fourteen volunteers (four women; mean ± SD age, 22 ± 1 yr; height, 176.9 ± 8.4 cm; weight, 69.7 ± 10.4 kg) participated in a randomized counterbalanced crossover design. A 100% incongruent Stroop color word test of 90 min was used to induce mental fatigue and the control task encompassed watching a 90-min documentary. Traditional FPT comprised a single-leg hop for distance, countermovement jump, and Y-balance test, whereas the neurocognitive FPT encompassed the reactive balance test (RBT). All FPTs were evaluated pre-post the 90-min task. Mental fatigue was assessed using the Stroop task, visual analog scale for mental fatigue, and the Eriksen-Flanker task. Mental fatigue was successfully induced, as shown by a significant increase in visual analog scale for mental fatigue (P < 0.001), with no decrease in performance on the Stroop and Eriksen-Flanker task. No interaction effect of mental fatigue was found for the Y-balance test, single-leg hop, and countermovement jump. For the RBT accuracy, a significant interaction effect of mental fatigue and time was observed (P = 0.024), with participants performing significantly worse when mentally fatigued. No interaction effect or main effect of condition and time was observed when considering the effect of mental fatigue on visuomotor reaction time in the RBT. Mental fatigue negatively affects a neurocognitive FPT, indicated by a decreased accuracy in response to visual stimuli in the RBT. Traditional FPT remained unaffected by mental fatigue.


Stabilization of electrocatalytic metal nanoparticles at metal-metal oxide-graphene triple junction points.
Carbon-supported precious metal catalysts are widely used in heterogeneous catalysis and electrocatalysis, and enhancement of catalyst dispersion and stability by controlling the interfacial structure is highly desired. Here we report a new method to deposit metal oxides and metal nanoparticles on graphene and form stable metal-metal oxide-graphene triple junctions for electrocatalysis applications. We first synthesize indium tin oxide (ITO) nanocrystals directly on functionalized graphene sheets, forming an ITO-graphene hybrid. Platinum nanoparticles are then deposited, forming a unique triple-junction structure (Pt-ITO-graphene). Our experimental work and periodic density functional theory (DFT) calculations show that the supported Pt nanoparticles are more stable at the Pt-ITO-graphene triple junctions. Furthermore, DFT calculations suggest that the defects and functional groups on graphene also play an important role in stabilizing the catalysts. These new catalyst materials were tested for oxygen reduction for potential applications in polymer electrolyte membrane fuel cells, and they exhibited greatly enhanced stability and activity.


Prevalence of autoimmune thyroid dysfunction in postpartum psychosis.
Postpartum psychosis is a life-threatening psychiatric emergency, which often occurs without significant premorbid symptoms. Although many studies have postulated an involvement of the immune and endocrine systems in the onset of postpartum psychosis, the specific aetiological factors have remained unknown. To examine the hypothesis that autoimmune thyroid dysfunction may be associated with the onset of postpartum psychosis. Thirty-one consecutive primiparous women with no prior psychiatric history were referred to our in-patient unit for postpartum psychosis. The control group (n = 117) comprised primiparous women with consecutive deliveries at a community practice. Blood samples were obtained from all participants at 4 weeks and 9 months postpartum. Thyroperoxidase antibody levels were quantified as immunological measures of autoimmune thyroid disease (AITD). Thyroid-stimulating hormone and free thyroxine levels were measured to assess clinical thyroid dysfunction. At 4 weeks postpartum and prior to the initiation of mood stabiliser therapy, 19% of women with postpartum psychosis had AITD compared with only 5% in the control group. Women with both postpartum psychosis and AITD had a dramatically higher risk of progression to clinical thyroid dysfunction (67%) than control participants with AITD (20%). Women with postpartum psychosis are at higher risk not only of AITD but also of clinical thyroid failure. These data implicate thyroid function as an important clinical outcome in patients with postpartum psychosis. Further, AITD represents a potentially strong aetiological factor for the development of postpartum psychosis. Therefore, screening for thyroperoxidase antibodies is warranted in patients with postpartum psychosis.


Practice-related effects demonstrate complementary roles of anterior cingulate and prefrontal cortices in attentional control.
The purpose of this study was to test the hypothesis that the dorsolateral prefrontal cortex (DLFPC), not the anterior cingulate cortex (ACC), plays the predominant role in implementing top-down attentional control. To do so, we used fMRI to examine practice-related changes in neural activity during a variant of the Stroop task. The results indicated that the DLPFC's activity decreased gradually as the need for control was reduced (as indexed by behavioral measures), while the ACC's activity dropped off rapidly. Such a pattern is consistent with the DLPFC taking a leading role in implementing top-down attentional control and the ACC being involved in other aspects of attentional control, such as response-related processes. In addition, with practice, there was a reduction in activity within cortical systems handling the processing of task-irrelevant information capable of interfering with task performance. This finding suggests that with practice the brain is capable of identifying and strategically inhibiting such processing.


Colicin import into E. coli cells: a model system for insights into the import mechanisms of bacteriocins.
Bacteriocins are a diverse group of ribosomally synthesized protein antibiotics produced by most bacteria. They range from small lanthipeptides produced by lactic acid bacteria to much larger multi domain proteins of Gram negative bacteria such as the colicins from Escherichia coli. For activity bacteriocins must be released from the producing cell and then bind to the surface of a sensitive cell to instigate the import process leading to cell death. For over 50years, colicins have provided a working platform for elucidating the structure/function studies of bacteriocin import and modes of action. An understanding of the processes that contribute to the delivery of a colicin molecule across two lipid membranes of the cell envelope has advanced our knowledge of protein-protein interactions (PPI), protein-lipid interactions and the role of order-disorder transitions of protein domains pertinent to protein transport. In this review, we provide an overview of the arrangement of genes that controls the synthesis and release of the mature protein. We examine the uptake processes of colicins from initial binding and sequestration of binding partners to crossing of the outer membrane, and then discuss the translocation of colicins through the cell periplasm and across the inner membrane to their cytotoxic site of action. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.


Factors associated with hepatitis C viremia in a large cohort of HIV-infected and -uninfected women.
Co-infection with hepatitis C virus (HCV) is common among HIV-infected women. To further our understanding of the risk factors for HCV viremia and the predictors of HCV viral load among women. We investigated sociodemographic, immunologic, and virologic factors associated with presence and level of HCV viremia among 1049 HCV-seropositive women, 882 of whom were HIV-infected and 167 HIV-uninfected at their entry into the Women's Interagency HIV Study. Plasma HCV RNA was detected in 852 (81%) of these 1049 women (range: 1.2-7.8 log(10)copies/ml). HCV-viremic women were more likely to have an HIV RNA level >100,000 copies/ml (P=0.0004), to have reported smoking (P=0.01), or to be Black (P=0.005). They were less likely to have current or resolved hepatitis B infection. HCV RNA levels were higher in women who were >35 years old, or HIV-infected. Current smoking and history of drug use (crack/freebase cocaine, marijuana, amphetamines, or heroin) were each associated with both presence and level of viremia. Substance abuse counseling aimed at eliminating ongoing use of illicit drugs and tobacco may reduce clinical progression, improve response to treatment, and decrease HCV transmission by lowering levels of HCV viremia in women.


