Scientific literacy and preferred resources used by Latin American medical students during the COVID-19 pandemic: A multinational survey.
Background: This study aims to identify the preferred sources for acquiring knowledge about COVID-19 and to evaluate basic knowledge on critical scientific literature appraisal in students from medical schools located in Spanish speaking countries in Latin America. Methods: We designed an online survey of 15 closed-ended questions related to demographics, preferred resources for COVID-19 training, and items to assess critical appraisal skills. A snowball method was used for sampling. We conducted a descriptive analysis and Chi-squared tests to compare the proportion of correct identification of the concept of a preprint and a predatory journal when considering a) self-perceived level of knowledge, b) public vs private school, c) inclusion of a scientific literature appraisal subject in the curriculum, and d) progress in medical school. Results: Our sample included 770 valid responses, out of which most of the participants included were from Mexico (n=283, 36.8%) and Ecuador (n=229, 29.7%). Participants preferred using evidence-based clinical resources (EBCRs) to learn more about COVID-19 (n=182, 23.6%). The preferred study design was case report/series (n=218, 28.1%). We found that only 265 participants correctly identified the concept of a preprint (34.4%), while 243 students (31.6%) correctly identified the characteristics of a predatory journal. We found no significant differences in the proportion of correct answers regardless of the self-perceived level of knowledge, progress in medical school, or scientific literature critical appraisal classes. Conclusion: This study is novel in its approach of identifying sources of knowledge used by Latin American medical students and provides insights into the need to reinforce training in critical appraisal of scientific literature during medical school.


Participatory implementation science to increase the impact of evidence-based cancer prevention and control.
It is critical to accelerate the integration of evidence-based programs, practices, and strategies for cancer prevention and control into clinical, community, and public health settings. While it is clear that effective translation of existing knowledge into practice can reduce cancer burden, it is less clear how best to achieve this. This gap is addressed by the rapidly growing field of implementation science. Given that context influences and is influenced by implementation efforts, engaging stakeholders in the co-production of knowledge and solutions offers an opportunity to increase the likelihood that implementation efforts are useful, scalable, and sustainable in real-world settings. We argue that a participatory implementation science approach is critical, as it supports iterative, ongoing engagement between stakeholders and researchers to improve the pathway between research and practice, create system change, and address health disparities and health equity. This article highlights the utility of participatory implementation science for cancer prevention and control research and addresses (a) the spectrum of participatory research approaches that may be of use, (b) benefits of participatory implementation science, and


Example-Based Image Colorization Using Locality Consistent Sparse Representation.
Image colorization aims to produce a natural looking color image from a given gray-scale image, which remains a challenging problem. In this paper, we propose a novel example-based image colorization method exploiting a new locality consistent sparse representation. Given a single reference color image, our method automatically colorizes the target gray-scale image by sparse pursuit. For efficiency and robustness, our method operates at the superpixel level. We extract low-level intensity features, mid-level texture features, and high-level semantic features for each superpixel, which are then concatenated to form its descriptor. The collection of feature vectors for all the superpixels from the reference image composes the dictionary. We formulate colorization of target superpixels as a dictionary-based sparse reconstruction problem. Inspired by the observation that superpixels with similar spatial location and/or feature representation are likely to match spatially close regions from the reference image, we further introduce a locality promoting regularization term into the energy formulation, which substantially improves the matching consistency and subsequent colorization results. Target superpixels are colorized based on the chrominance information from the dominant reference superpixels. Finally, to further improve coherence while preserving sharpness, we develop a new edge-preserving filter for chrominance channels with the guidance from the target gray-scale image. To the best of our knowledge, this is the first work on sparse pursuit image colorization from single reference images. Experimental results demonstrate that our colorization method outperforms the state-of-the-art methods, both visually and quantitatively using a user study.


NL1 expression level in Nrx1β and the excitability of PV interneurons in mice with POCD.
Effects of NL1 on the expression level of neurexin-1β (Nrx1β) and the excitability of parvalbumin (PV) interneurons in mice with postoperative cognitive dysfunction (POCD) were explored. Eighty 10-month-old C57BL/6 male mice were randomly divided into four groups: control group, control+empty vector group (Control+EV), anesthesia surgery+empty vector group (POCD+EV group) and anesthesia+NL1 overexpression group (POCD+NL1 group), (n=20 per group). The behavioral differences of mice in the four groups were analyzed by means of open field test and fear conditioning test. The expression levels of NL1, PV and Nrx1β were detected by western blot analysis, and the binding between NL1 and Nrx1β was determined by co-immunoprecipitation. The expression level of postsynaptic density protein 95 (PSD95) in hippocampus and changes in the excitability of PV interneurons were further detected. Control and Control+EV groups had no significant difference in each index (P>0.05). Compared with Control+EV group, the percentage of cued freezing time in POCD+EV group decreased significantly, while percentage of cued freezing time was significantly increased in POCD+NL1 group and POCD+EV group (P<0.01). The differences in freezing time were not statistically significant among the 4 groups in the tone-related fear test (P>0.05). Then NL1 was overexpressed in mice with POCD, the protein levels of PV, Nrx1β and PSD95 were subsequently increased, and the interaction between NL1 and Nrx1β protein was enhanced, dramatically increasing the excitability of PV interneurons. The overexpression of NL1 can upregulate the expression levels of PV, Nrx1β and PSD95 in mice with POCD, enhance the interaction between NL1 and Nrx1β and further increase the excitability of PV interneurons, thus restoring the hippocampus-dependent memorial and cognitive impairment in POCD.


Joint brain parametric T1-map segmentation and RF inhomogeneity calibration.
We propose a constrained version of Mumford and Shah's (1989) segmentation model with an information-theoretic point of view in order to devise a systematic procedure to segment brain magnetic resonance imaging (MRI) data for parametric T(1)-Map and T(1)-weighted images, in both 2-D and 3D settings. Incorporation of a tuning weight in particular adds a probabilistic flavor to our segmentation method, and makes the 3-tissue segmentation possible. Moreover, we proposed a novel method to jointly segment the T(1)-Map and calibrate RF Inhomogeneity (JSRIC). This method assumes the average T(1) value of white matter is the same across transverse slices in the central brain region, and JSRIC is able to rectify the flip angles to generate calibrated T(1)-Maps. In order to generate an accurate T(1)-Map, the determination of optimal flip-angles and the registration of flip-angle images are examined. Our JSRIC method is validated on two human subjects in the 2D T(1)-Map modality and our segmentation method is validated by two public databases, BrainWeb and IBSR, of T(1)-weighted modality in the 3D setting.


Renal protective effect of xiao-chai-hu-tang on diabetic nephropathy of type 1-diabetic mice.
Xiao-Chai-Hu-Tang (XCHT), a traditional Chinese medicine formula consisting of seven medicinal plants, is used in the treatment of various diseases. We show here that XCHT could protect type-1 diabetic mice against diabetic nephropathy, using streptozotocin (STZ)-induced diabetic mice and high-glucose (HG)-exposed rat mesangial cell (RMC) as models. Following 4 weeks of oral administration with XCHT, renal functions and renal hypertrophy significantly improved in the STZ-diabetic mice, while serum glucose was only moderately reduced compared to vehicle treatment. Treatment with XCHT in the STZ-diabetic mice and HG-exposed RMC resulted in a decrease in expression levels of TGF-β1, fibronectin, and collagen IV, with concomitant increase in BMP-7 expression. Data from DPPH assay, DHE stain, and CM-H(2)DCFDA analysis indicated that XCHT could scavenge free radicals and inhibit high-glucose-induced ROS in RMCs. Taken together, these results suggest that treatment with XCHT can improve renal functions in STZ-diabetic mice, an effect that is potentially mediated through decreasing oxidative stress and production of TGF-β1, fibronectin, and collagen IV in the kidney during development of diabetic nephropathy. XCHT, therefore merits further investigation for application to improve renal functions in diabetic disorders.


