Social Representation of "Loud Music" in Young Adults: A Cross-Cultural Study.
Exposure to recreational noise, particularly music exposure, is considered one of the biggest public health hazards of our time. Some important influencing factors such as socioeconomic status, educational background, and cross-cultural perspectives have previously been found to be associated with attitudes toward loud music and the use of hearing protection. Although culture seems to play an important role, there is relatively little known about how it influences perceptions regarding loud music exposure in young adults. The present study was aimed to explore cross-cultural perceptions of and reactions to loud music in young adults (18-25 yr) using the theory of social representations. The study used a cross-sectional survey design. The study sample included young adults (n = 534) from five different countries (India, Iran, Portugal, the United States, and the United Kingdom) who were recruited using convenience sampling. Data were collected using a questionnaire. Data were analyzed using a content analysis, co-occurrence analysis, and also χ² analysis. Fairly equal numbers of positive and negative connotations (∼40%) were noted in all countries. However, the χ² analysis showed significant differences between the countries (most positive connotations were found in India and Iran, whereas the most negative connotations were found in the United Kingdom and Portugal) regarding the informants' perception of loud music. The co-occurrence analysis results generally indicate that the category "negative emotions and actions" occurred most frequently, immediately followed by the category "positive emotions and actions." The other most frequently occurring categories included "acoustics," "physical aliment," "location," and "ear and hearing problems." These six categories formed the central nodes of the social representation of loud music exposure in the global index. Although some similarities and differences were noted among the social representations toward loud music among countries, it is noteworthy that more similarities than differences were noted among countries. The study results suggest that "loud music" is perceived to have both positive and negative aspects within society and culture. We suggest that the health promotion strategies should focus on changing societal norms and regulations to be more effective in decreasing the noise- and/or music-induced auditory symptoms among young adults.


Lateral reading and monetary incentives to spot disinformation about science.
Disinformation about science can impose enormous economic and public health burdens. A recently proposed strategy to help online users recognise false content is to follow the techniques of professional fact checkers, such as looking for information on other websites (lateral reading) and looking beyond the first results suggested by search engines (click restraint). In two preregistered online experiments (N = 5387), we simulated a social media environment and tested two interventions, one in the form of a pop-up meant to advise participants to follow such techniques, the other based on monetary incentives. We measured participants' ability to identify whether information was scientifically valid or invalid. Analysis of participants' search style reveals that both monetary incentives and pop-up increased the use of fact-checking strategies. Monetary incentives were overall effective in increasing accuracy, whereas the pop-up worked when the source of information was unknown. Pop-up and incentives, when used together, produced a cumulative effect on accuracy. We suggest that monetary incentives enhance content relevance, and could be combined with fact-checking techniques to counteract disinformation.


Blood transfusion and autologous donation: a survey of post-surgical patients, interest group members and the public.
Before planned surgery, patients may choose autologous donation in order to avoid the small, but potential, risks of receiving an allogeneic blood transfusion. This study examined the perceived risks of allogeneic blood transfusions, preferences and willingness to pay for autologous donation and the desired role in the decision-making process in three populations: post-surgical patients, special interest group members and the general public. Quantitative and qualitative data were collected from 206 respondents with the help of computer-assisted semi-structured telephone interviews. Thirty-three per cent of the sample voiced concerns about receiving allogeneic blood transfusions. The risks of hepatitis C virus, human immunodeficiency virus, variant Creutzfeldt-Jakob disease and a haemolytic reaction were perceived as being low, but were rated as numerically higher than those of other life events that have equal probability. Autologous donation was perceived as removing all the risks associated with transfusion, and respondents were willing to pay a median $976 AUD ($664 US) to use this technique. Over 80% of respondents preferred to be involved in making the decision about whether to use autologous donation. Even though autologous donation is not 'risk-free' and the blood supply is very safe, people overestimate the associated risks and have a preference for their own blood. Decision aids presenting balanced information on the advantages and disadvantages of both allogeneic and autologous blood may be required.


Determination of cardiac troponin I forms in the blood of patients with acute myocardial infarction and patients receiving crystalloid or cold blood cardioplegia.
To determine the forms of cardiac troponin I (cTnI) circulating in the bloodstream of patients with acute myocardial infarction (AMI) and patients receiving a cardioplegia during heart surgery, we developed three immunoenzymatic sandwich assays. The first assay involves the combination of two monoclonal antibodies (mAbs) specific for human cTnI. The second assay involves the combination of a mAb specific for troponin C (TnC) and an anti-cTnI mAb. The third assay was a combination of a mAb specific for human cardiac troponin T (cTnT) and an anti-cTnI mAb. Fifteen serum samples from patients with AMI, 10 serum samples from patients receiving crystalloid cardioplegia during heart surgery, and 10 serum samples from patients receiving cold blood cardioplegia during heart surgery were assayed by the three two-site immunoassays. We confirmed that cTnI circulates not only in free form but also complexed with the other troponin components (TnC and cTnT). We showed that the predominant form in blood is the cTnI-TnC binary complex (IC). Free cTnI, the cTnI-cTnT binary complex, and the cTnT-cTnI-TnC ternary complex were seldom present, and when present, were in small quantities compared with the binary complex IC. Similar results were obtained in both patient populations studied. These observations are essential for the development of new immunoassays with improved clinical sensitivity and for the selection of an appropriate cTnI primary calibrator.


Perceptions of wildfire and landscape change in the Kenai Peninsula, Alaska.
Despite a broad literature addressing the human dimensions of wildfire, current approaches often compartmentalize results according to disciplinary boundaries. Further, relatively few studies have focused on the public's evolving perceptions of wildfire as communities change over time. This paper responds to these gaps by exploring perceptions of landscape dynamics and wildfire between 2003 and 2007 using a typological framework of intersecting ecological, social, and cultural processes. Designed as a restudy, and using key informant interviews, this research allowed us to observe risk perception as they are related to community challenges and opportunities in the Kenai Peninsula, Alaska. Risk perceptions were examined as an integral part of community and landscape change. Wildfire was a concern among informants in 2003 and remained a concern in 2007, although informants were less likely to discuss it as a major threat compared to the original study. Informants in the western part of the peninsula tended to express more concern about wildfire than their eastern counterparts largely due to their experiences with recent fires. Other important factors residents considered included changing forest fuels, the expanding wildland urban interface, and contrasting values of new residents. Underscoring the localized nature of risk perceptions, informants had difficulty describing the probability of a wildfire event in a geographical context broader than the community scale. This paper demonstrates how a holistic approach can help wildfire and natural resource professionals, community members, and other stakeholders understand the social and physical complexities influencing collective actions or inactions to address the threat of wildfire.


MicroRNA-186 improves fracture healing through activating the bone morphogenetic protein signalling pathway by inhibiting SMAD6 in a mouse model of femoral fracture: An animal study.
MicroRNAs (miRNAs) have been reported as key regulators of bone formation, signalling, and repair. Fracture healing is a proliferative physiological process where the body facilitates the repair of a bone fracture. The aim of our study was to explore the effects of microRNA-186 (miR-186) on fracture healing through the bone morphogenetic protein (BMP) signalling pathway by binding to Smad family member 6 (SMAD6) in a mouse model of femoral fracture. Microarray analysis was adopted to identify the regulatory miR of SMAD6. 3D micro-CT was performed to assess the bone volume (BV), bone volume fraction (BVF, BV/TV), and bone mineral density (BMD), followed by a biomechanical test for maximum load, maximum radial degrees, elastic radial degrees, and rigidity of the femur. The positive expression of SMAD6 in fracture tissues was measured. Moreover, the miR-186 level, messenger RNA (mRNA) level, and protein levels of SMAD6, BMP-2, and BMP-7 were examined. MicroRNA-186 was predicted to regulate SMAD6. Furthermore, SMAD6 was verified as a target gene of miR-186. Overexpressed miR-186 and SMAD6 silencing resulted in increased callus formation, BMD and BV/TV, as well as maximum load, maximum radial degrees, elastic radial degrees, and rigidity of the femur. In addition, the mRNA and protein levels of SMAD6 were decreased, while BMP-2 and BMP-7 levels were elevated in response to upregulated miR-186 and SMAD6 silencing. In conclusion, the study indicated that miR-186 could activate the BMP signalling pathway to promote fracture healing by inhibiting SMAD6 in a mouse model of femoral fracture.Cite this article: Bone Joint Res 2019;8:550-562.


Raising the sauropod neck: it costs more to get less.
The long necks of gigantic sauropod dinosaurs are commonly assumed to have been used for high browsing to obtain enough food. However, this analysis questions whether such a posture was reasonable from the standpoint of energetics. The energy cost of circulating the blood can be estimated accurately from two physiological axioms that relate metabolic rate, blood flow rate and arterial blood pressure: (i) metabolic rate is proportional to blood flow rate and (ii) cardiac work rate is proportional to the product of blood flow rate and blood pressure. The analysis shows that it would have required the animal to expend approximately half of its energy intake just to circulate the blood, primarily because a vertical neck would have required a high systemic arterial blood pressure. It is therefore energetically more feasible to have used a more or less horizontal neck to enable wide browsing while keeping blood pressure low.