Noncovalently bound excited-state dimers: a perspective on current time-dependent density functional theory approaches applied to aromatic excimer models.
Excimers are supramolecular systems whose binding strength is influenced by many factors that are ongoing challenges for computational methods, such as charge transfer, exciton coupling, and London dispersion interactions. Treating the various intricacies of excimer binding at an adequate level is expected to be particularly challenging for time-dependent Density Functional Theory (TD-DFT) methods. In addition to well-known limitations for some TD-DFT methods in the description of charge transfer or exciton coupling, the inherent London dispersion problem from ground-state DFT translates to TD-DFT. While techniques to appropriately treat dispersion in DFT are well-developed for electronic ground states, these dispersion corrections remain largely untested for excited states. Herein, we aim to shed light on current TD-DFT methods, including some of the newest developments. The binding of four model excimers is studied across nine density functionals with and without the application of additive dispersion corrections against a wave function reference of SCS-CC2/CBS(3,4) quality, which approximates select CCSDR(3)/CBS data adequately. To our knowledge, this is the first study that presents single-reference wave function dissociation curves at the complete basis set level for the assessed model systems. It is also the first time range-separated double-hybrid density functionals are applied to excimers. In fact, those functionals turn out to be the most promising for the description of excimer binding followed by global double hybrids. Range-separated and global hybrids-particularly with large fractions of Fock exchange-are outperformed by double hybrids and yield worse dissociation energies and inter-molecular equilibrium distances. The deviation between each assessed functional and reference increases with system size, most likely due to missing dispersion interactions. Additive dispersion corrections of the DFT-D3(BJ) and DFT-D4 types reduce the average errors for TD-DFT methods but do so inconsistently and therefore do not offer a black-box solution in their ground-state parametrised form. The lack of appropriate description of dispersion effects for TD-DFT methods is likely hindering the practical application of the herein identified more efficient methods. Dispersion corrections parametrised for excited states appear to be an important next step to improve the applicability of TD-DFT methods and we hope that our work assists with the future development of such corrections.


Enhanced saccadic control in young people with Tourette syndrome despite slowed pro-saccades.
Tourette syndrome (TS) is a neurodevelopmental disorder characterized by motor and vocal tics. Tics are repetitive and uncontrolled behaviours that have been associated with basal ganglia dysfunction. We investigated saccadic eye movements in a group of young people with TS but without co-morbid ADHD. Participants performed two tasks. One required them to perform only pro-saccade responses (pure pro-saccade task). The other involved shifting, unpredictably, between executing pro- and anti-saccades (mixed saccade task). We show that in the mixing saccade task, the TS group makes significantly fewer errors than an age-matched control group, while responding equally fast. By contrast, on the pure pro-saccade task, the TS group were shown to be significantly slower to initiate and to complete the saccades (longer movement duration and decreased peak velocity) than controls, while movement amplitude and direction accuracy were not different. These findings demonstrate enhanced shifting ability despite slower reflexive responding in TS and are discussed with respect to a disorder-related adaptation for increased cognitive regulation of behaviour.


Chlorella virus Marburg topoisomerase II: high DNA cleavage activity as a characteristic of Chlorella virus type II enzymes.
Although the formation of a covalent enzyme-cleaved DNA complex is a prerequisite for the essential functions of topoisomerase II, this reaction intermediate has the potential to destabilize the genome. Consequently, all known eukaryotic type II enzymes maintain this complex at a low steady-state level. Recently, however, a novel topoisomerase II was discovered in Paramecium bursaria chlorella virus-1 (PBCV-1) that has an exceptionally high DNA cleavage activity [Fortune et al. (2001) J. Biol. Chem. 276, 24401-24408]. If robust DNA cleavage is critical to the physiological functions of chlorella virus topoisomerase II, then this remarkable characteristic should be conserved throughout the viral family. Therefore, topoisomerase II from Chlorella virus Marburg-1 (CVM-1), a distant family member, was expressed in yeast, isolated, and characterized. CVM-1 topoisomerase II is 1058 amino acids in length, making it the smallest known type II enzyme. The viral topoisomerase II displayed a high DNA strand passage activity and a DNA cleavage activity that was approximately 50-fold greater than that of human topoisomerase IIalpha. High DNA cleavage appeared to result from a greater rate of scission rather than promiscuous DNA site utilization, inordinately tight DNA binding, or diminished religation rates. Despite the fact that CVM-1 and PBCV-1 topoisomerase II share approximately 67% amino acid sequence identity, the two enzymes displayed clear differences in their DNA cleavage specificity/site utilization. These findings suggest that robust DNA cleavage is intrinsic to the viral enzyme and imply that chlorella virus topoisomerase II plays a physiological role beyond the control of DNA topology.


A Mixed-Methods Study to Examine the Role of Psychosocial Stress and Air Pollution on Hypertension in Mexican-Origin Hispanics.
Independent and combined effects of air pollution and psychosocial stressors on hypertension, a risk factor for cardiovascular disease, among Hispanics are not well studied. We administered a pilot-tested questionnaire on individual- and neighborhood-level psychosocial stressors, developed with community input, to nearly 2500 individuals from the MD Anderson Cancer Center cohort of Mexican-Americans. We used data from local air quality monitors to estimate individual exposures to ozone (O3) and fine particulate matter (PM2.5) for the 12-month period preceding enrollment using inverse distance interpolation. We applied logistic regression models to examine relationships between exposures to psychosocial stressors and air pollution with prevalent hypertension and used stratified analyses to examine the interacting effects of these two exposures on hypertension. RESULTS: There was a positive association between prevalent hypertension and a high frequency of feeling anxious or depressed (prevalence odds ratio (POR) = 1.36, 95% CI [1.06-1.75]) and experiencing aches and pains (POR = 1.29, 95% CI [1.01-1.64]). The odds of having hypertension were also elevated among those worrying about their own health (POR = 1.65, 95% CI [1.30-2.06]) or about not having enough money (POR = 1.27, 95% CI [1.01-1.6]). We observed an inverse association between O3 and hypertension. There was no interaction between psychosocial stressors and O3 on hypertension. Our findings add to the evidence of a positive association between individual and family stressors on hypertension among Hispanics and other racial/ethnic groups. Contrary to previous studies reporting positive associations, our results suggest that long-term exposure to O3 may be inversely related to prevalent hypertension.