Prenatal Tdap immunization and risk of maternal and newborn adverse events.
Many countries recommend combined tetanus toxoid, reduced diphtheria toxoid and acellular pertussis immunization (Tdap) during pregnancy to stimulate transplacental transmission of pertussis antibodies to newborns. The immune system can be altered during pregnancy, potentially resulting in differing immunization risks in pregnant women. The safety of widespread Tdap immunization during pregnancy needs to be established. Our objective was to assess whether prenatal Tdap immunization was associated with adverse birth outcomes, and to evaluate the effect of timing of Tdap administration on these outcomes. We identified pregnancies at delivery in a large insurance claims database (2010-2014). Tdap immunization was categorized as optimal prenatal (27+weeks), early prenatal (<27weeks), postpartum (≤7days post-delivery), or none. Medical claims were searched to identify maternal adverse immunization reactions (e.g. anaphylaxis, fever, Guillian-Barre syndrome [GBS]), adverse birth outcomes (e.g. preeclampsia/eclampsia, premature rupture or membranes, chorioamnionitis) and newborn outcomes (e.g. respiratory distress, pulmonary hypertension, neonatal jaundice). Women with optimal or early prenatal Tdap were compared to those not immunized in pregnancy, using propensity score-weighted log-binomial regression and Cox proportional hazards models to estimate risk ratios (RR) and hazard ratios (HR). We identified 1,079,034 deliveries and 677,075 linked newborns; 11.5% were immunized optimally and 2.3% immunized early. There were 1 case of post-immunization anaphylaxis, and 12 cases of maternal encephalopathy (all post- delivery); there were no cases of GBS. Optimally-timed immunization was associated with small increased relative risks of: chorioamnionitis [RR=1.11, (95% CI: 1.07-1.15), overall risk=2.8%], and postpartum hemorrhage [RR=1.23 (95% DI: 1.18-1.28), overall risk=2.4%]; however, these relative increases corresponded to low absolute risk increases. Tdap was not associated with increased risk of any adverse newborn outcome. Overall, prenatal Tdap immunization was not associated with newborn adverse events, but potential associations with chorioamnionitis consistent with one previous study and postpartum hemorrhage require further investigation.


The impact of sugar-sweetened beverage intake on rat cardiac function.
Although there is evidence linking sugar-sweetened beverage (SSB) intake with the development of cardio-metabolic diseases, the underlying mechanisms remain unclear. The current study therefore evaluated the effects of SSB consumption by establishing a unique in-house in vivo experimental model. Male Wistar rats were divided into two groups: a) one consuming a popular local SSB (SSB- Jive), and b) a control group (Control-water) for a period of three and six months (n = 6 per group), respectively. Rats were gavaged on a daily basis with an experimental dosage amounting to half a glass per day (in human terms) (SSB vs. water). Cardiac function was assessed at baseline (echocardiography) and following ex vivo ischemia-reperfusion of the isolated perfused working rat heart. Oral glucose tolerance tests and mitochondrial respiratory analyses were also performed. In addition, the role of non-oxidative glucose pathways (NOGPs), i.e. the polyol pathway, hexosamine biosynthetic pathway (HBP) and PKC were assessed. These data show that SSB intake: a) resulted in increased weight gain, but did not elicit major effects in terms of insulin resistance and cardiac function after three and six months, respectively; b) triggered myocardial NOGP activation after three months with a reversion after six months; and c) resulted in some impairment in mitochondrial respiratory capacity in response to fatty acid substrate supply after six months. SSB intake did not result in cardiac dysfunction or insulin resistance. However, early changes at the molecular level may increase risk in the longer term.


Preventing child maltreatment: an evidence-based update.
Child maltreatment is a significant public health problem associated with a broad range of negative outcomes in children and adolescents that can extend into adulthood. This review summarizes information about programs aimed at the prevention of child maltreatment evaluated by controlled trials, with a focus on home visitation programs. It does not include programs aimed at prevention of child sexual abuse, the subject of a separate review in this series. We discuss those programs that include one or more measures of child maltreatment and related outcomes (reports of abuse and neglect, injuries, hospitalizations and emergency room visits). Most programs targeting at-risk families have not shown evidence of effectiveness in preventing abuse or neglect. An important exception is the Nurse Family Partnership (NFP), a program provided by nurses to first-time socially disadvantaged mothers beginning prenatally that has undergone rigorous evaluation in three randomized controlled trials. It has shown consistent effects in reducing reports of maltreatment and associated outcomes as well as additional benefits in maternal and child health in high-risk families. A second exception is the promising Early Start program provided by nurses and social workers to at-risk families beginning postnatally. One randomized controlled trial of the program has shown reduced rates of parental reports of severe abuse and hospital attendance for injuries and poisonings, based on records. The characteristics of the NFP and Early Start programs are discussed with special emphasis on ways in which they differ from other home visitation programs.


HIV type 1 resistance in Kenyan sex workers is not associated with altered cellular susceptibility to HIV type 1 infection or enhanced beta-chemokine production.
A small group of women (n = 80) within the Nairobi-based Pumwani Sex Workers Cohort demonstrates epidemiologic resistance to HIV-1 infection. Chemokine receptor polymorphisms and beta-chemokine overproduction have been among the mechanisms suggested to be responsible for resistance to HIV-1 infection. This study attempts to determine if any of those mechanisms are protecting the HIV-1-resistant women. Genetic analysis of CCR5 and CCR3 from the resistant women demonstrated no polymorphisms associated with resistance. Expression levels of CCR5 among the resistant women were shown to be equivalent to that found in low-risk seronegative (negative) controls, while CXCR4 expression was greater among some of the resistant women. In vitro infection experiments showed that phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) from resistant women were as susceptible to infection to T cell- and macrophage-tropic North American and Kenyan HIV-1 isolates as were the PBMCs from negative controls. No significant difference in circulating plasma levels of MIP-1alpha and MIP-1beta were found between the resistant women and negative or HIV-1-infected controls. In vitro cultures of media and PHA-stimulated PBMCs indicated that the resistant women produced significantly less MIP-1alpha and MIP-1beta than did negative controls and no significant difference in RANTES levels were observed. In contrast to studies in Caucasian cohorts, these data indicate that CCR5 polymorphisms, altered CCR5 and CXCR4 expression levels, cellular resistance to in vitro HIV-1 infection, and increased levels of beta-chemokine production do not account for the resistance to HIV-1 infection observed among the women of the Pumwani Sex Workers Cohort.


Hearing myself with others: sound levels in choral performance measured with separation of one's own voice from the rest of the choir.
The choir singer has two acoustic signals to attend to: the sound of his or her own voice (feedback), and the sound of the rest of the choir (reference). The balance in loudness between feedback and reference is governed mainly by the room acoustics. Although earlier experiments have shown that singers have a fairly large tolerance for imbalance, with references ranging from -23 to +5 dB, experience suggests that, when singers are given control over this parameter, their preferences are much narrower. A quantification of the optimum balance would be useful in the design of concert stages and rehearsal halls. A method is described for measuring the feedback and reference levels as experienced by singers under live performance conditions. Recordings were made using binaural microphones worn by choir singer subjects. With the given combination of choir and room, it was possible to achieve adequate separation of the feedback and reference signals with simple signal processing. The feedback-to-reference ratio averaged over the 12 singers was found to be +3.9 dB, with extremes of +1.5 and +7.3 dB.