Severe hypomagnesemia and low-grade inflammation in metabolic syndrome.
To evaluate the association between severe hypomagnesemia and the low-grade inflammatory response in subjects with metabolic syndrome (MetS), ninety-eight individuals with new diagnosis of MetS were enrolled in a cross-sectional study. Pregnancy, smoking, alcohol intake, renal damage, hepatic disorders, infectious or chronic inflammatory diseases, malignancy, use of diuretics, statins, calcium antagonist, antioxidants, vitamins, anti-inflammatory drugs, or previous oral magnesium supplementation were exclusion criteria. According serum magnesium levels, participants were assigned to the following groups: 1) severe hypomagnesemia (≤1.2 mg/dL); 2) hypomagnesemia (>1.2≤1.8 mg/dL); 3) Normal serum magnesium levels (>1.8 mg/dL). The low-grade inflammatory response was defined by elevation of serum levels of (hsCRP >1.0 ≤10.0 mg/L) or TNF-alpha (TNF-α ≥3.5 pg/mL). Severe hypomagnesemia, hypomagnesemia, and normomagnesemia were identified in 21 (21.4%), 38 (38.8%), and 39 (39.8%) individuals. The ORs, adjusted by WC, showed that severe hypomagnesemia (OR: 8.1; CI 95%: 3.6-19.4 and OR: 3.7; CI 95%: 1.1-12.1), but not hypomagnesemia (OR: 1.8; CI 95%: 0.9-15.5 and OR: 1.6; CI 95%: 0.7-3.6), was strongly associated with elevated hsCRP and TNF-α levels, and that normomagnesemia exhibited a protective role (OR: 0.32; CI 95%: 0.1-0.7 and OR: 0.28; CI 95%: 0.1-0.6) for elevation of CRP and TNF-α. Results of this study show that, in subjects with MetS, severe hypomagnesemia, but not hypomagnesemia, is associated with elevated concentrations of CRP and TNF-α.


Hepatitis B testing among Vietnamese American men.
Vietnamese American men are over 10 times more likely to be diagnosed with liver cancer than their white counterparts. This health disparity is attributable to high rates of hepatitis B virus (HBV) infection. Our study objective was to examine factors associated with HBV testing among Vietnamese men. A population-based survey was conducted in Seattle. The questionnaire content was guided by an earlier qualitative study and the Health Behavior Framework. The survey was completed by 345 men (response rate: 80%). About one-third (34%) of the respondents reported they had not been tested for HBV. The following factors were associated (P < 0.01) with previous testing in bivariate comparisons: having a regular source of care and regular provider; knowing that HBV can be spread during childbirth; believing HBV can cause liver cancer; and doctor(s) had recommended testing as well as had asked doctor(s) for testing. Three variables were independently associated with HBV testing in a logistic regression model: regular source of care (OR = 4.5; 95% CI = 2.6-7.9), physician recommendation (OR = 2.3, 95% CI = 1.3-4.0), and knowing HBV can be spread during childbirth (OR = 2.1; 95% CI = 1.2-3.9). Low levels of HBV testing remain a public health problem in some Vietnamese American sub-groups. Health education about HBV transmission may stimulate patients to seek testing. Intervention programs should specifically target Vietnamese men without a regular source of health care and physicians who serve Vietnamese communities.


Repositioning tolcapone as a potent inhibitor of transthyretin amyloidogenesis and associated cellular toxicity.
Transthyretin (TTR) is a plasma homotetrameric protein implicated in fatal systemic amyloidoses. TTR tetramer dissociation precedes pathological TTR aggregation. Native state stabilizers are promising drugs to treat TTR amyloidoses. Here we repurpose tolcapone, an FDA-approved molecule for Parkinson's disease, as a potent TTR aggregation inhibitor. Tolcapone binds specifically to TTR in human plasma, stabilizes the native tetramer in vivo in mice and humans and inhibits TTR cytotoxicity. Crystal structures of tolcapone bound to wild-type TTR and to the V122I cardiomyopathy-associated variant show that it docks better into the TTR T4 pocket than tafamidis, so far the only drug on the market to treat TTR amyloidoses. These data indicate that tolcapone, already in clinical trials for familial amyloid polyneuropathy, is a strong candidate for therapeutic intervention in these diseases, including those affecting the central nervous system, for which no small-molecule therapy exists.


Measures of asthma control.
Over the past decade, the concept of asthma control as distinct from asthma severity has been clearly defined. Well controlled asthma is the goal of therapy in all asthma patients. This review is a comprehensive description of the tools currently available for a methodical assessment of different aspects of asthma control in clinical practice and research. Several questionnaires for assessing asthma control have been extensively validated in adults. In children, validation data are less extensive. Considerable overlap exists between asthma control measures and measures of asthma-specific quality of life. Asthma-specific quality-of-life questionnaires have been used as primary outcome measures in major clinical trials evaluating asthma therapy. Biomarkers that reflect eosinophilic inflammation of the airways are used as intermediate outcome measures to reflect the biological basis of asthma control. There is some controversy, however, over which biomarkers are best incorporated into therapeutic algorithms that attempt to achieve maximal asthma control while minimizing treatment intensity. In designing clinical studies to evaluate different asthma therapies, researchers will find this review to be a useful resource in terms of choosing the appropriate tool for assessing asthma control. This is also a valuable resource for a methodical assessment of response to asthma therapy in routine clinical care.


Effects of tongue cleaning on bacterial flora in tongue coating and dental plaque: a crossover study.
The effects of tongue cleaning on reconstruction of bacterial flora in dental plaque and tongue coating itself are obscure. We assessed changes in the amounts of total bacteria as well as Fusobacterium nucleatum in tongue coating and dental plaque specimens obtained with and without tongue cleaning. We conducted a randomized examiner-blind crossover study using 30 volunteers (average 23.7 ± 3.2 years old) without periodontitis. After dividing randomly into 2 groups, 1 group was instructed to clean the tongue, while the other did not. On days 1 (baseline), 3, and 10, tongue coating and dental plaque samples were collected after recording tongue coating score (Winkel tongue coating index: WTCI). After a washout period of 3 weeks, the same examinations were performed with the subjects allocated to the alternate group. Genomic DNA was purified from the samples and applied to SYBR® Green-based real-time PCR to quantify the amounts of total bacteria and F. nucleatum. After 3 days, the WTCI score recovered to baseline, though the amount of total bacteria in tongue coating was significantly lower as compared to the baseline. In plaque samples, the bacterial amounts on day 3 and 10 were significantly lower than the baseline with and without tongue cleaning. Principal component analysis showed that variations of bacterial amounts in the tongue coating and dental plaque samples were independent from each other. Furthermore, we found a strong association between amounts of total bacteria and F. nucleatum in specimens both. Tongue cleaning reduced the amount of bacteria in tongue coating. However, the cleaning had no obvious contribution to inhibit dental plaque formation. Furthermore, recovery of the total bacterial amount induced an increase in F. nucleatum in both tongue coating and dental plaque. Thus, it is recommended that tongue cleaning and tooth brushing should both be performed for promoting oral health.


A meta-analysis of single case research studies on aided augmentative and alternative communication systems with individuals with autism spectrum disorders.
Many individuals with autism cannot speak or cannot speak intelligibly. A variety of aided augmentative and alternative communication (AAC) approaches have been investigated. Most of the research on these approaches has been single-case research, with small numbers of participants. The purpose of this investigation was to meta-analyze the single case research on the use of aided AAC with individuals with autism spectrum disorders (ASD). Twenty-four single-case studies were analyzed via an effect size measure, the Improvement Rate Difference (IRD). Three research questions were investigated concerning the overall impact of AAC interventions on targeted behavioral outcomes, effects of AAC interventions on individual targeted behavioral outcomes, and effects of three types of AAC interventions. Results indicated that, overall, aided AAC interventions had large effects on targeted behavioral outcomes in individuals with ASD. AAC interventions had positive effects on all of the targeted behavioral outcome; however, effects were greater for communication skills than other categories of skills. Effects of the Picture Exchange Communication System and speech-generating devices were larger than those for other picture-based systems, though picture-based systems did have small effects.


Reproductive isolation in alpine gingers: How do coexisting Roscoea (R. purpurea and R. tumjensis) conserve species integrity?
Multiple barriers may contribute to reproductive isolation between closely related species. Understanding the relative strength of these barriers can illuminate the ecological factors that currently maintain species integrity and how these factors originally promoted speciation. Two Himalayan alpine gingers, Roscoea purpurea and R. tumjensis, occur sympatrically in central Nepal and have such similar morphology that it is not clear whether or how they maintain a distinct identity. Our quantitative measurements of the components of reproductive isolation show that they are, in fact, completely isolated by a combination of phenological displacement of flowering, earlier for R. tumjensis and later for R. purpurea, and complete fidelity of visitation by different pollinator species, bumblebees for R. tumjensis and a long-tongued fly for R. purpurea. Furthermore, the nectar of R. tumjensis flowers is available to the shorter tongued bumblebees while R. purpurea nectar is less accessible, requiring deep probing from long-tongued flies. Although flowering phenology is a strong current barrier that seemingly obviates any need for pollinator discrimination, this current pattern need not reflect selective forces occurring at the initial divergence of R. tumjensis. There has been considerable pollinator switching during the radiation of the Himalayan Roscoea, and the association of flowering time with type of pollinator in these sympatric species may have originated among the earliest or latest flowering individuals or populations of an ancestor to exploit either bumblebee activity early in the breeding season or long-tongued fly abundance later in the season. These two sympatric Roscoea species add to accumulating evidence of the primacy of prezygotic pollination traits in speciation among angiosperms even in the absence of postzygotic incompatibility.


Influence of vitamin D and retinoids on the induction of functional differentiation in vitro of canine osteosarcoma clonal cells.
The efficacy of 22-oxacalcitriol (OCT), calcitriol, cholecalciferol, all-trans retinoic acid (ATRA) and 9-cis retinoic acid (9-cis RA) to differentiate in vitro four clonal cells of the canine osteosarcoma cell line POS into cells having properties of a functionally mature osteoblast bone cell were investigated. The induction of intracellular alkaline phosphatase (ALP) activity, osteocalcin (GLA-OC) and type I collagen (PIP) production after 72 h treatment were used as markers of differentiation. At a concentration of 10(-8)M, OCT and calcitriol significantly induced all markers, and ATRA only the ALP of osteoblast, chondroblast and undifferentiated clonal cells. At the same concentration, 9-cis RA and cholecalciferol induced ALP of chondroblast and osteoblast cells, respectively; ATRA, 9-cis RA and cholecalciferol induced PIP of chondroblast and undifferentiated cells. None of the drugs significantly differentiated fibroblast cells. The ability of these agents to differentiate osteosarcoma cells into cells that exhibit properties of functionally mature osteoblastic bone cells may promote normal osteogenesis and reverse the loss of control of their differentiation.