Characterizing cryogenic amplifiers with a matched temperature-variable noise source.
We present a cryogenic microwave noise source with a characteristic impedance of 50 Ω, which can be installed in a coaxial line of a cryostat. The bath temperature of the noise source is continuously variable between 0.1 K and 5 K without causing significant back-action heating on the sample space. As a proof-of-concept experiment, we perform Y-factor measurements of an amplifier cascade that includes a traveling wave parametric amplifier and a commercial high electron mobility transistor amplifier. We observe system noise temperatures as low as 680-200 +20 mK at 5.7 GHz corresponding to 1.5-0.7 +0.1 excess photons. The system we present has immediate applications in the validation of solid-state qubit readout lines.


Binding and selectivity of the marine toxin neodysiherbaine A and its synthetic analogues to GluK1 and GluK2 kainate receptors.
Dysiherbaine (DH) and neodysiherbaine A (NDH) selectively bind and activate two kainate-type ionotropic glutamate receptors, GluK1 and GluK2. The ligand-binding domains of human GluK1 and GluK2 were crystallized as bound forms with a series of DH analogues including DH, NDH, 8-deoxy-NDH, 9-deoxy-NDH and 8,9-dideoxy-NDH (MSVIII-19), isolated from natural sources or prepared by total synthesis. Since the DH analogues exhibit a wide range of binding affinities and agonist efficacies, it follows that the detailed analysis of crystal structure would provide us with a significant opportunity to elucidate structural factors responsible for selective binding and some aspects of gating efficacy. We found that differences in three amino acids (Thr503, Ser706 and Ser726 in GluK1 and Ala487, Asn690 and Thr710 in GluK2) in the ligand-binding pocket generate differences in the binding modes of NDH to GluK1 and GluK2. Furthermore, deletion of the C(9) hydroxy group in NDH alters the ligand conformation such that it is no longer suited for binding to the GluK1 ligand-binding pocket. In GluK2, NDH pushes and rotates the side chain of Asn690 (substituted for Ser706 in GluK1) and disrupts an interdomain hydrogen bond with Glu409. The present data support the idea that receptor selectivities of DH analogues resulted from the differences in the binding modes of the ligands in GluK1/GluK2 and the steric repulsion of Asn690 in GluK2. All ligands, regardless of agonist efficacy, induced full domain closure. Consequently, ligand efficacy and domain closure did not directly coincide with DH analogues and the kainate receptors.


Changes in weight and weight-related quality of life in a multicentre, randomized trial of aripiprazole versus standard of care.
This is a secondary analysis of clinical trial data collected in 12 European countries. We examined changes in weight and weight-related quality of life among community patients with schizophrenia treated with aripiprazole (ARI) versus standard of care (SOC), consisting of other marketed atypical antipsychotics (olanzapine, quetiapine, and risperidone). Five-hundred and fifty-five patients whose clinical symptoms were not optimally controlled and/or experienced tolerability problems with current medication were randomized to ARI (10-30 mg/day) or SOC. Weight and weight-related quality of life (using the IWQOL-Lite) were assessed at baseline, and weeks 8, 18 and 26. Random regression analysis across all time points using all available data was used to compare groups on changes in weight and IWQOL-Lite. Meaningful change from baseline was also assessed. Participants were 59.7% male, with a mean age of 38.5 years (SD 10.9) and mean baseline body mass index of 27.2 (SD 5.1). ARI participants lost an average of 1.7% of baseline weight in comparison to a gain of 2.1% by SOC participants (p<0.0001) at 26 weeks. ARI participants experienced significantly greater increases in physical function, self-esteem, sexual life, and IWQOL-Lite total score. At 26 weeks, 20.7% of ARI participants experienced meaningful improvements in IWQOL-Lite score, versus 13.5% of SOC participants. A clinically meaningful change in weight was also associated with a meaningful change in quality of life (p<0.001). A potential limitation of this study was its funding by a pharmaceutical company. Compared to standard of care, patients with schizophrenia treated with aripiprazole experienced decreased weight and improved weight-related quality of life over 26 weeks. These changes were both statistically and clinically significant.


HIF-1α promotes autophagic proteolysis of Dicer and enhances tumor metastasis.
HIF-1α, one of the most extensively studied oncogenes, is activated by a variety of microenvironmental factors. The resulting biological effects are thought to depend on its transcriptional activity. The RNAse enzyme Dicer is frequently downregulated in human cancers, which has been functionally linked to enhanced metastatic properties; however, current knowledge of the upstream mechanisms regulating Dicer is limited. In the present study, we identified Dicer as a HIF-1α-interacting protein in multiple types of cancer cell lines and different human tumors. HIF-1α downregulated Dicer expression by facilitating its ubiquitination by the E3 ligase Parkin, thereby enhancing autophagy-mediated degradation of Dicer, which further suppressed the maturation of known tumor suppressors, such as the microRNA let-7 and microRNA-200b. Consequently, expression of HIF-1α facilitated epithelial-mesenchymal transition (EMT) and metastasis in tumor-bearing mice. Thus, this study uncovered a connection between oncogenic HIF-1α and the tumor-suppressive Dicer. This function of HIF-1α is transcription independent and occurs through previously unrecognized protein interaction-mediated ubiquitination and autophagic proteolysis.