Surface-enhanced spectroscopy on plasmonic oligomers assembled by AFM nanoxerography.
Surface-enhanced Raman scattering (SERS) and surface-enhanced fluorescence (SEF) from individual plasmonic oligomers are investigated by confocal Raman micro-spectroscopy and time-resolved fluorescence microscopy coupled to steady state micro-spectroscopy. The nanoparticle (NP) oligomers are made of either ligand protected Au or Au@SiO2 core-shell colloidal NPs, which were assembled into ordered arrays by atomic force microscopy (AFM) nanoxerography. A strong dependence of the SERS emission on the polarization of incident light relative to the specific geometry of the plasmonic oligomer was observed. The SEF studies, performed on a large collection of NP oligomers of various known configurations showed interesting fluorophore decay rate modification and red-shift of the emission spectra. The experimental results are analyzed theoretically by employing finite-difference time-domain (FDTD) simulations on equivalent realistic structures, within the local density of optical states (LDOS) framework. The presented results, together with the proven potential of the LDOS approach as a useful common tool for analyzing both SERS and SEF effects further the general understanding of plasmon-related phenomena in nanoparticle oligomers.


Universal Access to Surgical Care and Sustainable Development in Sub-Saharan Africa: A Case for Surgical Systems Research Comment on "Global Surgery - Informing National Strategies for Scaling Up Surgery in Sub-Saharan Africa".
National level experiences, lessons learnt from the Millennium Development Goal (MDG) era coupled with the academic evidence and proposals generated by the Lancet Commission on Global Surgery (LCoGS) together with the economic arguments and recommendations from the World Bank Group's "Essential Surgery" Disease Control Priorities (DCP3) publication, provided the impetus for political commitments to improve surgical care capacity at the primary level of the healthcare system in low- and middle-income countries (LMICs) as part of their drive towards universal health coverage (UHC) in the form of World Health Organization (WHO) Resolution A68.15. This global commitment from governments must be followed up with development of a Global Action Plan and a global coordination mechanism supported by regional implementation frameworks on the part of the WHO in order for the organisation to better coordinate all stakeholders and sustain the technical support needed to develop and implement national surgical health policy in the form of National Surgical Obstetric and Anaesthesia Plans (NSOAPs). As expounded by Gajewski et al, data and research output on surgical care is essential to informing policy development and programme implementation. This area still remains a challenge in sub-Saharan Africa (SSA) but it is envisaged that countries will include this key component in their ongoing national surgical healthcare policy development and programme implementation. In the Zambian case study, research in the area of Global Surgery investment-the surgical workforce scale-up is used to demonstrate the important role of implementation research in the development and implementation of the Zambian NSOAP as well as the need for international collaborations to this end. Scale-up reviews informed by implementation research to evaluate progress on the commitments contained in Resolution A68.15 and Decision A70.22 are essential to sustain the momentum and to help maintain focus on the gaps in all countries. There are opportunities for non-state actors especially local sub-regional academic institutions, non-governmental organizations (NGOs) and private sector to play a key role in surgical healthcare policy development and implementation research. Collection of and better information management of standardised surgical care indicators is essential for such research, for bi-annual WHO progress reporting and for demonstration of impact to justify and encourage further investments in surgical care.


Inherited variants in mitochondrial biogenesis genes may influence epithelial ovarian cancer risk.
Mitochondria contribute to oxidative stress, a phenomenon implicated in ovarian carcinogenesis. We hypothesized that inherited variants in mitochondrial-related genes influence epithelial ovarian cancer (EOC) susceptibility. Through a multicenter study of 1,815 Caucasian EOC cases and 1,900 controls, we investigated associations between EOC risk and 128 single nucleotide polymorphisms (SNPs) from 22 genes/regions within the mitochondrial genome (mtDNA) and 2,839 nuclear-encoded SNPs localized to 138 genes involved in mitochondrial biogenesis (BIO, n = 35), steroid hormone metabolism (HOR, n = 13), and oxidative phosphorylation (OXP, n = 90) pathways. Unconditional logistic regression was used to estimate OR and 95% CI between genotype and case status. Overall significance of each gene and pathway was evaluated by using Fisher's method to combine SNP-level evidence. At the SNP level, we investigated whether lifetime ovulation, hormone replacement therapy (HRT), and cigarette smoking were confounders or modifiers of associations. Interindividual variation involving BIO was most strongly associated with EOC risk (empirical P = 0.050), especially for NRF1, MTERF, PPARGC1A, ESRRA, and CAMK2D. Several SNP-level associations strengthened after adjustment for nongenetic factors, particularly for MTERF. Statistical interactions with cigarette smoking and HRT use were observed with MTERF and CAMK2D SNPs, respectively. Overall variation within mtDNA, HOR, and OXP was not statistically significant (empirical P > 0.10). We provide novel evidence to suggest that variants in mitochondrial biogenesis genes may influence EOC susceptibility. A deeper understanding of the complex mechanisms implicated in mitochondrial biogenesis and oxidative stress may aid in developing strategies to reduce morbidity and mortality from EOC.


Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition.
Purpose: Despite intense research, treatment options for patients with mesothelioma are limited and offer only modest survival advantage. We screened a large panel of compounds in multiple mesothelioma models and correlated sensitivity with a range of molecular features to detect biomarkers of drug response.Experimental design: We utilized a high-throughput chemical inhibitor screen in a panel of 889 cancer cell lines, including both immortalized and primary early-passage mesothelioma lines, alongside comprehensive molecular characterization using Illumina whole-exome sequencing, copy-number analysis and Affymetrix array whole transcriptome profiling. Subsequent validation was done using functional assays such as siRNA silencing and mesothelioma mouse xenograft models.Results: A subgroup of immortalized and primary MPM lines appeared highly sensitive to FGFR inhibition. None of these lines harbored genomic alterations of FGFR family members, but rather BAP1 protein loss was associated with enhanced sensitivity to FGFR inhibition. This was confirmed in an MPM mouse xenograft model and by BAP1 knockdown and overexpression in cell line models. Gene expression analyses revealed an association between BAP1 loss and increased expression of the receptors FGFR1/3 and ligands FGF9/18. BAP1 loss was associated with activation of MAPK signaling. These associations were confirmed in a cohort of MPM patient samples.Conclusions: A subgroup of mesotheliomas cell lines harbor sensitivity to FGFR inhibition. BAP1 protein loss enriches for this subgroup and could serve as a potential biomarker to select patients for FGFR inhibitor treatment. These data identify a clinically relevant MPM subgroup for consideration of FGFR therapeutics in future clinical studies. Clin Cancer Res; 24(1); 84-94. ©2017 AACR.


Simplified freeform optics design for complicated laser beam shaping.
Control of the optical fields of laser beams, i.e., laser beam shaping, is of great importance to many laser applications. Freeform optics offers plenty of advantages for complex beam shaping requirements, including precise beam control, energy efficiency, compact structure, and relatively low cost. We present a modified ray-mapping method to simplify the freeform optics design for complicated optical field control and achieve a challenging task of producing two prescribed beam profiles on two successive target planes. This method begins by calculating an approximate output ray sequence that connects the two prescribed beam profiles and a corresponding input ray sequence. After setting an initial profile of the first freeform optical surface on the input ray sequence, we can obtain the second freeform optical surface based on the optical path length constancy between the given input wavefront and the computed output wavefront. Then, we can acquire all the normal vectors of the first freeform optical surface using Snell's law and approximately reconstruct the first freeform optical surface by solving a relationship between the surface points and normal vectors using a fast least squares method. The surface construction process is repeated until the stop criterion is satisfied. We design three freeform lenses, and Monte Carlo simulations demonstrate their abilities of simultaneously producing two challenging beam profiles from a divergent Gaussian beam.


Adding flexibility to clinical trial designs: an example-based guide to the practical use of adaptive designs.
Adaptive designs for clinical trials permit alterations to a study in response to accumulating data in order to make trials more flexible, ethical, and efficient. These benefits are achieved while preserving the integrity and validity of the trial, through the pre-specification and proper adjustment for the possible alterations during the course of the trial. Despite much research in the statistical literature highlighting the potential advantages of adaptive designs over traditional fixed designs, the uptake of such methods in clinical research has been slow. One major reason for this is that different adaptations to trial designs, as well as their advantages and limitations, remain unfamiliar to large parts of the clinical community. The aim of this paper is to clarify where adaptive designs can be used to address specific questions of scientific interest; we introduce the main features of adaptive designs and commonly used terminology, highlighting their utility and pitfalls, and illustrate their use through case studies of adaptive trials ranging from early-phase dose escalation to confirmatory phase III studies.