Dissociation between systemic and mucosal humoral immune responses in coeliac disease.
We examined humoral immunity in coeliac disease as expressed in serum (systemic immunity), and in saliva, jejunal aspirate, and whole gut lavage fluid (mucosal immunity). The aims were to define features of the secretory immune response (IgA and IgM concentrations and antibody values to gliadin and other food proteins measured by enzyme linked immunosorbent assay (ELISA)) in active disease and remission, and to establish whether secretions obtained by relatively non-invasive techniques (saliva and gut lavage fluid) can be used for indirect measurements of events in the jejunum. Serum, saliva, and jejunal aspirate from 26 adults with untreated coeliac disease, 22 treated patients, and 28 immunologically normal control subjects were studied, together with intestinal secretions obtained by gut lavage from 15 untreated and 19 treated patients with coeliac disease and 25 control subjects. Jejunal aspirate IgA and IgM and gut lavage fluid IgM concentrations were significantly raised in patients with untreated coeliac disease; the lavage fluid IgM concentration remained higher in patients with treated coeliac disease than in controls. Serum and salivary immunoglobulin concentrations were similar in the three groups. Patients with untreated coeliac disease had higher values of antibodies to gliadin compared with treated patients and control subjects in all body fluids tested; these were predominantly of IgA and IgG classes in serum, and of IgA and IgM classes in jejunal aspirate and gut lavage fluid. Values of salivary IgA antibodies to gliadin were significantly higher in untreated coeliacs, though antibody values were generally low, with a large overlap between coeliac disease patients and control subjects. In treated patients, with proved histological recovery on gluten free diet, serum IgA antigliadin antibody values fell to control values, though serum IgG antigliadin antibody values remained moderately raised. In contrast, there was persistence of secretory antigliadin antibodies in treated patients (particularly IgM antibody) in both jejunal aspirate and gut lavage fluid. Antibody responses to betalactoglobulin and ovalbumin were similar to those for gliadin, including persistence of high intestinal antibody values in patients with treated coeliac disease. There was a positive correlation between antibody values in jejunal aspirate and gut lavage fluid, but not between saliva and jejunal aspirate; thus salivary antibodies do not reflect intestinal humoral immunity.


The Preoperative Neutrophil-to-lymphocyte Ratio is a Novel Biomarker for Predicting Worse Clinical Outcomes in Non-muscle Invasive Bladder Cancer Patients with a Previous History of Smoking.
We speculated that a heterogeneous population of non-muscle invasive bladder cancer (NMIBC) patients with a previous history of smoking may be more precisely stratified by a biomarker associated with tumor aggressiveness and then focused on the preoperative neutrophil-to-lymphocyte ratio (pre-NLR), which is a simple index of systemic inflammation. Our study population comprised 605 patients initially diagnosed with NMIBC at our 3 institutions between 1995 and 2013. We analyzed the relationships between pre-NLR levels and clinical outcomes in NMIBC. A pre-NLR level of ≥2.2 was defined as elevated according to a calculation by a receiver-operating curve analysis. In overall, a total of 296 patients (48.9 %) had pre-NLR ≥ 2.2, and the pre-NLR level was one of independent risk factors for tumor recurrence and stage progression. Among 344 patients with a previous history of smoking, 184 (53.5 %) had pre-NLR ≥ 2.2 and the pre-NLR level was one of independent risk factors for tumor recurrence and stage progression. The 5-year recurrence-free survival and progression-free survival rates in patients with pre-NLR < 2.2 were 66.3 and 97.5 %, respectively, which were significantly higher than those in their counterparts (31.7 and 90.4 %, p < 0.001). In either subgroup of patients who were current smokers (N = 175) or former smokers (N = 169), the pre-NLR level was the only independent risk factor for tumor recurrence. The pre-NLR level was not associated with tumor recurrence or stage progression in 261 nonsmoking patients. Pre-NLR levels may be a useful marker for identifying worse clinical outcomes in NMIBC patients, particularly those with a previous history of smoking.


White matter hyperintensities in late life depression: a systematic review.
White matter hyperintensities in MRI scans are age related but appear to be more prevalent in depressed patients. They may be more pronounced in late onset depression. This finding, if confirmed, would potentially illuminate the heterogeneity of depression in elderly subjects. We conducted a systematic literature search of studies investigating white matter changes in late life depression, identifying 98 studies. The 30 remaining eligible studies were scrutinised for the presence and severity measures of periventricular and deep white matter changes in late life, late onset and, if available, early onset depression as well as in controls. Comparisons between groups were entered into random effects meta-analyses using odds ratios and Cohen's d, as appropriate. Correlations with potential confounders, such as age difference between groups, were explored. Late life depression and, to a greater extent, late onset depression in late life were characterised by more frequent and intense white matter abnormalities. In particular, the odds of having white matter changes were over 4 for late compared with early onset depression. Similarly, on severity scales, late onset depression had scores of 0.7-0.8 standard deviations above early onset patients. Significant differences between early and late onset depression suggest different aetiological mechanisms, in accordance with a theory of "cerebrovascular" depression of late onset. Greater duration of depressive symptoms, signs and treatment does not appear to have a measurable impact on white matter signal in MRI scans.


Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation.
Enrichments for anaerobic organotrophic hyperthermophiles were performed with hydrothermal chimney samples collected at the Guaymas Basin (27 degrees 01' N, 111 degrees 24' W). Positive enrichments were submitted to gamma-irradiation at a dose of 30 kGy. One of the resistant strains, designated strain EJ3(T), formed regular motile cocci. The new strain grew between 55 and 95 degrees C, with an optimum growth temperature of 88 degrees C. The optimal pH for growth was 6.0, and the optimum NaCl concentration for growth was around 20 g l(-1). Strain EJ3(T) was an obligately anaerobic heterotroph that utilized yeast extract, tryptone and peptone. Elemental sulfur or cystine was required for growth and reduced to hydrogen sulfide. The G + C content of the genomic DNA was 51.3 mol%. As determined by 16S rRNA gene sequence analysis, the organism was most closely related to Thermococcus celer, Thermococcus guaymasensis, Thermococcus hydrothermalis, Thermococcus profundus and Thermococcus gorgonarius. However, no significant homology was observed between them by DNA-DNA hybridization. The novel organism also possessed phenotypic traits that differ from those of its closest phylogenetic relatives. Therefore, it is proposed that this isolate, which constitutes the most radioresistant hyperthermophilic archaeon known to date, should be described as the type strain of a novel species, Thermococcus gammatolerans sp. nov. The type strain is EJ3(T) (= DSM 15229(T) = JCM 11827(T)).


Aldosterone induces cardiotrophin-1 expression in HL-1 adult cardiomyocytes.
Aldosterone (ALDO) may induce cardiac hypertrophy by nonhemodynamic mechanisms that are not completely defined. Cardiotrophin-1 (CT-1) is a cytokine that exerts hypertrophic actions on isolated cardiomyocytes and promotes cardiac hypertrophy in vivo. We investigated whether ALDO induces CT-1 expression in HL-1 cardiomyocytes aiming at the possibility that the cytokine is involved in ALDO-induced cardiomyocyte hypertrophy. mRNA and protein expression were quantified by RT-PCR and Western blot. Cardiomyocyte area, as an index of hypertrophy, was assayed by image analysis in phalloidin-stained HL-1 cells. ALDO addition to adult HL-1 cardiomyocytes increased (P<0.01) CT-1 mRNA and protein expression in a concentration-dependent manner. This effect was abrogated by actinomycin D, the mineralocorticoid and glucocorticoid receptor antagonists spironolactone and RU486, respectively, and the p38 MAPK blocker SB203580. CT-1 signaling pathway blockade with specific antibodies against the cytokine and its two receptor subunits avoided (P<0.01) alpha-sarcomeric actin and c-fos protein overexpression as well as cell size increase induced by ALDO in HL-1 cells. In vivo, a single ALDO injection acutely increased (P<0.01) the myocardial expression of CT-1 in C57BJ6 wild-type mice but not CT-1-null mice. The bolus of the mineralocorticoid increased (P<0.01) ANP and c-fos mRNA expression in the myocardium of wild-type mice, whereas no changes were observed in CT-1-null mice. In summary, ALDO induces CT-1 expression in adult HL-1 cardiomyocytes via genomic and nongenomic mechanisms. CT-1 up-regulation could have relevance in the direct hypertrophic effects of ALDO in cardiomyocytes.


Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3.
Filarial nematode parasites cause serious diseases such as elephantiasis and river blindness in humans, and heartworm infections in dogs. Third stage filarial larvae (L3) are a critical stage in the life cycle of filarial parasites, because this is the stage that is transmitted by arthropod vectors to initiate infections in mammals. Improved understanding of molecular mechanisms associated with this transition may provide important leads for development of new therapies and vaccines to prevent filarial infections. This study explores changes in gene expression associated with the transition of Brugia malayi third stage larvae (BmL3) from mosquitoes into mammalian hosts and how these changes are affected by radiation. Radiation effects are especially interesting because irradiated L3 induce partial immunity to filarial infections. The underlying molecular mechanisms responsible for the efficacy of such vaccines are unkown. Expression profiles were obtained using a new filarial microarray with 18, 104 64-mer elements. 771 genes were identified as differentially expressed in two-way comparative analyses of the three L3 types. 353 genes were up-regulated in mosquito L3 (L3i) relative to cultured L3 (L3c). These genes are important for establishment of filarial infections in mammalian hosts. Other genes were up-regulated in L3c relative to L3i (234) or irradiated L3 (L3ir) (22). These culture-induced transcripts include key molecules required for growth and development. 165 genes were up-regulated in L3ir relative to L3c; these genes encode highly immunogenic proteins and proteins involved in radiation repair. L3ir and L3i have similar transcription profiles for genes that encode highly immunogenic proteins, antioxidants and cuticle components. Changes in gene expression that normally occur during culture under conditions that support L3 development and molting are prevented or delayed by radiation. This may explain the enhanced immunogenicity of L3ir. Gene Ontology and KEGG analyses revealed altered pathways between L3 types. Energy and "immune pathways" are up-regulated and may be needed for L3i invasion and survival, while growth and development are priorities for L3c. This study has improved our understanding of molecules involved in parasite invasion and immune evasion, potential targets of protective immunity, and molecules required for parasite growth and development.