Cellular, subcellular, and subsynaptic distribution of AMPA-type glutamate receptor subunits in the neostriatum of the rat.
Glutamate released in the basal ganglia is involved in the expression of clinical symptoms of neurodegenerative diseases like Parkinson's or Huntington's. Neostriatal neurons are the targets of glutamatergic inputs derived from the cortex and the thalamus acting via AMPA-type as well as other glutamate receptors. To determine the location of subunits of the AMPA subclass of glutamate receptors (GluR) in the rat neostriatum, we applied multiple immunocytochemical techniques using anti-peptide antibodies against the GluR1, GluR2/3, and GluR4 subunits at both the light and electron microscopic levels. All medium spiny efferent neurons, some of which were identified as striatonigral neurons, displayed immunoreactivity for GluR1 and GluR2/3 subunits. Double immunofluorescence revealed that at least 70-90% of parvalbumin-immunopositive GABAergic interneurons were immunoreactive for each of GluR1, GluR2/3, or GluR4 subunits and that at least 40% of choline acetyltransferase-immunopositive cholinergic interneurons were immunopositive for GluR1 or GluR4 subunits. The majority of nitric oxide synthase-immunopositive neurons had no detectable immunoreactivity for any of the AMPA receptor subunits. Electron microscopic analysis confirmed the presence of immunoreactivity for GluR1 and GluR2/3 in the perikarya of spiny neurons and interneurons and GluR4 in perikarya of interneurons only. GluR1 and GluR2/3 subunits were detected in dendrites and spines. A significant population of extrasynaptic receptors was revealed by pre-embedding immunogold labeling along the plasma membranes of perikarya, dendrites, and spines. Receptors were concentrated in the postsynaptic membrane specialization of asymmetrical synapses, as revealed by the postembedding immunogold method. Quantitative analysis demonstrated that immunoreactivity for the GluR1 and GluR2/3 subunits is higher at the periphery than at the middle of the postsynaptic membrane specialization. Our results demonstrate that AMPA receptor subunits are distributed widely and heterogeneously among striatal neurons and are concentrated on the postsynaptic membrane of asymmetrical synaptic specializations, although extrasynaptic receptors are also present.


Characterizing the effects of heparin gel stiffness on function of primary hepatocytes.
In the liver, hepatocytes are exposed to a large array of stimuli that shape hepatic phenotype. This in vivo microenvironment is lost when hepatocytes are cultured in standard cell cultureware, making it challenging to maintain hepatocyte function in vitro. Our article focused on one of the least studied inducers of the hepatic phenotype-the mechanical properties of the underlying substrate. Gel layers comprised of thiolated heparin (Hep-SH) and diacrylated poly(ethylene glycol) (PEG-DA) were formed on glass substrates via a radical mediated thiol-ene coupling reaction. The substrate stiffness varied from 10 to 110 kPa by changing the concentration of the precursor solution. ELISA analysis revealed that after 5 days, hepatocytes cultured on a softer heparin gel were synthesizing five times higher levels of albumin compared to those on a stiffer heparin gel. Immunofluorescent staining for hepatic markers, albumin and E-cadherin, confirmed that softer gels promoted better maintenance of the hepatic phenotype. Our findings point to the importance of substrate mechanical properties on hepatocyte function.


Overnight urinary isoflavone excretion in a population of women living in the United States, and its relationship to isoflavone intake.
Dietary isoflavones are biologically active in humans, but few observational data exist on the relationship between isoflavone intake and excretion in Western populations. We examined associations between self-reported soy intakes and overnight urinary isoflavone excretion in a population-based sample of western Washington State women, and we investigated the usefulness of one versus two overnight urine samples, collected 48 h apart, as a biomarker of intake. Isoflavones (genistein, daidzein, O-desmethylangolensin, and equol) were measured in two overnight urine collections from 363 women recruited from a health maintenance organization. Soy food intakes were assessed using two 1-day diet records completed on each day prior to the urine collections and a food frequency questionnaire (FFQ) that had been completed by 312 of the women with regard to their dietary habits 3.5 years (range, 2-5 years) before the urine collections. Twenty-one percent of the women consumed soy on either day of the diet recall, and 13% and 34% of the women consumed soy at least once a week or at least once a month, respectively, according to the FFQ. Women who consumed soy at either of the two diet recalls or at the FFQ (at least once a week or at least once a month) had a significantly higher urinary excretion of isoflavones than women who did not consume soy (P < 0.01). Among women who consumed soy at either of the two diet recalls or at the FFQ (soy consumed at least once a month), isoflavone intake and excretion correlated significantly (P < 0.01). Excretion of the individual isoflavones correlated significantly between the two urine samples collected 48 h apart (genistein, r = 0.41 and P < 0.001; daidzein, r = 0.30 and P < 0.001; O-desmethylangolensin, r = 0.46 and P < 0.001; equol, r = 0.60 and P < 0.001). Differences between soy consumers and nonconsumers and associations between intakes and excretion remained significant whether one or both urine collections were considered. Measuring isoflavone excretion in one overnight urine collection serves as a biomarker of recent or past isoflavone intake, even in populations whose intake of soy foods is relatively low.


Roles of serum and biliary CEA, CA19-9, VEGFR3, and TAC in differentiating between malignant and benign biliary obstructions.
Despite the presence of many diagnostic methods, the differential diagnosis between benign and malignant biliary obstructions is still not easy. We aimed to evaluate the role of serum/biliary carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA 19-9), vascular endothelial growth factor receptor-3(VEGFR-3), and total antioxidant capacity (TAC) tests in this differential diagnosis. Patients (n:225; 110♂, 115♀) with diagnosis of malignant (n:96) or benign (n:129) biliary obstruction were included in this cross-sectional study. Serum and biliary CEA, CA 19-9, VEGFR-3, and TAC tests were analyzed, statistics were obtained, and significance was defined as p<0.05. Mean age was 54.9±16.4 for the benign and 54.2±19.6 for the malignant group (p=0.89). Head of pancreas cancer (18.2%), cholangiocarcinoma (11.4%) and choledochal stone (48%) were the most common etiologies. The area under the curve (AUC)s by ROC analysis of serum/biliary CA 19-9, VEGFR-3, and TAC and serum CEA were 0.701/0.616, 0.622/0.663, 0.602/0.581, and 0713, respectively. Serum TAC had higher sensitivity (61.1%) and CEA had lower sensitivity (42.7%), whereas CEA had higher specificity (89.9%) and TAC had lower specificity (60.5%). In biliary tumor markers, CA 19-9 had higher sensitivity (74%) and VEGFR-3 had lower sensitivity (56.2%); however, VEGFR-3 had higher specificity (79.1%) and CA 19-9 had lower specificity (34.1%). Additionally, combination of serum CEA (p<0.001), CA 19-9 (p<0.001), VEGFR-3 (p<0.001), and biliary CA 19-9 (p=0.028) markers achieved 95% estimation probability, and the sensitivity, specificity, and accuracy were 88.5%, 45.7%, and 64%, respectively. Serum and biliary CEA, CA 19-9, VEGFR-3, and TAC tests would not be useful in the differentiation between malignant and benign biliary obstructions.


Ecological stress and sex evolution in soil microfungi.
The elucidation of the origin and maintenance of sex is a major unsolved problem in evolutionary biology. A number of hypotheses have been elaborated, but the scarcity of empirical data limits further progress. During recent years, the general inclination has changed towards pluralistic models of sex evolution, due partly to an increased diversity of studied organisms. Fungi are among the most promising organisms for testing sexual causation, as demonstrated in recent laboratory experiments. However, reconciling theory and evidence necessitates critical field observations. Here, we report new estimates of the distribution of morphologically sexual and asexual soil microfungi in nature, which indicate a remarkable trend towards increased sexuality with increasing climatic stress.