Distance-based microfluidic quantitative detection methods for point-of-care testing.
Equipment-free devices with quantitative readout are of great significance to point-of-care testing (POCT), which provides real-time readout to users and is especially important in low-resource settings. Among various equipment-free approaches, distance-based visual quantitative detection methods rely on reading the visual signal length for corresponding target concentrations, thus eliminating the need for sophisticated instruments. The distance-based methods are low-cost, user-friendly and can be integrated into portable analytical devices. Moreover, such methods enable quantitative detection of various targets by the naked eye. In this review, we first introduce the concept and history of distance-based visual quantitative detection methods. Then, we summarize the main methods for translation of molecular signals to distance-based readout and discuss different microfluidic platforms (glass, PDMS, paper and thread) in terms of applications in biomedical diagnostics, food safety monitoring, and environmental analysis. Finally, the potential and future perspectives are discussed.


Antibiotic resistance in uropathogens across northern Australia 2007-20 and impact on treatment guidelines.
Urinary tract infections are common and are increasingly resistant to antibiotic therapy. Northern Australia is a sparsely populated region with limited access to healthcare, a relatively high burden of disease, a substantial regional and remote population, and high rates of antibiotic resistance in skin pathogens. To explore trends in antibiotic resistance for common uropathogens Escherichia coli and Klebsiella pneumoniae in northern Australia, and how these relate to current treatment guidelines in the community and hospital settings. We used data from an antibiotic resistance surveillance system. We calculated the monthly and yearly percentage of isolates that were resistant in each antibiotic class, by bacterium. We analysed resistance proportions geographically and temporally, stratifying by healthcare setting. Using simple linear regression, we investigated longitudinal trends in monthly resistance proportions and correlation between community and hospital isolates. Our analysis included 177 223 urinary isolates from four pathology providers between 2007 and 2020. Resistance to most studied antibiotics remained <20% (for E. coli and K. pneumoniae, respectively, in 2019: amoxicillin/clavulanate 16%, 5%; cefazolin 17%, 8%; nitrofurantoin 1%, 31%; trimethoprim 36%, 17%; gentamicin 7%, 2%; extended-spectrum cephalosporins 8%, 5%), but many are increasing by 1%-3% (absolute) per year. Patterns of resistance were similar between isolates from community and hospital patients. Antibiotic resistance in uropathogens is increasing in northern Australia, but treatment guidelines generally remain appropriate for empirical therapy of patients with suspected infection (except trimethoprim in some settings). Our findings demonstrate the importance of local surveillance data (HOTspots) to inform clinical decision making and guidelines.


Animal-appropriate housing of ball pythons (Python regius)-Behavior-based evaluation of two types of housing systems.
Considering animal welfare, animals should be kept in animal-appropriate and stress-free housing conditions in all circumstances. To assure such conditions, not only basic needs must be met, but also possibilities must be provided that allow animals in captive care to express all species-typical behaviors. Rack housing systems for snakes have become increasingly popular and are widely used; however, from an animal welfare perspective, they are no alternative to furnished terrariums. In this study, we therefore evaluated two types of housing systems for ball pythons (Python regius) by considering the welfare aspect animal behavior. In Part 1 of the study, ball pythons (n = 35) were housed individually in a conventional rack system. The pythons were provided with a hiding place and a water bowl, temperature control was automatic, and the lighting in the room served as indirect illumination. In Part 2 of the study, the same ball pythons, after at least 8 weeks, were housed individually in furnished terrariums. The size of each terrarium was correlated with the body length of each python. The terrariums contained substrate, a hiding place, possibilities for climbing, a water basin for bathing, an elevated basking spot, and living plants. The temperature was controlled automatically, and illumination was provided by a fluorescent tube and a UV lamp. The shown behavior spectrum differed significantly between the two housing systems (p < 0.05). The four behaviors basking, climbing, burrowing, and bathing could only be expressed in the terrarium. Abnormal behaviors that could indicate stereotypies were almost exclusively seen in the rack system. The results show that the housing of ball pythons in a rack system leads to a considerable restriction in species-typical behaviors; thus, the rack system does not meet the requirements for animal-appropriate housing.


Beta-Band Functional Connectivity is Reorganized in Mild Cognitive Impairment after Combined Computerized Physical and Cognitive Training.
Physical and cognitive idleness constitute significant risk factors for the clinical manifestation of age-related neurodegenerative diseases. In contrast, a physically and cognitively active lifestyle may restructure age-declined neuronal networks enhancing neuroplasticity. The present study, investigated the changes of brain's functional network in a group of elderly individuals at risk for dementia that were induced by a combined cognitive and physical intervention scheme. Fifty seniors meeting Petersen's criteria of Mild Cognitive Impairment were equally divided into an experimental (LLM), and an active control (AC) group. Resting state electroencephalogram (EEG) was measured before and after the intervention. Functional networks were estimated by computing the magnitude square coherence between the time series of all available cortical sources as computed by standardized low resolution brain electromagnetic tomography (sLORETA). A statistical model was used to form groups' characteristic weighted graphs. The introduced modulation was assessed by networks' density and nodes' strength. Results focused on the beta band (12-30 Hz) in which the difference of the two networks' density is maximum, indicating that the structure of the LLM cortical network changes significantly due to the intervention, in contrast to the network of AC. The node strength of LLM participants in the beta band presents a higher number of bilateral connections in the occipital, parietal, temporal and prefrontal regions after the intervention. Our results show that the combined training scheme reorganizes the beta-band functional connectivity of MCI patients. ClinicalTrials.gov Identifier: NCT02313935 https://clinicaltrials.gov/ct2/show/NCT02313935.


Colombian experience with transcatheter aortic valve implantation of medtronic CoreValve.
At our institutions, increasing numbers of aortic stenosis patients were not candidates for surgical aortic valve replacement. Accordingly, we initiated the Cali Colombian Transcatheter Aortic Valve Implantation (TAVI) program. From March 2008 through January 2011, 53 consecutive patients (mean age, 79 ± 6 yr; men, 58%) underwent TAVI with the Medtronic CoreValve System, and data were prospectively collected. Our study's endpoints conformed with Valve Academic Research Consortium recommendations. We report our clinical results.Predicted mortality rates were 25% (interquartile range, 17%-34%) according to logistic EuroSCORE and 6% (interquartile range, 3%-8%) according to the Society of Thoracic Surgeons score. The 30-day mortality rate was 9% (3 intraprocedural deaths, 5 total). The combined 30-day safety endpoint was 30% (major vascular sequelae, 23%; life-threatening bleeding, 12%; myocardial infarction, 4%; major stroke, 4%; and acute kidney injury [stage 3], 2%). Eight patients (15%) required post-implantation balloon dilation and 2 (4%) required valve-in-valve implantation, for a technical device success rate of 77%. Mean peak transvalvular gradient decreased from 74 ± 29 to 17 ± 8 mmHg and mean transvalvular gradient from 40 ± 17 to 8 ± 4 mmHg (both P=0.001). Moderate or severe aortic regurgitation decreased from 32% to 18% (P=0.12) and mitral regurgitation from 32% to 13% (P=0.002). The 1-year survival rate was 81%.We found that TAVI with the CoreValve prosthesis was safe and feasible, with sustained long-term results, for treating aortic stenosis in patients at excessive surgical risk; nonetheless, serious adverse events occurred in 30% of the patients.