Salmonella Typhi Vi capsule prime-boost vaccination induces convergent and functional antibody responses.
Vaccine development to prevent Salmonella Typhi infections has accelerated over the past decade, resulting in licensure of new vaccines, which use the Vi polysaccharide (Vi PS) of the bacterium conjugated to an unrelated carrier protein as the active component. Antibodies elicited by these vaccines are important for mediating protection against typhoid fever. However, the characteristics of protective and functional Vi antibodies are unknown. In this study, we investigated the human antibody repertoire, avidity maturation, epitope specificity, and function after immunization with a single dose of Vi-tetanus toxoid conjugate vaccine (Vi-TT) and after a booster with plain Vi PS (Vi-PS). The Vi-TT prime induced an IgG1-dominant response, whereas the Vi-TT prime followed by the Vi-PS boost induced IgG1 and IgG2 antibody production. B cells from recipients who received both prime and boost showed evidence of convergence, with shared V gene usage and CDR3 characteristics. The detected Vi antibodies showed heterogeneous avidity ranging from 10 μM to 500 pM, with no evidence of affinity maturation after the boost. Vi-specific antibodies mediated Fc effector functions, which correlated with antibody dissociation kinetics but not with association kinetics. We identified antibodies induced by prime and boost vaccines that recognized subdominant epitopes, indicated by binding to the de–O-acetylated Vi backbone. These antibodies also mediated Fc-dependent functions, such as complement deposition and monocyte phagocytosis. Defining strategies on how to broaden epitope targeting for S. Typhi Vi and enriching for antibody Fc functions that protect against typhoid fever will advance the design of high-efficacy Vi vaccines for protection across diverse populations.


alpha 2 integrin subunit cytoplasmic domain-dependent cellular migration requires p38 MAPK.
The alpha(2) integrin subunit cytoplasmic domain uniquely supported epidermal growth factor (EGF)-stimulated migration on type I collagen. p38 MAP kinase- and phosphatidylinositol 3-kinase-specific inhibitors, but not a MEK-specific inhibitor, eliminated EGF-stimulated and unstimulated alpha(2)-cytoplasmic domain-dependent migration. Following adhesion to collagenous matrices, cells expressing the full-length alpha(2) integrin subunit, but not cells expressing a chimeric alpha(2) integrin subunit in which the alpha(2)-cytoplasmic domain was replaced by the cytoplasmic domain of the alpha(1)-subunit, exhibited sustained and robust phosphorylation of p38 MAP kinase. Expression of dominant negative p38 MAP kinase inhibited alpha(2)-cytoplasmic domain-dependent, EGF-stimulated migration as well as unstimulated migration on collagen. Expression of constitutively active Rac1(Val-12) augmented p38 MAP kinase activation and alpha(2)-cytoplasmic domain-dependent migration. It also rescued the ability of cells expressing the alpha(1)-cytoplasmic domain to activate p38 MAPK and to migrate. These results suggest that the alpha(2) integrin cytoplasmic domain uniquely stimulates the p38 MAP kinase pathway that is required for unstimulated and EGF-stimulated migration on type I collagen.


Benefit of ventriculoperitoneal cerebrospinal fluid shunting and intrathecal chemotherapy in neoplastic meningitis: a retrospective, case-controlled study.
Neoplastic meningitis (NM) is a debilitating and increasingly frequent neurological complication of cancer characterized by infiltration of tumor cells into the leptomeninges and the subarachnoid space. Although NM is rarely curable, combined intrathecal chemotherapy and focal radiation can improve disease-related symptoms and survival. Hydrocephalus occurs in a significant proportion of patients, is associated with poor prognosis and reduced quality of life, and usually precludes the use of intrathecal therapy. Since January of 2005, the authors have used a combined treatment approach for patients with both NM and hydrocephalus that employs a subcutaneously placed reservoir connected in series to an on/off valve and a ventriculoperitoneal shunt for both diversion of CSF and injection of intrathecal chemotherapy. They conducted a retrospective, case-controlled study from 2 independent institutions to review their experience. Twenty-four patients with NM and hydrocephalus underwent placement of a CSF reservoir-on/off valve-ventriculoperitoneal shunt (RO-VPS) construct. There was no perioperative mortality, and there were only 2 minor complications. One shunt failure and no shunt-associated infections were observed over a median of 28 weeks of follow-up. Symptomatic improvement and improved performance status were seen in 20 patients (83.3%) and were sustained over 6 months. Eighteen patients received intraventricular chemotherapy without unexpected toxicity, and cytological responses were found in 11 patients (61.1%). Median progression-free and overall survival was 14 and 31 weeks, respectively. Compared with a contemporaneous comparison group of 24 demographically matched patients with NM who underwent CSF reservoir placement only, those who received RO-VPS constructs (p = 0.02) and had primary diagnosis of breast cancer (p = 0.04) had significant advantage in overall survival. A combined RO-VPS system is safe and practical to install, results in symptomatic improvement in most patients, and allows uncomplicated and effective administration of intrathecal chemotherapy in patients with NM. Cerebrospinal fluid diversion surgery should be considered in NM patients in conjunction with intrathecal and systemic treatments.


Replication stress induces accumulation of FANCD2 at central region of large fragile genes.
During mild replication stress provoked by low dose aphidicolin (APH) treatment, the key Fanconi anemia protein FANCD2 accumulates on common fragile sites, observed as sister foci, and protects genome stability. To gain further insights into FANCD2 function and its regulatory mechanisms, we examined the genome-wide chromatin localization of FANCD2 in this setting by ChIP-seq analysis. We found that FANCD2 mostly accumulates in the central regions of a set of large transcribed genes that were extensively overlapped with known CFS. Consistent with previous studies, we found that this FANCD2 retention is R-loop-dependent. However, FANCD2 monoubiquitination and RPA foci formation were still induced in cells depleted of R-loops. Interestingly, we detected increased Proximal Ligation Assay dots between FANCD2 and R-loops following APH treatment, which was suppressed by transcriptional inhibition. Collectively, our data suggested that R-loops are required to retain FANCD2 in chromatin at the middle intronic region of large genes, while the replication stress-induced upstream events leading to the FA pathway activation are not triggered by R-loops.


A bivariate parametric model for survival and intermediate event times.
In diseases such as acquired immune deficiency syndrome (AIDS), there is great interest in describing the frequency of secondary diagnoses that occur during the course of the disease and their effect on survival. Casting this situation in a more general framework, one distinguishes a terminal event (TE) and an intermediate event (IE) that may or may not occur. In epidemiologic applications the TE is usually death. Earlier studies of IE and TE times have used the latter to censor the IE time for individuals who do not present it. For such cases, we argue that more appropriately the TE removes the individual from the risk set for the IE. With this view, one distinguishes observations of four types, each with a different formula for its likelihood contribution. We propose an approach that uses separate parametric models for the marginal distribution of the survival time D and for the conditional distribution of the time R to the IE given D = d and R < or = D. A central quantity is the probability of presenting the IE given the occurrence of the TE at time d. This function of d can reveal important connections between the two events. We suggest a model derived from Weibull distributions where the parameters control the shape of this function. One can obtain inferences about other probabilities of interest such as the proportion of individuals who present the IE, P(R < or = D), the marginal distribution of R among the IE cases, P(R > r [symbol: see text] R < or = D) and the residual survival after the IE occurs, P(D - R > v [symbol: see text] R < or = D, R = r). We apply the model to the analysis of time to secondary Kaposi's sarcoma (KS) diagnosis and time to death in a large cohort study of homosexual men infected with the human immunodeficiency virus type 1 (HIV) and who had an initial non-KS AIDS diagnosis.


Paediatric External Ventricular Drains: Experience from a tertiary care hospital of a Developing Country.
The aim of the study was to describe indications and complications of external ventricular drain (EVD) placement in children aged between 1 month and 16 years. This retrospective chart review was conducted at the Aga Khan University Hospital, Karachi, and comprised all children who underwent EVD placement from January 2007 to December 2014. Of the 177 patients identified, 117(66%) were males 60(34%) were girls. The overall mean age was 5.4±5.2 years. The median Glasgow Coma Scale score on presentation and discharge was 13 (interquartile range [IQR]: 7) and 15 (IQR: 4), respectively. Major diagnosis included intracranial tumour 60(34%), bacterial meningitis 34(19%), tuberculous meningitis 33(18.6%), and haemorrhage 23(13%). Clinical indications for EVD insertion were acute hydrocephalus secondary to infection 64(36.2%), tumour 54(30.5%), and haemorrhage 23(13%) ventriculoperitoneal shunt malfunction or infection 25(14.1%) and traumatic brain injury 11(6.2%). Complications were observed in 47(26%) patients including infections 25(14.1%), malfunction 11(6.2%), haemorrhage 6(3.4%), misplacement 3(1.7%) and obstruction 2(1.1%). Staphylococcus was the main organism isolated. Moreover, 25(14%) patients expired. Acute hydrocephalus was the major indication and EVD infection was the major complication.