Enhanced ghrelin secretion in rats with cysteamine-induced duodenal ulcers.
Ghrelin, produced and secreted by the A-like cells of the stomach, stimulates growth hormone secretion, gastric motility, and food intake. Cysteamine inhibits the release of somatostatin and induces the formation of duodenal ulcers in rats. The present study was conducted to investigate the dynamics of ghrelin secretion in rats treated with cysteamine. Male Wistar rats (7 wk old) were administered three doses of cysteamine (400 mg/kg) orally; at 50 h after the first dose, duodenal ulcers were induced, and the plasma level of somatostatin and gastric density of somatostatin-immunoreactive cells were significantly reduced. The plasma total and active ghrelin levels were significantly higher in the cysteamine-treated rats than in the control rats, whereas the gastric ghrelin levels, number of gastric ghrelin-immunoreactive cells, and preproghrelin mRNA expression levels were significantly lower. Even at the time points of 2 and 10 h after the first dose of cysteamine, at which time no significant ulcer formation or antral neutrophil accumulation was yet noted, a significant increase in the plasma ghrelin level and decrease in the gastric ghrelin level were observed. Furthermore, although lansoprazole treatment attenuated the duodenal ulceration induced by cysteamine, the increase in the plasma level of ghrelin could still be demonstrated. Because an inverse correlation was found between the plasma ghrelin and somatostatin levels, the inhibition of somatostatin secretion may be associated with the increased ghrelin secretion. In conclusion, an increase in the plasma ghrelin level precedes the formation of duodenal ulcers in rats treated with cysteamine.


Suicidality and antiepileptic drugs: is there a link?
The main purpose of the present article is to review the possible risk factors for suicidal behaviour in epilepsy with a special emphasis on the different antiepileptic drugs (AEDs). Epidemiological data show that, in general, the suicide rate among patients with epilepsy is 5-fold higher than that in the general population, while in temporal lobe epilepsy and complex partial seizures it is approximately 25-fold higher. A certain psychiatric comorbidity may provoke suicidality in patients with epilepsy, and depression and cognitive impairment seem to be the main risk factors for suicidality in epilepsy. In addition, depression and cognitive deterioration in epilepsy may share common neuropsychological mechanisms in terms of hypofrontality. This may cause similar psychopathological signs in both diagnostic categories, including suicidality. Analysis of the literature has shown that serotonin metabolism disturbances are involved in the pathogenesis of suicidal behaviour irrespective of primary diagnosis. Serotonin disturbances also seem to be a common link between depression, suicidality and even epilepsy itself. The various AEDs differ not only in their mechanisms of action, but also in influences on cognition and mood in epileptic patients and suicidality, respectively. Until now, only Ketter's hypothesis has been proposed to explain the psychotropic effects of different AEDs, although it does not explain the positive psychotropic effects of some AEDs, such as carbamazepine and oxcarbazepine. According to this model, all psychotropic effects of AEDs may be the result of effects on the function of two types of receptor functions: gamma-aminobutyric acid (GABA) ergic and antiglutamatergic; other possible mechanisms have not been incorporated. Presumably, other neurochemical mechanisms, and a serotonergic mechanism in particular, should also be taken into account when explaining the psychotropic effects of different AEDs. Based on these data, it has been suggested that AEDs with certain serotonergic properties should reduce the suicidality risk because they exert effects similar to antidepressants (i.e. selective serotonin reuptake inhibitors), whereas AEDs that lack serotonergic mechanisms would not be effective in suicidality prevention. In line with this paradigm, phenobarbital and phenytoin seem to be the only drugs with proven suicidality risk. On the other hand, carbamazepine, oxcarbazepine, valproate and lamotrigine could be regarded as drugs with antisuicidal properties because they all improve cognitive functions and mood in epileptic patients, and possess serotonergic mechanisms of action. The other AEDs, including topiramate, tiagabine, vigabatrin, levetiracetam and zonisamide, all exert negative effects on mood and cognition, although their influence on suicidality has not been proven in evidence-based studies yet. Although zonizamide has serotonergic properties, it exerts negative psychotropic effects, whereas gabapentin is devoid of serotonergic properties but has positive psychotropic effects on mood and cognition. To more fully explain the positive and negative psychotropic effects and influence on suicidality of AEDs, Ketter's paradigm should be supplemented by an understanding of the serotonergic mechanisms of different AEDs. Further trials are required to prove or refute this model.


A critical role for extracellular protein disulfide isomerase during thrombus formation in mice.
Thiol isomerases, including protein disulfide isomerase (PDI), catalyze disulfide oxidation, reduction, and isomerization, thereby playing an important role in protein synthesis. To determine whether extracellular PDI mediates thrombus formation in an animal model, PDI expression, platelet accumulation, and fibrin generation were monitored in the blood vessels of mice by intravital fluorescence microscopy following laser-induced arteriolar injury. A time-dependent increase in PDI was observed in murine thrombi following injury. Infusion of the PDI inhibitor bacitracin or a blocking monoclonal antibody against PDI inhibited platelet thrombus formation and fibrin generation. Fibrin deposition is normal in mice lacking the G protein-coupled platelet receptor Par4, although there is no stable accumulation of platelets. Infusion of monoclonal antibodies against PDI into the circulation of Par4(-/-) mice prior to vessel wall injury inhibited fibrin generation. These results indicate that PDI is required in vivo in mice for both fibrin generation and platelet thrombus formation.


Family planning and resilience: associations found in a Population, Health, and Environment (PHE) project in Western Tanzania.
Using 2016 household survey data from Tanzania, we define and measure resilience within the context of Population, Health, and Environment programming and quantify the link between resilience and family planning. We created a multicomponent model using confirmatory factor analysis in a structural equation modeling context. Factor loadings for eight defined latent factors of resilience were statistically significant (p < 0.001). We created a factor called "FP-MCH" reflecting awareness, attitudes, and access to family planning (FP) and health care services and use of maternal and child health care (MCH) facilities. Analysis, with controls, shows that a 1 standard deviation (SD) increase in FP/MCH was associated with a 0.68 SD increase in resilience (p < 0.01), suggesting that the association between FP/MCH and resilience is robust across a range of factors. Analyses showed that the association between FP/MCH is broadly related to the construct of resilience and not through any single component. This study supports the importance of including FP/MCH as part of integrated projects to enhance resilience.