Do we really need vision? How blind people "see" the actions of others.
Observing and learning actions and behaviors from others, a mechanism crucial for survival and social interaction, engages the mirror neuron system. To determine whether vision is a necessary prerequisite for the human mirror system to develop and function, we used functional magnetic resonance imaging to compare brain activity in congenitally blind individuals during the auditory presentation of hand-executed actions or environmental sounds, and the motor pantomime of manipulation tasks, with that in sighted volunteers, who additionally performed a visual action recognition task. Congenitally blind individuals activated a premotor-temporoparietal cortical network in response to aurally presented actions that overlapped both with mirror system areas found in sighted subjects in response to visually and aurally presented stimuli, and with the brain response elicited by motor pantomime of the same actions. Furthermore, the mirror system cortex showed a significantly greater response to motor familiar than to unfamiliar action sounds in both sighted and blind individuals. Thus, the mirror system in humans can develop in the absence of sight. The results in blind individuals demonstrate that the sound of an action engages the mirror system for action schemas that have not been learned through the visual modality and that this activity is not mediated by visual imagery. These findings indicate that the mirror system is based on supramodal sensory representations of actions and, furthermore, that these abstract representations allow individuals with no visual experience to interact effectively with others.


Streptococcus pyogenes M1T1 Variants Induce an Inflammatory Neutrophil Phenotype Including Activation of Inflammatory Caspases.
Invasive infections due to group A Streptococcus (GAS) advance rapidly causing tissue degradation and unregulated inflammation. Neutrophils are the primary immune cells that respond to GAS. The neutrophil response to GAS was characterised in response to two M1T1 isolates; 5448 and animal passaged variant 5448AP. Co-incubation of neutrophils with 5448AP resulted in proliferation of GAS and lowered the production of reactive oxygen species when compared with 5448. Infection with both strains invoked neutrophil death, however apoptosis was reduced in response to 5448AP. Both strains induced neutrophil caspase-1 and caspase-4 expression in vitro, with inflammatory caspase activation detected in vitro and in vivo. GAS infections involving strains such as 5448AP that promote an inflammatory neutrophil phenotype may contribute to increased inflammation yet ineffective bacterial eradication, contributing to the severity of invasive GAS infections.


A replication defective recombinant Ad5 vaccine expressing Ebola virus GP is safe and immunogenic in healthy adults.
Ebola virus causes irregular outbreaks of severe hemorrhagic fever in equatorial Africa. Case mortality remains high; there is no effective treatment and outbreaks are sporadic and unpredictable. Studies of Ebola virus vaccine platforms in non-human primates have established that the induction of protective immunity is possible and safety and human immunogenicity has been demonstrated in a previous Phase I clinical trial of a 1st generation Ebola DNA vaccine. We now report the safety and immunogenicity of a recombinant adenovirus serotype 5 (rAd5) vaccine encoding the envelope glycoprotein (GP) from the Zaire and Sudan Ebola virus species, in a randomized, placebo-controlled, double-blinded, dose escalation, Phase I human study. Thirty-one healthy adults received vaccine at 2×10(9) (n=12), or 2×10(10) (n=11) viral particles or placebo (n=8) as an intramuscular injection. Antibody responses were assessed by ELISA and neutralizing assays; and T cell responses were assessed by ELISpot and intracellular cytokine staining assays. This recombinant Ebola virus vaccine was safe and subjects developed antigen specific humoral and cellular immune responses.


Denoising and copy attacks resilient watermarking by exploiting prior knowledge at detector.
Watermarking with both oblivious detection and high robustness capabilities is still a challenging problem. In this paper, we tackle the aforementioned problem. One easy way to achieve blind detection is to use denoising for filtering out the hidden watermark, which can be utilized to create either a false positive (copy attack) or false negative (denoising and remodulation attack). Our basic design methodology is to exploit prior knowledge available at the detector side and then use it to design a "nonblind" embedder. We prove that the proposed scheme can resist two famous watermark estimation-based attacks, which have successfully cracked many existing watermarking schemes. False negative and false positive analyses are conducted to verify the performance of our scheme. The experimental results show that the new method is indeed powerful.


Direct measurement of the substrate preference of uracil-DNA glycosylase.
Site-directed mutants of the herpes simplex virus type 1 uracil-DNA glycosylase lacking catalytic activity have been used to probe the substrate recognition of this highly conserved and ubiquitous class of DNA-repair enzyme utilizing surface plasmon resonance. The residues aspartic acid-88 and histidine-210, implicated in the catalytic mechanism of the enzyme (Savva, R., McAuley-Hecht, K., Brown, T., and Pearl, L. (1995) Nature 373, 487-493; Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E. and Tainer, J. A. (1996) Nature 384, 87-92) were separately mutated to asparagine to allow investigations of substrate recognition in the absence of catalysis. The mutants were shown to be correctly folded and to lack catalytic activity. Binding to single- and double-stranded oligonucleotides, with or without uracil, was monitored by real-time biomolecular interaction analysis using surface plasmon resonance. Both mutants exhibited comparable rates of binding and dissociation on the same uracil-containing substrates. Interaction with single-stranded uracil-DNA was found to be stronger than with double-stranded uracil-DNA, and the binding to Gua:Ura mismatches was significantly stronger than that to Ade:Ura base pairs suggesting that the stability of the base pair determines the efficiency of interaction. Also, there was negligible interaction between the mutants and single- or double-stranded DNA lacking uracil, or with DNA containing abasic sites. These results suggest that it is uracil in the DNA, rather than DNA itself, that is recognized by the uracil-DNA glycosylases.


Learning from hackers: open-source clinical trials.
Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. A similar gap was addressed in the software industry by their open-source software movement. Here, we examine how the social and technical principles of the movement can guide the growth of an open-source clinical trial community.


Etiology of Ageratum Yellow Vein Diseases in South China.
Ageratum conyzoides is a common weed in agricultural regions in Asia. A. conyzoides plants exhibiting yellow vein symptoms were collected from Yunnan and Guangxi provinces of China. Polymerase chain reaction detection and sequence analysis showed that samples collected from Yunnan were mainly infected by Tobacco curly shoot virus (TbCSV) associated with Ageratum yellow vein China betasatellite (AYVCNB), while samples from Guangxi were mostly infected by Papaya leaf curl China virus (PaLCuCNV) and AYVCNB, or by Ageratum yellow vein China virus (AYVCNV) and AYVCNB, with a few exhibiting dual infections by PaLCuCNV, AYVCNV, and AYVCNB. Agrobacterium-mediated inoculation of infectious clones showed that both TbCSV and AYVCNB or PaLCuCNV and AYVCNB produced typical yellow vein symptoms in A. conyzoides. Consequently, Ageratum yellow vein diseases in Yunnan and Guangxi provinces were caused by TbCSV/AYVCNB, PaLCuCNV/AYVCNB, or AYVCNV/ AYVCNB. The implications of these results in relation to the prevalence of begomoviruses in cultivated plants are discussed.


Females are more vulnerable to Internet gaming disorder than males: Evidence from cortical thickness abnormalities.
Male predominance is a well-known feature of Internet gaming disorder (IGD), with a reported male to female ratio of 3:1. Because of the overwhelming focus on males, little is known about the neural basis of sex differences in IGD, especially neuroanatomical features. Thus, investigations on sex differences with an adequate sample size are critical for improving the understanding of biological mechanisms underlying IGD. Structural magnetic resonance imaging data were acquired from 62 IGD subjects (29 males, 33 females) and 71 recreational game users (RGUs) (37 males, 34 females) with well-matched age and education levels. Group-by-sex interaction in cortical thickness was analyzed, and the correlations between cortical thickness and addiction severity were calculated. We detected a group-by-sex interaction in the bilateral rostral middle frontal gyri (MFG), left superior frontal gyrus (SFG), left supramarginal gyrus (SMG), right posterior cingulate cortex (PCC), and right superior parietal lobule (SPL). Post-hoc analyses revealed that, compared with same-sex RGUs, male IGD subjects had increased cortical thickness and female IGD subjects had reduced cortical thickness beside their right PCC. By contrast, male IGD subjects had reduced cortical thickness and female IGD subjects had increased cortical thickness in their right PCC. Moreover, only females showed significant negative correlations between the cortical thickness and their self-reported cravings and Internet addiction test scores. For female IGD subjects, the reduced cortical thickness, combined with the negative correlations of addiction severities, suggests the great effect created by IGD in the brain regions. Males and females may be affected differently by IGD, with females being more vulnerable to it.