Multi-source dataset of e-commerce products with attributes for property matching.
Schema/ontology matching consists in finding matches between types, properties and entities in heterogeneous sources of data in order to integrate them, which has become increasingly relevant with the development of web technologies and open data initiatives. One of the involved tasks is the matching of data properties, which attempts to try to find correspondences between the attributes of the entities. This is challenging due to the at times different names of equivalent properties. Furthermore, some properties may not be equivalent, but still match in 1..n relationships. These difficulties create the need for varied evaluation datasets for two reasons. First, they are needed to evaluate existing techniques in a variety of scenarios. Second, they enable the training of supervised techniques that may even become context-independent if trained with data from diverse enough contexts. To support the evaluation and training of data property matching techniques, we present a collection dataset consisting of product records from four different contexts. These datasets are the result of transforming two different existing datasets. In one of the datasets, some properties were filtered for being too noisy. The resulting processed dataset consists of json files with a listing of the product records and their properties, and a separate grouping of the properties that determines which ones match. It contains information about 2860 entities, with 4386 properties and 13350 pairwise matches.


Computational physiology and the Physiome Project.
Bioengineering analyses of physiological systems use the computational solution of physical conservation laws on anatomically detailed geometric models to understand the physiological function of intact organs in terms of the properties and behaviour of the cells and tissues within the organ. By linking behaviour in a quantitative, mathematically defined sense across multiple scales of biological organization--from proteins to cells, tissues, organs and organ systems--these methods have the potential to link patient-specific knowledge at the two ends of these spatial scales. A genetic profile linked to cardiac ion channel mutations, for example, can be interpreted in relation to body surface ECG measurements via a mathematical model of the heart and torso, which includes the spatial distribution of cardiac ion channels throughout the myocardium and the individual kinetics for each of the approximately 50 types of ion channel, exchanger or pump known to be present in the heart. Similarly, linking molecular defects such as mutations of chloride ion channels in lung epithelial cells to the integrated function of the intact lung requires models that include the detailed anatomy of the lungs, the physics of air flow, blood flow and gas exchange, together with the large deformation mechanics of breathing. Organizing this large body of knowledge into a coherent framework for modelling requires the development of ontologies, markup languages for encoding models, and web-accessible distributed databases. In this article we review the state of the field at all the relevant levels, and the tools that are being developed to tackle such complexity. Integrative physiology is central to the interpretation of genomic and proteomic data, and is becoming a highly quantitative, computer-intensive discipline.


MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.
Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity. The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. The isolation of dozens of species in cellulolytic microbial consortia, including a novel species of myxobacteria that has the smallest genome among all sequenced aerobic myxobacteria, was easily achieved using the binning software. This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. MaxBin is available at https://sourceforge.net/projects/maxbin/.


Analysis of serum inflammatory mediators identifies unique dynamic networks associated with death and spontaneous survival in pediatric acute liver failure.
Tools to predict death or spontaneous survival are necessary to inform liver transplantation (LTx) decisions in pediatric acute liver failure (PALF), but such tools are not available. Recent data suggest that immune/inflammatory dysregulation occurs in the setting of acute liver failure. We hypothesized that specific, dynamic, and measurable patterns of immune/inflammatory dysregulation will correlate with outcomes in PALF. We assayed 26 inflammatory mediators on stored serum samples obtained from a convenience sample of 49 children in the PALF study group (PALFSG) collected within 7 days after enrollment. Outcomes were assessed within 21 days of enrollment consisting of spontaneous survivors, non-survivors, and LTx recipients. Data were subjected to statistical analysis, patient-specific Principal Component Analysis (PCA), and Dynamic Bayesian Network (DBN) inference. Raw inflammatory mediator levels assessed over time did not distinguish among PALF outcomes. However, DBN analysis did reveal distinct interferon-gamma-related networks that distinguished spontaneous survivors from those who died. The network identified in LTx patients pre-transplant was more like that seen in spontaneous survivors than in those who died, a finding supported by PCA. The application of DBN analysis of inflammatory mediators in this small patient sample appears to differentiate survivors from non-survivors in PALF. Patterns associated with LTx pre-transplant were more like those seen in spontaneous survivors than in those who died. DBN-based analyses might lead to a better prediction of outcome in PALF, and could also have more general utility in other complex diseases with an inflammatory etiology.


Diet-induced developmental acceleration independent of TOR and insulin in C. elegans.
Dietary composition has major effects on physiology. Here, we show that developmental rate, reproduction, and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells.


Optical component: nonreciprocal three-way divider based on magneto-optical resonator.
We suggest and analyze a new compact nonreciprocal optical component based on a magneto-optical (MO) resonator. This component fulfills simultaneously two functions, namely, equal division of the input signal between three output ports and isolation of the input port from output ones. Using group theory, we analyze the scattering matrix of this symmetrical component. Our numerical results for one of the possible schemes of the divider based on 2D photonic crystal with MO material demonstrate that, at the central frequency, the division of the signal between the three output ports is about -6.4 dB. The variation of the division levels in the output ports in this band is (-6.4±0.4) dB. For two of the output ports, the calculated bandwidth for the level -20 dB of the isolation is around 219 GHz at the wavelength 1.55 μm. For the third output port, the isolation at the central frequency is about -6 dB.


Interferon gamma induces retrograde dendritic retraction and inhibits synapse formation.
The expression of interferon gamma (IFNgamma) increases after neural injury, and it is sustained in chronic inflammatory conditions such as multiple sclerosis and infection with human immunodeficiency virus. To understand how exposure to this proinflammatory cytokine might affect neural function, we examined its effects on cultures of neurons derived from the central and peripheral nervous systems. IFNgamma inhibits initial dendritic outgrowth in cultures of embryonic rat sympathetic and hippocampal neurons, and this inhibitory effect on process growth is associated with a decrease in the rate of synapse formation. In addition, in older cultures of sympathetic neurons, IFNgamma also selectively induces retraction of existing dendrites, ultimately leading to an 88% decrease in the size of the arbor. Dendritic retraction induced by IFNgamma represents a specific cellular response because it occurs without affecting axonal outgrowth or cell survival, and it is not observed with tumor necrosis factor alpha or other inflammatory cytokines. IFNgamma-induced dendritic retraction is associated with the phosphorylation and nuclear translocation of signal transducer and activator of transcription 1 (STAT1), and expression of a dominant-negative STAT1 construct attenuates the inhibitory effect of IFNgamma. Moreover, retrograde dendritic retraction is observed when distal axons are selectively exposed to IFNgamma. These data imply that IFNgamma-mediated STAT1 activation induces both dendritic atrophy and synaptic loss and that this occurs both at the sites of IFNgamma release and at remote loci. Regressive actions of IFNgamma on dendrites may contribute to the neuropathology of inflammatory diseases.


CO2 and SO2 activation by a Cr-Cr quintuple bond.
A quintuply bonded dichromium complex stabilized by aminopyridinato ligands activates CO2 and SO2 by reducing the (formal) bond order of the metal-metal bonds. Oxygen abstraction is observed during CO2 activation. SO2 activation proceeds via formation of a unique dithionite complex/coordination. Furthermore, N2O activation was investigated and the formation of a tetrameric Cr-oxo complex was observed.


The first two years of practice: a longitudinal perspective on the learning and professional development of promising novice physical therapists.
Physical therapists work in complex health care systems requiring professional competence in clinical reasoning and confidence in decision-making skills. For novice physical therapists, the initial practice years are a time for developing professional identity and practical knowledge. The study purpose was to extend previous research describing the experiences, learning, and professional development of 11 promising novice therapists during their first year of practice. The present study examined the continued development of the same therapists during their second year of clinical practice. Seven researchers from 4 physical therapist educational programs in the eastern and midwestern United States used a longitudinal, qualitative, multiple case study approach. Eleven physical therapist graduates identified as "promising novices" were recruited using purposive sampling. Participants ranged in age from 24 to 29 years and entered varied practice settings. Data were collected for 2 years using semistructured interviews, reflective journals, and participant observation. A conceptual model describing the participants' ongoing development during the second year of practice emerged. The 3 themes were formal and informal learning, increasing confidence and expansion of skills, and engagement in an environment characterized by collaborative exchange and opportunities for teaching. The second year represented consolidation and elaboration of practice-based learning and skills. The expansion of confidence, skills, and responsibilities and the externalization of learning the participants experienced promoted professional role formation. Learning previously directed inward and self-focused turned outward, fueled by growing self-confidence. Research illuminating the professional role formation experienced during early clinical practice is not widely available. The current study and further research into the learning and development of novice practitioners may assist educators in the design of pedagogical strategies and learning environments that enhance the professional development of physical therapists.


Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue.
Formalin-fixed, paraffin-embedded (FFPE) tissue is the most common specimen available for molecular assays on tissue after diagnostic histopathological examination. RNA from FFPE tissue suffers from strand breakage and cross-linking. Despite excellent extraction methods, RNA quality from FFPE material remains variable. To address the RNA quality factors within FFPE tissues, we studied RNA quality, isolating individual elements of the tissue fixation and processing including length of fixation in formalin and the type of buffer incorporated in the fixative. We examined the impact of the length of the tissue processing cycle as well. The optimal fixation period of 12-24 hr in phosphate-buffered formalin resulted in better-quality RNA. Longer tissue processing times were associated with higher quality RNA. We determined that the middle region of gene suffers less damage by these processes as shown by real-time quantitative RT-PCR. These data provide key information for the development of methods of analysis of gene expression in archival FFPE tissues and contribute to the establishment of objective standards for the processing and handling of tissue in surgical pathology. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.