Factors associated with comfort level of occupational therapy practitioners in providing low vision services.
OBJECTIVE. We describe the perceived adequacy of educational preparation for and comfort level of occupational therapy practitioners in providing services to clients with low vision and identify factors associated with the practitioners' comfort level. METHOD. One hundred occupational therapists who were not specialists in low vision rehabilitation completed a survey. RESULTS. Fifty-two percent of the respondents perceived that they had received adequate preparation in occupational therapy school to address low vision. Between 54% and 63% of respondents were comfortable performing visual screening and providing interventions for clients with low vision. Multivariable analyses indicated that having received adequate preparation in occupational therapy school, having a partnership with an eye-care professional, and having provided services to a larger percentage of clients with low vision were significantly associated with perceived comfort in providing services to this population. CONCLUSION. Findings provide an initial direction to improve low vision content in occupational therapy education curricula.


Population expansion, clonal growth, and specific differentiation patterns in primary cultures of hepatocytes induced by HGF/SF, EGF and TGF alpha in a chemically defined (HGM) medium.
Mature adult parenchymal hepatocytes, typically of restricted capacity to proliferate in culture, can now enter into clonal growth under the influence of hepatocyte growth factor (scatter factor) (HGF/SF), epidermal growth factor (EGF), and transforming growth factor alpha (TGFalpha) in the presence of a new chemically defined medium (HGM). The expanding populations of hepatocytes lose expression of hepatocyte specific genes (albumin, cytochrome P450 IIB1), acquire expression of markers expressed by bile duct epithelium (cytokeratin 19), produce TGFalpha and acidic FGF and assume a very simplified morphologic phenotype by electron microscopy. A major change associated with this transition is the decrease in ratio between transcription factors C/EBPalpha and C/EBPbeta, as well as the emergence in the proliferating hepatocytes of transcription factors AP1, NFkappaB. The liver associated transcription factors HNFI, HNF3, and HNF4 are preserved throughout this process. After population expansion and clonal growth, the proliferating hepatocytes can return to mature hepatocyte phenotype in the presence of EHS gel (Matrigel). This includes complete restoration of electron microscopic structure and albumin expression. The hepatocyte cultures however can instead be induced to form acinar/ductular structures akin to bile ductules (in the presence of HGF/SF and type I collagen). These transformations affect the entire population of the hepatocytes and occur even when DNA synthesis is inhibited. Similar acinar/ductular structures are seen in embryonic liver when HGF/SF and its receptor are expressed at high levels. These findings strongly support the hypothesis that mature hepatocytes can function as or be a source of bipotential facultative hepatic stem cells (hepatoblasts). These studies also provide evidence for the growth factor and matrix signals that govern these complex phenotypic transitions of facultative stem cells which are crucial for recovery from acute and chronic liver injury.


B1 lymphocytes develop independently of Notch signaling during mouse embryonic development.
B1 lymphocytes are a small but unique component of the innate immune-like cells. However, their ontogenic origin is still a matter of debate. Although it is widely accepted that B1 cells originate early in fetal life, whether or not they arise from hematopoietic stem cells (HSCs) is still unclear. In order to shed light on the B1 cell origin, we set out to determine whether their lineage specification is dependent on Notch signaling, which is essential for the HSC generation and, therefore, all derivatives lineages. Using mouse embryonic stem cells (mESCs) to recapitulate murine embryonic development, we have studied the requirement for Notch signaling during the earliest B-cell lymphopoiesis and found that Rbpj-deficient mESCs are able to generate B1 cells. Their Notch independence was confirmed in ex vivo experiments using Rbpj-deficient embryos. In addition, we found that upregulation of Notch signaling induced the emergence of B2 lymphoid cells. Taken together, these findings indicate that control of Notch signaling dose is crucial for different B-cell lineage specification from endothelial cells and provides pivotal information for their in vitro generation from PSCs for therapeutic applications. This article has an associated 'The people behind the papers' interview.


Bipartite Community Structure of eQTLs.
Genome Wide Association Studies (GWAS) and expression quantitative trait locus (eQTL) analyses have identified genetic associations with a wide range of human phenotypes. However, many of these variants have weak effects and understanding their combined effect remains a challenge. One hypothesis is that multiple SNPs interact in complex networks to influence functional processes that ultimately lead to complex phenotypes, including disease states. Here we present CONDOR, a method that represents both cis- and trans-acting SNPs and the genes with which they are associated as a bipartite graph and then uses the modular structure of that graph to place SNPs into a functional context. In applying CONDOR to eQTLs in chronic obstructive pulmonary disease (COPD), we found the global network "hub" SNPs were devoid of disease associations through GWAS. However, the network was organized into 52 communities of SNPs and genes, many of which were enriched for genes in specific functional classes. We identified local hubs within each community ("core SNPs") and these were enriched for GWAS SNPs for COPD and many other diseases. These results speak to our intuition: rather than single SNPs influencing single genes, we see groups of SNPs associated with the expression of families of functionally related genes and that disease SNPs are associated with the perturbation of those functions. These methods are not limited in their application to COPD and can be used in the analysis of a wide variety of disease processes and other phenotypic traits.


Light-induced second-harmonic generation in azo-dye polymers.
The permanent all-optical poling of an azo-aromatic acrylic copolymer is experimentally demonstrated by seeding preparation in a backward phase-conjugation geometry. The microscopic mechanism involves an orientational hole burning followed by orientational redistribution caused by trans-to-cis isomerization of the azo-dye chromophores. The characteristic kinetics of monitored by second-harmonic generation.


COVID-19 and the policy sciences: initial reactions and perspectives.
The world is in the grip of a crisis that stands unprecedented in living memory. The COVID-19 pandemic is urgent, global in scale, and massive in impacts. Following Harold D. Lasswell's goal for the policy sciences to offer insights into unfolding phenomena, this commentary draws on the lessons of the policy sciences literature to understand the dynamics related to COVID-19. We explore the ways in which scientific and technical expertise, emotions, and narratives influence policy decisions and shape relationships among citizens, organizations, and governments. We discuss varied processes of adaptation and change, including learning, surges in policy responses, alterations in networks (locally and globally), implementing policies across transboundary issues, and assessing policy success and failure. We conclude by identifying understudied aspects of the policy sciences that deserve attention in the pandemic's aftermath.