Factors affecting British teenagers' contraceptive use at first intercourse: the importance of partner communication.
Despite the growing body of knowledge about teenager's sexual and contraceptive behavior in the United Kingdom, much quantitative work has failed to consider the broader social contexts in which this behavior occurs. A 1999 survey of 963 full-time students aged 16-18 gathered information on individual, contextual and background factors. Logistic regression analyses were conducted to investigate how these factors determine use of a modern method at first sex and whether such use is discussed beforehand. Three factors were significantly associated with the odds of contraceptive use at first sex among young men-discussing contraception beforehand (odds ratios, 5.7-13.8), giving an intimate reason for having sex the first time (6.4) and having parents who portrayed sexuality positively during childhood and the early teenage years (1.2). For young women, five factors significantly predicted use-communication (odds ratios, 6.2-15.0), age at first sex (1.8), not having visited a service provider (5.0), feeling comfortable interacting with teenage males (1.2) and "sort of" or not expecting to have sex (0.2 and 0.4, respectively). Among young men, the factors significantly associated with the odds of having discussed contraception were the level of social deprivation, the length of the relationship and parents' openness to talking about sex; among young women, the factors were the number of intimate reasons given for having sex and the warmth and availability of parents. Efforts to increase young people's ability to negotiate sexual and contraceptive decision-making should be multifaceted. It is essential that parents provide a supportive climate throughout childhood and adolescence, where discussions of sexual issues are acceptable and where families feel comfortable talking openly.


Explaining variance of avian malaria infection in the wild: the importance of host density, habitat, individual life-history and oxidative stress.
Avian malaria (Plasmodium sp.) is globally widespread, but considerable variation exists in infection (presence/absence) patterns at small spatial scales. This variation can be driven by variation in ecology, demography, and phenotypic characters, in particular those that influence the host's resistance. Generation of reactive oxygen species (ROS) is one of the host's initial immune responses to combat parasitic invasion. However, long-term ROS exposure can harm the host and the redox response therefore needs to be adjusted according to infection stage and host phenotype. Here we use experimental and correlational approaches to assess the relative importance of host density, habitat composition, individual level variation and redox physiology for Plasmodium infection in a wild population of great tits, Parus major. We found that 36% of the great tit population was infected with Plasmodium (22% P. relictum and 15% P. circumflexum prevalence) and that patterns of infection were Plasmodium species-specific. First, the infection of P. circumflexum was significantly higher in areas with experimental increased host density, whereas variation in P. relictum infection was mainly attributed to age, sex and reproduction. Second, great tit antioxidant responses - total and oxidizied glutathione - showed age- , sex- and Plasmodium species-specific patterns between infected and uninfected individuals, but reactive oxygen metabolites (ROM) showed only a weak explanatory power for patterns of P. relictum infection. Instead ROM significantly increased with Plasmodium parasitaemia. These results identify some key factors that influence Plasmodium infection in wild birds, and provide a potential explanation for the underlying physiological basis of recently documented negative effects of chronic avian malaria on survival and reproductive success.


Prevalence of metabolic syndrome in a rural area of Brazil.
Metabolic syndrome (MS) is recognized worldwide as an important public health concern. However, little information is available for rural populations in Brazil. The aim was to determine the prevalence and risk factors associated with MS in a rural village in Brazil in 2004. Cross-sectional population-based study, in Virgem das Graças, a rural community in the Jequitinhonha Valley, State of Minas Gerais. MS was the dependent variable, defined as any three of these risk factors: arterial hypertension, high glucose or triglyceride concentrations, low high-density lipoprotein cholesterol and abdominal obesity. MS prevalence, according to selected socioeconomic and demographic variables (age, skin color, marital status, schooling and smoking habits), was determined in 251 subjects aged 20-88 years. Multivariate logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals. MS prevalence was 21.6% (7.7% for men and 33.6% for women); the age-adjusted prevalence was 19.0%. The highest prevalences were observed for women > 60 years of age (52.9%) and women with body mass index (BMI) >or= 25 kg/m(2) (64%). Age, sex and BMI were associated risk factors for MS, while skin color was only significantly associated with MS for women. The models were adjusted for age, smoking habits, marital status, skin color and schooling. BMI and age were independently associated factors for MS in this rural community. These findings provide important evidence on the prevalence of MS as a public health problem, particularly for women and overweight individuals.


Integration of hepatitis B vaccination into rural African primary health care programmes.
To determine the efficacy of hepatitis B vaccine when added to the routine expanded programme on immunisation under field conditions in rural Africa. Infants were immunised according to two schedules--an early schedule at birth, 3 months, and 6 months and a later schedule to correspond with routine vaccination in the expanded programme on immunisation at 3 months, 4 1/2 months, and 6 months. Venda, northern Transvaal, South Africa, a self governing region of 7460 square kilometers varying from rural villages to small towns. The 1989 birth cohort of Venda. Coverage for hepatitis B vaccine at first, second, and third doses; serological assessment of vaccine efficacy by prevalence of antibodies to hepatitis B surface antigen in infants who had completed the three dose course of immunisation; antibodies to hepatitis B core antigen to determine if natural infection occurred. Vaccine coverage for hepatitis B dropped sharply from 99% to 53% to 39% for the first, second, and third dose respectively. In contrast, vaccine coverage was maintained at 97-99% for the three doses of poliomyelitis vaccine. Serological evaluation of vaccine efficacy showed that only 3.5% of recipients of all three doses failed to develop antibodies to hepatitis B surface antigen. Only 6.6% of vaccine recipients were vaccinated according to either the early or later schedules whereas 93.4% received their doses of vaccine at intervals beyond the limits of either of the planned schedules. There was, however, no significant difference in seroconversion to the surface antigen between the "unscheduled" or scheduled groups of those who were vaccinated according to the early or late schedules. The pattern of prevalence of antibodies to hepatitis B core antigen, which showed a sharp fall in children aged over 7 months, suggested that the antibodies were acquired passively rather than by active infection. Supplementation of the present expanded programme on immunisation with hepatitis B vaccine in rural Africa is fraught with difficulties. However, the vaccine was effective within a fairly wide spacing of dosage. Adding hepatitis B vaccine to diphtheria, tetanus, and pertussis as a tetravalent vaccine is proposed as a means of effectively integrating it into the expanded programme on immunisation in Third World settings.


Role of the msaABCR Operon in Cell Wall Biosynthesis, Autolysis, Integrity, and Antibiotic Resistance in Staphylococcus aureus.
Staphylococcus aureus is an important human pathogen in both community and health care settings. One of the challenges with S. aureus as a pathogen is its acquisition of antibiotic resistance. Previously, we showed that deletion of the msaABCR operon reduces cell wall thickness, resulting in decreased resistance to vancomycin in vancomycin-intermediate S. aureus (VISA). In this study, we investigated the nature of the cell wall defect in the msaABCR operon mutant in the Mu50 (VISA) and USA300 LAC methicillin-resistant Staphylococcus aureus (MRSA) strains. Results showed that msaABCR mutant cells had decreased cross-linking in both strains. This defect is typically due to increased murein hydrolase activity and/or nonspecific processing of murein hydrolases mediated by increased protease activity in mutant cells. The defect was enhanced by a decrease in teichoic acid content in the msaABCR mutant. Therefore, we propose that deletion of the msaABCR operon results in decreased peptidoglycan cross-linking, leading to increased susceptibility toward cell wall-targeting antibiotics, such as β-lactams and vancomycin. Moreover, we also observed significantly downregulated transcription of early cell wall-synthesizing genes, supporting the finding that msaABCR mutant cells have decreased peptidoglycan synthesis. More specifically, the msaABCR mutant in the USA300 LAC strain (MRSA) showed significantly reduced expression of the murA gene, whereas the msaABCR mutant in the Mu50 strain (VISA) showed significantly reduced expression of glmU, murA, and murD Thus, we conclude that the msaABCR operon controls the balance between cell wall synthesis and cell wall hydrolysis, which is required for maintaining a robust cell wall and acquiring resistance to cell wall-targeting antibiotics, such as vancomycin and the β-lactams.