Fourteen-Year Temporal Trends in Patients Hospitalized for Mitral Regurgitation: The Increasing Burden of Mitral Valve Prolapse in Men.
Mitral regurgitation (MR) is the second most common valvular heart disease in Europe. The aging of the population and the increase in post-infarction survival could increase the prevalence of MR. To estimate the burden of patients hospitalized for MR in France in 2019 and temporal trends by etiology and sex from 2006 to 2020, we selected all patients hospitalized for MR using the national hospital database. In 2019, 49.2% of such patients had mitral valve prolapse (MVP), 17.1% had ischemic MR, 9.9% had rheumatic MR and 4.4% had MR with cardiomyopathy. The mean age of MVP patients was 67.8 years, and 34% were women. Among 89% of MVP inpatients who had received mitral valve repair or replacement, 55% received surgical repair, 13% received percutaneous repair and 25% received replacement. The all-cause mortality of one year after a mitral procedure of MVP was 5.4%. Among ischemic MR inpatients, 29% have had a mitral valve replacement, 16% a surgical repair and 19% a percutaneous repair. Between 2006 and 2019, the age-standardized rates of patients hospitalized for MVP have increased by 60%, especially in men (+80%) with 5.3/100,000 Person-Years (PY). The age-standardized rates of patients hospitalized for ischemic MR have increased by 25% with 1.8/100,000 PY; that of rheumatic MR has decreased by 36%. The study found that the burden of MVP in hospitals has increased substantially, especially among men. These results emphasize the need to monitor these temporal trends and anticipate care needs in the coming years.


Efficacy of the Military Tactical Emergency Tourniquet for Lower Extremity Arterial Occlusion Compared with the Combat Application Tourniquet: A Randomized Crossover Study.
Extremity bleeding and subsequent hemorrhagic shock is one of the main causes of preventable battlefield death, leading to mass-fielding of modern tourniquets, such as the Combat Application Tourniquet (CAT; Composite Resources). Numerous look-alike tourniquets, such as the Military Tactical Emergency Tourniquet (MTET; SZCTKlink), flood commercial markets, offering visually near-identical tourniquets for drastically reduced prices. We examined the performance of the MTET compared with that of the CAT. We undertook a randomized crossover trial to observe self-applied tourniquets to the lower extremity by combat medics, comparing the CAT to the MTET in application time and success rates, proven by loss of distal pulse assessed by Doppler ultrasound in <1 minute. All 50 participants (100%) successfully applied the CAT versus 40 participants (80%) using the MTET (p = .0001). Median application time for the CAT (29.03 seconds; range, 18.63 to 59.50 seconds) was significantly less than those of successful MTET applications (35.27 seconds; range, 17.00 to 58.90 seconds) or failed MTET applications (72.26 seconds; range, 62.84 to 83.96 seconds) (p = .0012). Of 10 MTET failures, three (30%) were from application time >1 minute and seven (70%) from tourniquet mechanical failure. The MTET performed worse than the CAT did in all observed areas. Despite identical appearance, look-alike tourniquets should not be assumed to be equivalent in quality or functionality to robustly tested tourniquets.


Time-optimal trajectories for cooperative multi-manipulator systems.
We present two schemes for planning the time-optimal trajectory for cooperative multi-manipulator system (CMMS) carrying a common object. We assume that the desired path is given and parameterizable by an arclength variable. Both approaches take into account the dynamics of the manipulators and object. The first approach employs linear programming techniques, and it allows us to obtain the time-optimal execution of the given task utilizing the maximum torque capacities of the joint motors. The second approach is a sub-time-optimal method that is computationally very efficient. In the second approach the given load is divided into a share for each robot in the CMMS in a manner in which the trajectory acceleration/deceleration is maximized, hence the trajectory execution time is minimized. This load distribution approach uses optimization schemes that degenerate to a linear search algorithm for the case of two robots manipulating a common load, and this results in significant reduction of computation time. The load distribution scheme not only enables us to reduce the computation time, but also gives us the possibility of applying this method in real-time planning and control of CMMS. Further, we show that for certain object trajectories the load distribution scheme yields truly time-optimal trajectories.


Childhood adversity and borderline personality disorder: a meta-analysis.
The aim of this meta-analysis was to better understand the magnitude and consistency of the association between childhood adversity and borderline personality disorder (BPD) across case-control, epidemiological and prospective cohort studies. Following the review protocol (reference: CRD42017075179), search terms pertaining to adversity and BPD were entered into three search engines. Random-effects meta-analysis synthesised the size and consistency of the effects. A total of 97 studies compared BPD to non-clinical (k = 40) and clinical (k = 70) controls. Meta-analysis of case-control studies indicated that individuals with BPD are 13.91 (95% CI 11.11-17.43) times more likely to report childhood adversity than non-clinical controls. This effect was smaller when considering retrospective cohort (OR: 2.59; 95% CI 0.93-7.30) and epidemiological (OR: 2.56, 95% CI 1.24-5.30) studies. Findings were significant across adversity subtypes with emotional abuse (OR: 38.11, 95% CI: 25.99-55.88) and neglect (OR: 17.73, 95% CI = 13.01-24.17) demonstrating the largest effects. Individuals with BPD were 3.15 (95% CI 2.62-3.79) times more likely to report childhood adversity than other psychiatric groups. This meta-analysis corroborates theoretical proposals that exposure to adverse life experiences is associated with BPD. It highlights the importance of considering childhood adversity when treating people diagnosed with BPD.


Ion trace detection algorithm to extract pure ion chromatograms to improve untargeted peak detection quality for liquid chromatography/time-of-flight mass spectrometry-based metabolomics data.
Able to detect known and unknown metabolites, untargeted metabolomics has shown great potential in identifying novel biomarkers. However, elucidating all possible liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS) ion signals in a complex biological sample remains challenging since many ions are not the products of metabolites. Methods of reducing ions not related to metabolites or simply directly detecting metabolite related (pure) ions are important. In this work, we describe PITracer, a novel algorithm that accurately detects the pure ions of a LC/TOF-MS profile to extract pure ion chromatograms and detect chromatographic peaks. PITracer estimates the relative mass difference tolerance of ions and calibrates the mass over charge (m/z) values for peak detection algorithms with an additional option to further mass correction with respect to a user-specified metabolite. PITracer was evaluated using two data sets containing 373 human metabolite standards, including 5 saturated standards considered to be split peaks resultant from huge m/z fluctuation, and 12 urine samples spiked with 50 forensic drugs of varying concentrations. Analysis of these data sets show that PITracer correctly outperformed existing state-of-art algorithm and extracted the pure ion chromatograms of the 5 saturated standards without generating split peaks and detected the forensic drugs with high recall, precision, and F-score and small mass error.


Successful catheter ablation reduces the risk of cardiovascular events in atrial fibrillation patients with CHA2DS2-VASc risk score of 1 and higher.
It is not known if successful catheter ablation for atrial fibrillation (AF) improves the patient's long-term cardiovascular outcomes. This study investigated the long-term outcomes and mortality of AF patients at high risk who received antiarrhythmic medication and catheter ablation. The propensity scores for AF were calculated for each patient and were used to assemble a cohort of 174 AF patients with ablation who were compared with an equal number of AF patients without ablation. Composite cardiovascular end points (major adverse cardiovascular event, MACE), including mortality and vascular events in the medically treated patients representing the control group (group 1), were compared with those in the ablation-treated patients (group 2). The rates of the total mortality (2.95% vs. 0.74% per year; P < 0.01), cardiovascular death (1.77% vs. 0% per year; P = 0.001), and ischaemic stroke/transient ischaemic attack (2.21% vs. 0.59% per year; P = 0.02) were higher in group 1 than group 2, respectively. A multivariate Cox regression analysis of the MACE scores showed that a higher CHA2DS2-VASc score [hazard ratio (HR) = 1.309 per increment of score, 95% confidence interval (CI) = 1.06-1.617; P = 0.01] and the performance of the ablation procedure (HR = 0.225, CI = 0.076-0.671; P = 0.007) were independent predictors of a MACE. In patients who received catheter ablation, recurrence of any atrial arrhythmia was a predictor of vascular events and total mortality (P < 0.05). In AF patients with CHA2DS2-VASc score ≥1, catheter ablation of AF reduced the risk of the total/cardiovascular mortality and total vascular events. Atrial fibrillation recurrence predicts long-term cardiovascular outcomes, as well as the CHA2DS2-VASc score.


Does morphological and anatomical plasticity during the vegetative stage make wheat more tolerant of water deficit stress than rice?
Water scarcity and the increasing severity of water deficit stress are major challenges to sustaining irrigated rice (Oryza sativa) production. Despite the technologies developed to reduce the water requirement, rice growth is seriously constrained under water deficit stress compared with other dryland cereals such as wheat (Triticum aestivum). We exposed rice cultivars with contrasting responses to water deficit stress and wheat cultivars well adapted to water-limited conditions to the same moisture stress during vegetative growth to unravel the whole-plant (shoot and root morphology) and organ/tissue (root anatomy) responses. Wheat cultivars followed a water-conserving strategy by reducing specific leaf area and developing thicker roots and moderate tillering. In contrast, rice 'IR64' and 'Apo' adopted a rapid water acquisition strategy through thinner roots under water deficit stress. Root diameter, stele and xylem diameter, and xylem number were more responsive and varied with different positions along the nodal root under water deficit stress in wheat, whereas they were relatively conserved in rice cultivars. Increased metaxylem diameter and lower metaxylem number near the root tips and exactly the opposite phenomena at the root-shoot junction facilitated the efficient use of available soil moisture in wheat. Tolerant rice 'Nagina 22' had an advantage in root morphological and anatomical attributes over cultivars IR64 and Apo but lacked plasticity, unlike wheat cultivars exposed to water deficit stress. The key traits determining the adaptation of wheat to dryland conditions have been summarized and discussed.