Risk adjustment for inter-hospital comparison of caesarean delivery rates in low-risk deliveries.
Caesarean delivery (CD) rates have been frequently used as quality measures for maternity service comparisons. More recently, primary CD rates (CD in women without previous CD) or CD rates within selected categories such as nulliparous, term, cephalic singleton deliveries (NTCS) have been used. The objective of this study is to determine the extent to which risk adjustment for clinical and socio-demographic variables is needed for inter-hospital comparisons of CD rates in women without previous CD and in NTCS deliveries. Hospital discharge records of women who delivered in Emilia-Romagna Region (Italy) from January, 2007 to June 2009 and in Tuscany Region for year 2009 were linked with birth certificates. Adjusted RRs of CD in women without a previous Caesarean and NTCS were estimated using Poisson regression. Percentage differences in RR before and after adjustment were calculated and hospital rankings, based on crude and adjusted RRs, were examined. Adjusted RR differed substantially from crude RR in women without a previous Caesarean and only marginally in NTCS group. Hospital ranking was markedly affected by adjustment in women without a previous CD, but less in NTCS. Risk adjustment is warranted for inter-hospital comparisons of primary CD rates but not for NTCS CD rates. Crude NTCS CD rates are a reliable estimate of adjusted NTCS CD.


Immunolocalisation of E-cadherin and beta-catenin in human pterygium.
The pterygium represents an invasion of a wing of altered ocular surface tissue into the normal cornea. The head itself is slightly elevated and white, which is the only site of firm adhesion to the globe. The mechanisms of cell proliferation and adhesion in pterygium epithelium, however, are unknown. The aim of this study was to analyse the expression of cell adhesion molecules in pterygium tissues. Six pterygia were surgically removed using the bare-sclera procedure, and two normal corneas and a normal bulbar conjunctiva were also obtained. Formalin-fixed, paraffin-embedded tissues were analysed by immunohistochemistry with anti-E-cadherin and beta-catenin antibodies. Immunoreactivity for E-cadherin was not detected in the normal cornea and conjunctiva. In contrast, all corneal and conjunctival epithelial cells showed a weak homogeneous immunoreaction for beta-catenin on the cell membrane. In the pterygium head, the thickness was relatively marked compared with the body, and normal conjunctival and corneal epithelia. E-cadherin as well as beta-catenin was heterogeneously expressed in the cell membrane and cytoplasm of a variety of epithelial cells, whereas the expression was less marked in the body. Several epithelial cells showed intense nuclear immunoreactivity for beta-catenin. Immunoreactivity of beta-catenin, but not E-cadherin, was detected in only a few stromal cells, which were less marked than in epithelial cells. It is suggested that E-cadherin and beta-catenin are concentrated in pterygium tissue, and are possibly involved with epithelial proliferation and adhesion.


Identification of TEL-AML1 (ETV6-RUNX1) associated DNA and its impact on mRNA and protein output using ChIP, mRNA expression arrays and SILAC.
The contribution of the most common reciprocal translocation in childhood B-cell precursor leukemia t(12;21)(p13;q22) to leukemia development is still under debate. Direct as well as secondary indirect effects of the TEL-AML1 fusion protein are commonly recorded by using cell lines and patient samples, often bearing the TEL-AML1 fusion protein for decades. To identify direct targets of the fusion protein a short-term induction of TEL-AML1 is needed. We here describe in detail the experimental procedure, quality controls and contents of the ChIP, mRNA expression and SILAC datasets associated with the study published by Linka and colleagues in the Blood Cancer Journal [1] utilizing a short term induction of TEL-AML1 in an inducible precursor B-cell line model.


Selective COX-2 inhibition by a Pterocarpus marsupium extract characterized by pterostilbene, and its activity in healthy human volunteers.
In this study, an extract of Pterocarpus marsupium Roxb. containing pterostilbene has been evaluated for its PGE2-inhibitory activity in LPS-stimulated PBMC. In addition, the COX-1/2 selective inhibitory activity of P. marsupium (PM) extract was investigated. Biological activity, as well as safety of PM extract was evaluated in healthy human volunteers. PM extract, pterostilbene and resveratrol inhibited PGE2 production from LPS-stimulated human peripheral blood mononuclear cells (PBMC) with IC50 values of 3.2 +/- 1.3 microg/mL, 1.0 +/- 0.6 microM and 3.2 +/- 1.4 microM, respectively. When pterostilbene content of PM extract is calculated, PGE2 production inhibition of PM extract is comparable to PGE2 production inhibition of purified pterostilbene. Furthermore, in a COX-1 whole blood assay (WBA) PM extract was not effective while in a COX-2 WBA, PM extract decreased PGE2 production indicating COX-2 specific inhibition. In healthy human volunteers, the oral use of 450 mg PM extract did not decrease PGE2 production ex vivo in a WBA. Pterostilbene levels in serum were increased, but were 5-fold lower than the observed IC50 for PGE2 inhibition in LPS-stimulated PBMC. No changes from base-line of the safety parameters were observed and no extract-related adverse events occurred during the study. In conclusion, this is the first study to describe the selective COX-2 inhibitory activity of a Pterocarpus marsupium extract. Moreover, the PGE2 inhibitory activity of PM extract was related to its pterostilbene content. In humans, 450 mg PM extract resulted in elevated pterostilbene levels in serum, which were below the active concentration observed in vitro. In addition, short-term supplementation of 450 mg PM extract is considered to be a safe dose based on the long history of use, the absence of abnormal blood cell counts and blood chemistry values and the absence of extract-related adverse events. This strongly argues for a dose-finding study of PM extract in humans to corroborate the in vitro observed inhibitory activity on PGE2 production in order to resolve the potential use of PM extract in inflammatory disorders and/or inflammatory pain.


Facial emotion recognition from moving and static point-light images in schizophrenia.
It is well established that schizophrenia is associated with difficulties recognising facial expressions of emotion. It has been suggested that this impairment could be specific to moving faces [Archer, J., Hay, D., Young, A., 1994. Movement, face processing and schizophrenia: evidence of a differential deficit in expression analysis. British Journal of Clinical Psychology, 33, 517-528]. The current study used point-light images to assess whether people with schizophrenia can interpret emotions from isolated patterns of facial movement in the absence of featural cues. Emotion recognition from moving and static images was assessed using a forced choice design with two sets of three emotions (anger, sadness and surprise; disgust, fear and happiness). The schizophrenia group was significantly better at recognising the emotions from moving images than static images. Although the control group was more accurate overall than the schizophrenia group, both groups presented the same characteristic patterns of performance across tasks. For example, in terms of which emotions were better recognised than others and the types of misidentifications that were made. Hence, it is concluded that people with schizophrenia are sensitive to the motion patterns which underlie individual expressions of emotion and can use this information to accurately recognise emotions.