Genetic population structure of Italy. I. Geographic patterns of gene frequencies.
The diversity of spatial patterns of 61 allele frequencies for 20 genetic systems (15 loci) in Italy is presented. Blood antigens, enzymes, and proteins were analyzed. The total number of data points over all systems and localities was 1119. We used homogeneity tests, one-dimensional and directional spatial correlograms, and SYMAP interpolated surfaces. The data matrices were reduced by clustering techniques to reveal the principal patterns. Only a few allele frequency surfaces are strongly correlated across loci. All systems but one (ADA) exhibit significant heterogeneity in allele frequencies among the localities. Significant spatial patterns are shown by 27 of the 61 surfaces. Only one pattern (cde; system 4.19) is clinal; another (PGM1) exhibits a pure isolation by distance pattern; the others show long-range differentiation in addition to the short-distance decline of autocorrelation expected under isolation by distance. There is a marked decline in overall genetic similarity with distance for most variables. The 27 spatially significant alleles in Italy are also significantly patterned in Europe, but in all but 2 cases the country-wide and continent-wide patterns differ. The Italian patterns are due to forces specific to Italy. Differential selection for alleles associated with malaria is still evident. Whereas short-range differentiation can with malaria is still evident. Whereas short-range differentiation can be explained by isolation by distance, long-range differentiation appears to be due to demographic changes in certain populations that may be maintained by physical and linguistic isolation.


Renal function outcomes in patients treated for renal masses smaller than 4 cm by ablative and extirpative techniques.
We examined the effect of radical nephrectomy, partial nephrectomy and radio frequency ablation on renal function in patients with stage T1a renal masses. A total of 242 consecutive patients from July 1995 to March 2005 undergoing primary treatment for unilateral renal masses smaller than 4 cm and a normal contralateral kidney were identified. Renal function was calculated using the modified Modification of Diet in Renal Disease equation. The rate of decrease in the glomerular filtration rate below 60 ml per minute 1.73 m2 was compared among the 3 treatment modalities. A total of 86, 85 and 71 patients were treated with radio frequency ablation, partial nephrectomy and radical nephrectomy, respectively. Preoperatively stage 3 chronic kidney disease (glomerular filtration rate less than 60 ml per minute per 1.73 m2) was identified in 65 patients (26.7%), including 26.7%, 27.1% and 26.8% who underwent radio frequency ablation, partial nephrectomy and radical nephrectomy, respectively. Following intervention the 3-year freedom from a glomerular filtration rate decrease of below 60 ml per minute per 1.73 m2 for radio frequency ablation, partial nephrectomy and radical nephrectomy was 95.2%, 70.7% and 39.9%, respectively (p <0.001). Multivariate analysis showed that radical nephrectomy was an independent risk factor vs radio frequency ablation and partial nephrectomy for stage 3 chronic kidney disease (HR 34.3, 95% CI 4.28-275 and 10.9, 95% CI 1.36-88.7, respectively). Decreased renal function is prevalent in patients with small unilateral renal tumors even with a normal contralateral kidney. Ablative or extirpative nephron sparing techniques are effective for preserving renal function in these patients.


Imaging Brain Dynamics Using Independent Component Analysis.
The analysis of electroencephalographic (EEG) and magnetoencephalographic (MEG) recordings is important both for basic brain research and for medical diagnosis and treatment. Independent component analysis (ICA) is an effective method for removing artifacts and separating sources of the brain signals from these recordings. A similar approach is proving useful for analyzing functional magnetic resonance brain imaging (fMRI) data. In this paper, we outline the assumptions underlying ICA and demonstrate its application to a variety of electrical and hemodynamic recordings from the human brain.


Parents' and children's reactions to taking blood in a nutrition survey.
To assess the reactions of parents and their children to the request for a blood sample and an attempt to take blood. 1859 children aged 1.5-4.5 years took part in a national survey of diet and nutrition. A retrospective inquiry of the parents' and children's reported reactions was carried out six to 18 months later by postal questionnaire sent only to the 1157 who had given consent for an attempt to take blood. 866 questionnaires were returned; 790 were from parents of children in whom an attempt to take blood had been successful. Thirteen per cent said that their child had given blood previously. About 30% discussed the request with the family doctor or nurse. Some 90% said that they were given enough information and that the phlebotomist was sympathetic. Attempting to take blood caused upset in over 50%, which, in most, lasted for less than five minutes. A substantial minority were upset for up to 30 minutes and a few much longer. Bruising or bleeding occurred in 20-27%. Degree and duration of upset were both adversely associated with a failed attempt to obtain blood. The majority of preschool children experienced no more than a little upset of short duration after an attempt to take blood, but a substantial minority exhibited a greater degree of upset. These responses should be taken into account when assessing the benefits and risks of the procedure. The best equipment and expertise should be employed for taking blood as successful attempts are less upsetting.


Collateral vessel number, plaque burden, and functional decline in peripheral artery disease.
Associations of collateral vessels and lower extremity plaque with functional decline are unknown. Among people with peripheral artery disease (PAD), we determined whether greater superficial femoral artery (SFA) plaque burden combined with fewer lower extremity collateral vessels was associated with faster functional decline, compared to less plaque and/or more numerous collateral vessels. A total of 226 participants with ankle-brachial index (ABI) <1.00 underwent magnetic resonance imaging of lower extremity collateral vessels and cross-sectional imaging of the proximal SFA. Participants were categorized as follows: Group 1 (best), maximum plaque area < median and collateral vessel number ≥6 (median); Group 2, maximum plaque area < median and collateral vessel number <6; Group 3, maximum plaque area > median and collateral vessel number ≥6; Group 4 (worst), maximum plaque area > median and collateral vessel number <6. Functional measures were performed at baseline and annually for 2 years. Analyses adjust for age, sex, race, comorbidities, and other confounders. Annual changes in usual-paced walking velocity were: Group 1, +0.01 m/s; Group 2, -0.02 m/s; Group 3, -0.01 m/s; Group 4, -0.05 m/s (p-trend=0.008). Group 4 had greater decline than Group 1 (p<0.001), Group 2 (p=0.029), and Group 3 (p=0.010). Similar trends were observed for fastest-paced 4-meter walking velocity (p-trend=0.018). Results were not substantially changed when analyses were repeated with additional adjustment for ABI. However, there were no associations of SFA plaque burden and collateral vessel number with decline in 6-minute walk. In summary, a larger SFA plaque burden combined with fewer collateral vessels is associated with a faster decline in usual and fastest-paced walking velocity in PAD.