No effect of short-term testosterone manipulation on exercise substrate metabolism in men.
Compared with women, men use proportionately more carbohydrate and less fat during exercise at the same relative intensity. Estrogen and progesterone have potent effects on substrate use during exercise in women, but the role of testosterone (T) in mediating substrate use is unknown. The purpose of this investigation was to assess how large variations in the concentration of blood T would impact substrate use during exercise in men. Nine healthy, active men were studied in three distinct hormonal conditions: physiological T (no intervention), low T (pharmacological suppression of endogenous T with a gonadotrophin-releasing hormone antagonist), and high T (supplementation with transdermal T). Total carbohydrate oxidation, blood glucose rate of disappearance, and estimated muscle glycogen use were assessed by using stable isotope dilution and indirect calorimetry at rest and while bicycling at approximately 60% of peak O2 consumption for 90 min. Relative to the physiological condition (T = 5.5 +/- 0.5 ng/ml), total plasma T was considerably suppressed in low T (0.8 +/- 0.1) and elevated in high T (10.9 +/- 1.1). Despite the large changes in plasma T, carbohydrate oxidation, glucose rate of disappearance, and estimated muscle glycogen use were very similar across the three conditions. There were also no differences in plasma concentrations of glucose, insulin, lactate, or free fatty acids. Plasma estradiol (E) concentrations were elevated in high T, but correlations between substrate use and plasma concentrations of T, E, or the T-to-E ratio were very weak (r2 < 0.20). In conclusion, unlike the effect of acute elevation in E to constrain carbohydrate use in women, acute changes in circulating T concentrations do not appear to alter substrate use during exercise in men.


Ror2, encoding a receptor-like tyrosine kinase, is required for cartilage and growth plate development.
Receptor tyrosine kinases often have critical roles in particular cell lineages by initiating signalling cascades in those lineages. Examples include the neural-specific TRK receptors, the VEGF and angiopoietin endothelial-specific receptors, and the muscle-specific MUSK receptor. Many lineage-restricted receptor tyrosine kinases were initially identified as 'orphans' homologous to known receptors, and only subsequently used to identify their unknown growth factors. Some receptor-tyrosine-kinase-like orphans still lack identified ligands as well as biological roles. Here we characterize one such orphan, encoded by Ror2 (ref. 12). We report that disruption of mouse Ror2 leads to profound skeletal abnormalities, with essentially all endochondrally derived bones foreshortened or misshapen, albeit to differing degrees. Further, we find that Ror2 is selectively expressed in the chondrocytes of all developing cartilage anlagen, where it essential during initial growth and patterning, as well as subsequently in the proliferating chondrocytes of mature growth plates, where it is required for normal expansion. Thus, Ror2 encodes a receptor-like tyrosine kinase that is selectively expressed in, and particularly important for, the chondrocyte lineage.


The Instant Spontaneous Neuronal Activity Modulation of Transcutaneous Auricular Vagus Nerve Stimulation on Patients With Primary Insomnia.
Primary insomnia (PI) is associated with increased spontaneous neuronal activity. Transcutaneous auricular vagus nerve stimulation (taVNS) modulates brain function, and it is an effective treatment for primary insomnia. However, whether taVNS alleviates insomnia through modulating spontaneous neuronal activity is not fully clarified. This study aims to investigate the instant effect of taVNS in modulating spontaneous neuronal activity in PI patients using resting-state functional magnetic resonance imaging (rs-fMRI). Twenty-two PI subjects underwent rs-fMRI scanning prior and immediately after 30 min treatment of taVNS controlled by twenty healthy adults. Amplitude of low frequency fluctuations (ALFF) analysis was employed to assess the difference in spontaneous neuronal activity between PI patients and healthy adults, as well as between pre-treatment and post-treatment of taVNS. The taVNS-induced altered ALFF brain areas were then selected as regions of interest to perform the resting state functional connectivity (RSFC) analysis in PI patients. The right precuneus showed significantly increased ALFF in PI patients. After immediate taVNS treatment, the ALFF was significantly decreased in the right precuneus and increased in the left middle occipital gyrus. The RSFC in right precuneus with right angular, right superior frontal gyrus, and right middle frontal gyrus was significantly decreased. This study provides insights into the instant brain effects of taVNS on PI patients.


Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope.
Epidermal growth factor receptor (EGFR) signaling is initiated by a large ligand-favored conformational change of the extracellular domain (ECD) from a closed, self-inhibited tethered monomer, to an open untethered state, which exposes a loop required for strong dimerization and activation. In glioblastomas (GBMs), structurally heterogeneous missense and deletion mutations concentrate at the ECD for unclear reasons. We explore the conformational impact of GBM missense mutations, combining elastic network models (ENMs) with multiple molecular dynamics (MD) trajectories. Our simulations reveal that the main missense class, located at the I-II interface away from the self-inhibitory tether, can unexpectedly favor spontaneous untethering to a compact intermediate state, here validated by small-angle X-ray scattering (SAXS). Significantly, such intermediate is characterized by the rotation of a large ECD fragment (N-TR1), deleted in the most common GBM mutation, EGFRvIII, and that makes accessible a cryptic epitope characteristic of cancer cells. This observation suggested potential structural equivalence of missense and deletion ECD changes in GBMs. Corroborating this hypothesis, our FACS, in vitro, and in vivo data demonstrate that entirely different ECD variants all converge to remove N-TR1 steric hindrance from the 806-epitope, which we show is allosterically coupled to an intermediate kinase and hallmarks increased oncogenicity. Finally, the detected extraintracellular coupling allows for synergistic cotargeting of the intermediate with mAb806 and inhibitors, which is proved herein.


HLA haplotype A1 B8 DR3 as a risk factor for HIV-related disease.
Of 32 patients exposed to a single batch of factor VIII contaminated with human immunodeficiency virus (HIV), 18 became antibody positive. Serial T cell subset analyses over the succeeding four years have shown a progressive decline in circulating T4 cells in those 18 but no change in the 14 who remain seronegative. 2 of the seroconverters have died and a further 7 have symptoms attributable to HIV infection. In the group as a whole, the HLA haplotype A1 B8 DR3 was weakly associated with an increased risk of seroconversion on exposure to the virus while, in those who seroconverted, it was strongly associated with a rapid decline in T4 cells and development of HIV-related symptoms within four years of infection.


Nausea and nutrition.
Nausea and vomiting are symptoms associated with a wide variety of diseases and particular life conditions, such as pregnancy. The symptoms may occur in acute form or chronically depending on the underlying pathogenesis. In some cases, nausea and vomiting are directly triggered by food, e.g. in patients suffering from food allergy or food intolerances. In other cases, food is not the primary cause but dietetic manipulations may still contribute to the management of the nausea and vomiting. Therefore, food plays an important pathophysiological and therapeutic role in nausea and vomiting. In the present article, we describe the most relevant nutrient triggers for nausea and vomiting, discuss food allergy and intolerance as cause of nausea and vomiting, propose a clinical classification of nausea and vomiting, and present in detail dietetic and other therapeutic strategies of relevance for the management of nausea and vomiting.


Prevalence and determinants of chronic kidney disease in the Swiss population.
The prevalence of chronic kidney disease (CKD) is increasing worldwide, corresponding to an increased risk of cardiovascular disease. The latest study on prevalence of CKD involving the three linguistic regions of Switzerland dates back to 2002-2003 and definitions have changed since then. We aimed to assess the current prevalence and determinants of CKD in the Swiss general population. We analysed the data of 1353 participants from a cross-sectional population-based survey performed in 2010-2012 in the three linguistic regions of Switzerland. The prevalence of CKD and the derived cardiovascular risk categories were assessed according to the Kidney Disease - Improving Global Outcomes (KDIGO) 2012 classification, using estimated glomerular filtration rate (GFR; CKD-Epidemiological Collaboration equation) and albuminuria level. Multivariate logistic regression was used to analyse factors associated with CKD. We included 660 men and 693 women, equally distributed in four age categories (15-29, 30-44, 45-59 and over 60 years). The overall prevalence of CKD was 10.4%. The prevalence in the low, moderate, high and very high risk KDIGO categories were 89.6%, 8.4%, 1.6% and 0.5%, respectively. The prevalence of CKD was similar in all linguistic regions. In multivariate analysis, female gender, older age, diabetes and uric acid were independently associated with CKD in persons ≥45 y. In younger participants, diabetes and lower educational level were associated with CKD. In the general Swiss population, CKD affects one in ten adults. Subjects older than 60 years, as well as patients with diabetes and hypertension, show a high prevalence of CKD. Systematic screening may be recommended in this population.


Association of Polymorphisms in the Regulatory Region of the Cyclophilin a Gene (PPIA) with Gene Expression and HIV/AIDS Disease Progression.
Human cyclophilin A (CypA) encoded by peptidyl prolyl isomerase A gene (PPIA), enhances HIV-1 replication by aiding capsid uncoating. The association of genetic variation in the PPIA regulatory region with susceptibility to HIV-1 infection, disease progression, and gene expression among black South Africans at risk for infection or infected with HIV-1 is unknown. We genotyped 539 participants from 2 longitudinal study cohorts of black South Africans at high risk for infection or infected with HIV-1 for PPIA regulatory single nucleotide polymorphisms by polymerase chain reaction-restriction fragment length polymorphism. Minor allele (G) of SNP rs6850 (rs6850 G) significantly associated with higher viral loads (mean 4.85 versus 4.46 log copies/mL, P = 0.0006) and lower CD4 T-cell counts (mean 506 versus 557 cells/μL, P = 0.0256) during the acute phase of infection in the Centre for the AIDS Programme of Research in South Africa (CAPRISA) 002 cohort. Consistently, rs6850 G significantly associated with higher viral loads (mean 4.49 versus 4.01 log copies/mL, P < 0.0001) and lower CD4 T-cell counts (mean 442 versus 494 cells/μL, P = 0.0002) during the early chronic phase of infection in the CAPRISA 002 cohort; rs6850 G further associated significantly with rapid CD4 T-cell decline in the CAPRISA 002 cohort (P = 0.0481) and Sinikithemba chronic infection cohort (P = 0.0156). Interestingly, rs6850 G significantly associated with elevated CypA mRNA levels in HIV-1-positive individuals (P = 0.0061). These data suggest that rs6850 G enhances HIV-1 replication through upregulation of CypA expression following HIV-1 infection. The data support ongoing efforts to develop anti-HIV-1 drugs that block interaction of HIV-1 and cellular proteins.