A DNA-dependent stress response involving DNA-PK occurs in hypoxic cells and contributes to cellular adaptation to hypoxia.
DNA-dependent protein kinase (DNA-PK) is involved in DNA double-strand break (DSB) signalling and repair. We report that DNA-PK is activated by mild hypoxia conditions (0.1-1% O₂) as shown by (1) its autophosphorylation on Ser2056, and (2) its mobilisation from a soluble nucleoplasmic compartment to a less extractable nuclear fraction. The recruitment of DNA-PK was not followed by activation and recruitment of the XRCC4-DNA-ligase-IV complex, suggesting that DSBs are not responsible for activation of DNA-PK. To unravel the mechanism of DNA-PK activation, we show that exposure of cells to trichostatin A, a histone deacetylase inhibitor, leads to DNA-PK autophosphorylation and relocalisation to DNA. Histone acetylation (mainly H3K14) is increased in hypoxic cells and treatment with anacardic acid, an inhibitor of histone acetyl transferase, prevented both histone modifications and DNA-PK activation in hypoxic conditions. Importantly, in using either silenced DNA-PK cells or cells exposed to a specific DNA-PK inhibitor (NU7026), we demonstrated that hypoxic DNA-PK activation positively regulates the key transcription factor HIF-1 and one subsequent target gene, GLUT1. Our results show that hypoxia initiates chromatin modification and consequently DNA-PK activation, which positively regulate cellular oxygen-sensing and oxygen-signalling pathways.


U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF(65) is faced with the paradoxical tasks of accurately targeting polypyrimidine (Py) tracts preceding 3' splice sites while adapting to both cytidine and uridine nucleotides with nearly equivalent frequencies. To understand how U2AF(65) recognizes degenerate Py tracts, we determined six crystal structures of human U2AF(65) bound to cytidine-containing Py tracts. As deoxy-ribose backbones were required for co-crystallization with these Py tracts, we also determined two baseline structures of U2AF(65) bound to the deoxy-uridine counterparts and compared the original, RNA-bound structure. Local structural changes suggest that the N-terminal RNA recognition motif 1 (RRM1) is more promiscuous for cytosine-containing Py tracts than the C-terminal RRM2. These structural differences between the RRMs were reinforced by the specificities of wild-type and site-directed mutant U2AF(65) for region-dependent cytosine- and uracil-containing RNA sites. Small-angle X-ray scattering analyses further demonstrated that Py tract variations select distinct inter-RRM spacings from a pre-existing ensemble of U2AF(65) conformations. Our results highlight both local and global conformational selection as a means for universal 3' splice site recognition by U2AF(65).


Pathomx: an interactive workflow-based tool for the analysis of metabolomic data.
Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility. However, the development of robust methods for the analysis of metabolomic data is a work-in-progress. The tools that do exist are often not well integrated, requiring manual data handling and custom scripting on a case-by-case basis. Furthermore, existing tools often require experience with programming environments such as MATLAB® or R to use, limiting accessibility. Here we present Pathomx, a workflow-based tool for the processing, analysis and visualisation of metabolomic and associated data in an intuitive and extensible environment. The core application provides a workflow editor, IPython kernel and a HumanCyc™-derived database of metabolites, proteins and genes. Toolkits provide reusable tools that may be linked together to create complex workflows. Pathomx is released with a base set of plugins for the import, processing and visualisation of data. The IPython backend provides integration with existing platforms including MATLAB® and R, allowing data to be seamlessly transferred. Pathomx is supplied with a series of demonstration workflows and datasets. To demonstrate the use of the software we here present an analysis of 1D and 2D (1)H NMR metabolomic data from a model system of mammalian cell growth under hypoxic conditions. Pathomx is a useful addition to the analysis toolbox. The intuitive interface lowers the barrier to entry for non-experts, while scriptable tools and integration with existing tools supports complex analysis. We welcome contributions from the community.


Geographic clustering and seroprevalence of schistosomiasis in Puerto Rico (1995).
A systematic, island-wide survey for schistosomiasis in Puerto Rico has not been conducted for more than 40 years. In 1974, a thorough survey of Boqueron de Las Piedras, a small community, showed a prevalence of 40%. No additional information on prevalence in Puerto Rico has been obtained during the ensuing 21 years. Concern for the public health of residents and visitors prompted the formation of the Bilharzia Commission in 1994 and the systematic serosurvey reported herein. Two thousand nine hundred fifty-five plasma samples from healthy donors were obtained randomly from the Red Cross in March and April 1995. Sex, resident municipalities, and age of the donors were recorded. The donors were from all but three of 79 municipalities in Puerto Rico. No sample was available from the three out island municipalities of Mona, Vieques, and Culebra. Male donors (n = 2,027) outnumbered females (n = 928) by more than 2:1, ages ranged from nine to 76 years with most (85.3%) between 19 and 51 years of age. All samples were tested with the Falcon assay screening test:enzyme-linked immunosorbent assay (FAST:ELISA) with microsomal antigens of Schistosoma mansoni. All FAST:ELISA+ samples were confirmed by enzyme-linked immunoelectrotransfer blot (EITB). Our data showed that 15.4% were FAST:ELISA+, and 10.6% were confirmed by EITB; 13.5% of the males and 4.1% of the females were EITB+. If we exclude those municipalities with fewer than five samples, the prevalence of EITB+ ranged from 0% to 38.5%, with the highest seroprevalence rates (21.1-38.5%) concentrated in 17 municipalities, which accounted for 48% of all seropositive samples. These 17 municipalities, however, contain only 18% of the total population of Puerto Rico. Two areas of high seroprevalence rates center around Jayuya (38.5%) and Naguabo (36.4%). The previously surveyed area of Boqueron is located in Las Piedras (35.3%), adjacent to Naguabo. In addition, we found 10% (21) of our total 215 donors less than 25 years of age to be EITB+ and all but two are residents of the high prevalence districts. These data strongly support the contention that schistosomiasis has been transmitted in a focal fashion during the past approximately 20 years.


Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis.
Despite recent intensive research efforts in functional genomics, the functions of only a limited number of Arabidopsis (Arabidopsis thaliana) genes have been determined experimentally, and improving gene annotation remains a major challenge in plant science. As metabolite profiling can characterize the metabolomic phenotype of a genetic perturbation in the plant metabolism, it provides clues to the function(s) of genes of interest. We chose 50 Arabidopsis mutants, including a set of characterized and uncharacterized mutants, that resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry. To make the data set available as an efficient public functional genomics tool for hypothesis generation, we developed the Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO). It allows the evaluation of whether a mutation affects metabolism during normal plant growth and contains images of mutants, data on differences in metabolite accumulation, and interactive analysis tools. Nonprocessed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by the Metabolomics Standards Initiative and are freely downloadable. Proof-of-concept analysis suggests that MeKO is highly useful for the generation of hypotheses for genes of interest and for improving gene annotation. MeKO is publicly available at http://prime.psc.riken.jp/meko/.