[Endothelial cell cytoskeleton reorganization during functional monolayer formation in vitro].
The endothelium lining the inner surface of blood vessels regulates vascular permeability, permitting the exchange between the blood circulating in vessels and tissue fluid, and performs thereby the barrier function. Endothelial cells cultured in vitro retain the ability to perform a barrier function that is inherent in vascular endothelial cells in vivo. Endothelial monolayer in vitro is a unique model system that allows studying the interaction of cytoskeletal and adhesive structures of endothelial cells from the earliest stages of its formation. In this paper we describe and characterize quantitatively the changes in the cytoskeleton of endothelial cells from the time of endothelial cells spreading on the glass and formation of the first contacts between neighboring cells un- til the formation of a functional confluent monolayer. The main type of intermediate filaments of endothelial cells were vimentin filaments. The location of vimentin filaments and their number did not change at different stages of the endothelial monolayer formation, they occupied more than 80% of the cells. The system of actin filaments in endothelial cells was represented by the cortical actin at the cell periphery and bundles of actin stress fibers arranged in parallel. Upon the formation of contacts with neighboring cells the number and thickness of actin filaments increased. In addition, the formation of the endothelial monolayer led to changes in microtubule network, which was evident from the increase in the number of microtubules at the cell edge. Further, at all stages of assembling the endothelial monolayer, the number of microtubules formed at the cell margin in the area of cell-cell contacts exceeded the number of microtubules in the area of the free lamellae.


DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of function. A powerful predictive model for the function of non-coding DNA can have enormous benefit for both basic science and translational research because over 98% of the human genome is non-coding and 93% of disease-associated variants lie in these regions. To address this need, we propose DanQ, a novel hybrid convolutional and bi-directional long short-term memory recurrent neural network framework for predicting non-coding function de novo from sequence. In the DanQ model, the convolution layer captures regulatory motifs, while the recurrent layer captures long-term dependencies between the motifs in order to learn a regulatory 'grammar' to improve predictions. DanQ improves considerably upon other models across several metrics. For some regulatory markers, DanQ can achieve over a 50% relative improvement in the area under the precision-recall curve metric compared to related models. We have made the source code available at the github repository http://github.com/uci-cbcl/DanQ.


Neocentromeres form efficiently at multiple possible loci in Candida albicans.
Centromeres are critically important for chromosome stability and integrity. Most eukaryotes have regional centromeres that include long tracts of repetitive DNA packaged into pericentric heterochromatin. Neocentromeres, new sites of functional kinetochore assembly, can form at ectopic loci because no DNA sequence is strictly required for assembly of a functional kinetochore. In humans, neocentromeres often arise in cells with gross chromosome rearrangements that rescue an acentric chromosome. Here, we studied the properties of centromeres in Candida albicans, the most prevalent fungal pathogen of humans, which has small regional centromeres that lack pericentric heterochromatin. We functionally delimited centromere DNA on Chromosome 5 (CEN5) and then replaced the entire region with the counter-selectable URA3 gene or other marker genes. All of the resulting cen5Delta::URA3 transformants stably retained both copies of Chr5, indicating that a functional neocentromere had assembled efficiently on the homolog lacking CEN5 DNA. Strains selected to maintain only the cen5Delta::URA3 homolog and no wild-type Chr5 homolog also grew well, indicating that neocentromere function is independent of the presence of any wild-type CEN5 DNA. Two classes of neocentromere (neoCEN) strains were distinguishable: "proximal neoCEN" and "distal neoCEN" strains. Neocentromeres in the distal neoCEN strains formed at loci about 200-450 kb from cen5Delta::URA3 on either chromosome arm, as detected by massively parallel sequencing of DNA isolated by CENP-A(Cse4p) chromatin immunoprecipitation (ChIP). In the proximal neoCEN strains, the neocentromeres formed directly adjacent to cen5Delta::URA3 and moved onto the URA3 DNA, resulting in silencing of its expression. Functional neocentromeres form efficiently at several possible loci that share properties of low gene density and flanking repeated DNA sequences. Subsequently, neocentromeres can move locally, which can be detected by silencing of an adjacent URA3 gene, or can relocate to entirely different regions of the chromosome. The ability to select for neocentromere formation and movement in C. albicans permits mechanistic analysis of the assembly and maintenance of a regional centromere.


Hoeffding's inequality for general Markov chains with its applications to statistical learning.
This paper establishes Hoeffding's lemma and inequality for bounded functions of general-state-space and not necessarily reversible Markov chains. The sharpness of these results is characterized by the optimality of the ratio between variance proxies in the Markov-dependent and independent settings. The boundedness of functions is shown necessary for such results to hold in general. To showcase the usefulness of the new results, we apply them for non-asymptotic analyses of MCMC estimation, respondent-driven sampling and high-dimensional covariance matrix estimation on time series data with a Markovian nature. In addition to statistical problems, we also apply them to study the time-discounted rewards in econometric models and the multi-armed bandit problem with Markovian rewards arising from the field of machine learning.


Spectral response variation of a negative-electron-affinity photocathode in the preparation process.
In order to research the spectral response variation of a negative electron affinity (NEA) photocathode in the preparation process, we have done two experiments on a transmission-type GaAs photocathode. First, an automatic spectral response recording system is described, which is used to take spectral response curves during the activation procedure of the photocathode. By this system, the spectral response curves of a GaAs:Cs-O photocathode measured in situ are presented. Then, after the cathode is sealed with a microchannel plate and a fluorescence screen into the image tube, we measure the spectral response of the tube by another measurement instrument. By way of comparing and analyzing these curves, we can find the typical variation in spectral-responses. The reasons for the variation are discussed. Based on these curves, spectral matching factors of a GaAs cathode for green vegetation and rough concrete are calculated. The visual ranges of night-vision goggles under specific circumstances are estimated. The results show that the spectral response of the NEA photocathode degraded in the sealing process, especially at long wavelengths. The variation has also influenced the whole performance of the intensifier tube.


Metabolic mapping of functional activity in the hypothalamo-neurohypophysial system of the rat.
Physiological stimulation of the hypothalamo-neurohypophysial system by salt loading of rats resulted in a dramatically increased glucose utilization in the posterior pituitary but not in the paraventricular or supraoptic nuclei. The good correlation between glucose utilization and neural activity in the posterior pituitary (that is, nerve terminals) contrasted with the lack of correlation in the paraventricular and supraoptic nuclei (that is, the sites of the cell bodies of the same neurons). This difference in the metabolic response to functional activity between the two regions of these neurons can be explained by the differences in surface-to-volume ratios of these regions.


Insights into preventive measures for dental erosion.
Dental erosion is defined as the loss of tooth substance by acid exposure not involving bacteria. The etiology of erosion is related to different behavioral, biological and chemical factors. Based on an overview of the current literature, this paper presents a summary of the preventive strategies relevant for patients suffering from dental erosion. Behavioral factors, such as special drinking habits, unhealthy lifestyle factors or occupational acid exposure, might modify the extent of dental erosion. Thus, preventive strategies have to include measures to reduce the frequency and duration of acid exposure as well as adequate oral hygiene measures, as it is known that eroded surfaces are more susceptible to abrasion. Biological factors, such as saliva or acquired pellicle, act protectively against erosive demineralization. Therefore, the production of saliva should be enhanced, especially in patients with hyposalivation or xerostomia. With regard to chemical factors, the modification of acidic solutions with ions, especially calcium, was shown to reduce the demineralization, but the efficacy depends on the other chemical factors, such as the type of acid. To enhance the remineralization of eroded surfaces and to prevent further progression of dental wear, high-concentrated fluoride applications are recommended. Currently, little information is available about the efficacy of other preventive strategies, such as calcium and laser application, as well as the use of matrix metalloproteinase inhibitors. Further studies considering these factors are required. In conclusion, preventive strategies for patients suffering from erosion are mainly obtained from in vitro and in situ studies and include dietary counseling, stimulation of salivary flow, optimization of fluoride regimens, modification of erosive beverages and adequate oral hygiene measures.


Exogenous cyclic AMP, cholera toxin, and endotoxin induce expression of the lipopolysaccharide receptor CD14 in murine bone marrow cells: role of purinoreceptors.
Little is known about the mechanisms of lipopolysaccharide (LPS) signaling in immature cells that do not express the LPS receptor CD14 yet. Bone marrow granulocytes do not constitutively express CD14 but can be stimulated by low doses of LPS in the absence of serum and then express an inducible form of LPS receptor (iLpsR). We show that in addition to LPS, cholera toxin (CT) and various cyclic AMP (cAMP) analogs can also induce the expression of iLpsR, which was identified as CD14. Induction was independent of intracellular cAMP. The hypothesis that cAMP analogs act via a cell surface receptor was suggested by the unresponsiveness of trypsin-treated cells to these inducers and by the specific binding of [(3)H]cAMP to the cells. This binding was not inhibited by LPS or CT but was inhibited by various purine derivatives. However, the receptor involved is not a conventional purinoreceptor since both an agonist and an antagonist of such receptors were able to induce iLpsR expression. The results suggest that cAMP analogs and other purine derivatives induce iLpsR after interaction with an unconventional, trypsin-sensitive, purinoreceptor distinct from LPS and CT receptors.