Individual Baseline Performance and Electrode Montage Impact on the Effects of Anodal tDCS Over the Left Dorsolateral Prefrontal Cortex.
Anodal transcranial direct current stimulation (tDCS), applied over the left dorsolateral prefrontal cortex (lDLPFC), can produce significant effects on working memory (WM) performance and associated neurophysiological activity. However, results from previous studies are inconsistent and occasionally contradictory. This inconsistency may be attributed to methodological and individual differences during experiments. This study therefore investigated two hypotheses: (1) A multichannel-optimized montage was expected to be more effective than a classical bipolar montage, because of increased focality. (2) The subjects were expected to benefit differently from the stimulation depending on their initial task performance. In a sham-controlled crossover study, 24 healthy participants received bipolar, multichannel, and sham stimulation for 20 min in randomized order, targeting the lDLPFC while performing a 2-back WM task. After stimulation, electroencephalography (EEG) was recorded at rest and during 2-back and nontarget continuous performance task (CPT) performance. Bipolar and multichannel stimulations were both well tolerated and effectively blinded. We found no effect of stimulation on behavioral performance or neuronal oscillations comparing the classical bipolar or multichannel montage with sham stimulation. We did, however, find an interaction between stimulation and initial task performance. For multichannel stimulation, initially low-performing participants tended to improve their WM performance while initially high-performing participants tended to worsen their performance compared to sham stimulation. Both tDCS montages induced changes in neural oscillatory power, which correlated with baseline performance. The worse the participants' initial WM performance was, the more task-related theta power was induced by multichannel and bipolar stimulation. The same effect was observed for alpha power in the nontarget task following multichannel stimulation. Notably, we were not able to show a superiority of multichannel stimulation compared to bipolar stimulation. Still, comparing both montages with sham stimulation, multichannel stimulation led to stronger effects than bipolar stimulation. The current study highlights the importance of investigating different parameters with potential influence on tDCS effects in combination. Our results demonstrate how individual differences in cognitive performance and electrode montages influence effects of tDCS on neuropsychological performance. These findings support the idea of an individualized and optimized stimulation setting, potentially leading to increased tDCS effects.


Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.


Leisure-Time Spent Sitting and Site-Specific Cancer Incidence in a Large U.S. Cohort.
Time spent sitting is distinctly different from accumulating too little physical activity and may have independent deleterious effects. Few studies have examined the association between sitting time and site-specific cancer incidence. Among 69,260 men and 77,462 women who were cancer-free and enrolled in the American Cancer Society Cancer Prevention Study II Nutrition Cohort, 18,555 men and 12,236 women were diagnosed with cancer between 1992 and 2009. Extended Cox proportional hazards regression was used to estimate multivariable-adjusted relative risks (RR) and 95% confidence intervals (CI) of leisure-time spent sitting with total and site-specific cancer incidence. Longer leisure-time spent sitting, after adjustment for physical activity, BMI, and other factors, was associated with risk of total cancer in women (RR = 1.10; 95% CI, 1.04-1.17 for ≥6 hours vs. <3 hours per day), but not men (RR = 1.00; 95% CI, 0.96-1.05). In women, sitting time was associated with risk of multiple myeloma (RR = 1.65; 95% CI, 1.07-2.54), invasive breast cancer (RR = 1.10; 95% CI, 1.00-1.21), and ovarian cancer (RR = 1.43; 95% CI, 1.10-1.87). There were no associations between sitting time and site-specific cancers in men. Longer leisure-time spent sitting was associated with a higher risk of total cancer risk in women, and specifically with multiple myeloma, breast, and ovarian cancers, but sitting time was not associated with cancer risk in men. Further research is warranted to better understand the differences in associations between men and women. For women, these findings support American Cancer Society guidelines for cancer prevention to reduce sitting time when possible.


Population-related variation in plant defense more strongly affects survival of an herbivore than its solitary parasitoid wasp.
The performance of natural enemies, such as parasitoid wasps, is affected by differences in the quality of the host's diet, frequently mediated by species or population-related differences in plant allelochemistry. Here, we compared survival, development time, and body mass in a generalist herbivore, the cabbage moth, Mamestra brassicae, and its solitary endoparasitoid, Microplitis mediator, when reared on two cultivated (CYR and STH) and three wild (KIM, OH, and WIN) populations of cabbage, Brassica oleracea. Plants either were undamaged or induced by feeding of larvae of the cabbage butterfly, Pieris rapae. Development and biomass of M. brassicae and Mi. mediator were similar on both cultivated and one wild cabbage population (KIM), intermediate on the OH population, and significantly lower on the WIN population. Moreover, development was prolonged and biomass was reduced on herbivore-induced plants. However, only the survival of parasitized hosts (and not that of healthy larvae) was affected by induction. Analysis of glucosinolates in leaves of the cabbages revealed higher levels in the wild populations than cultivars, with the highest concentrations in WIN plants. Multivariate statistics revealed a negative correlation between insect performance and total levels of glucosinolates (GS) and levels of 3-butenyl GS. However, GS chemistry could not explain the reduced performance on induced plants since only indole GS concentrations increased in response to herbivory, which did not affect insect performance based on multivariate statistics. This result suggests that, in addition to aliphatic GS, other non-GS chemicals are responsible for the decline in insect performance, and that these chemicals affect the parasitoid more strongly than the host. Remarkably, when developing on WIN plants, the survival of Mi. mediator to adult eclosion was much higher than in its host, M. brassicae. This may be due to the fact that hosts parasitized by Mi. mediator pass through fewer instars, and host growth is arrested when they are only a fraction of the size of healthy caterpillars. Certain aspects of the biology and life-history of the host and parasitoid may determine their response to chemical challenges imposed by the food plant.


A Qualitative Exploration of the Meaning and Understanding of Male Partner Involvement in Pregnancy-Related Care among men in rural South Africa.
Male partner involvement (MPI) during antenatal care has been promoted as an effective intervention to improve maternal and newborn health outcomes. Although MPI is commonly defined as men attending antenatal clinic visits with their female partner, few men attend antenatal clinic visits in rural communities in the province of Mpumalanga, South Africa. The study aimed to qualitatively explore the meaning and understanding of MPI as perceived by men visiting primary health care clinics in rural communities in Mpumalanga. Six focus groups discussions (n = 53) were conducted, digitally recorded, simultaneously transcribed, and translated verbatim into English. Data were analyzed using thematic content analysis. Perceptions of male roles during and after pregnancy differed among men. Male involvement was understood as giving instrumental support to female partners through financial help, helping out with physical tasks, and providing emotional support. Accompanying female partners to the clinic was also viewed as partner support, including behaviors such as holding a spot for her in the clinic queues. Community attitudes, traditional beliefs, and negative experiences in health facilities were barriers for MPI. This study provides support for concerted efforts to work with both men and women within the cultural context to explore the important roles of all members of the family in working together to provide the best possible health outcomes for mother and infant. In particular, future interventions should focus on making antenatal care services more responsive to male partners, and improving male partner accessibility in health care facilities.


The relative roles of electrostatics and dispersion in the stabilization of halogen bonds.
In this work we highlight recent work aimed at the characterization of halogen bonds. Here we discuss the origins of the σ-hole, the modulation of halogen bond strength by changing of neighboring chemical groups (i.e. halogen bond tuning), the performance of various computational methods in treating halogen bonds, and the strength and character of the halogen bond, the dihalogen bond, and two hydrogen bonds in bromomethanol dimers (which serve as model complexes) are compared. Symmetry adapted perturbation theory analysis of halogen bonding complexes indicates that halogen bonds strongly depend on both dispersion and electrostatics. The electrostatic interaction that occurs between the halogen σ-hole and the electronegative halogen bond donor is responsible for the high degree of directionality exhibited by halogen bonds. Because these noncovalent interactions have a strong dispersion component, it is important that the computational method used to treat a halogen bonding system be chosen very carefully, with correlated methods (such as CCSD(T)) being optimal. It is also noted here that most forcefield-based molecular mechanics methods do not describe the halogen σ-hole, and thus are not suitable for treating systems with halogen bonds. Recent attempts to improve the molecular mechanics description of halogen bonds are also discussed.


Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain.
The continual evolution of SARS-CoV-2 and the emergence of variants that show resistance to vaccines and neutralizing antibodies threaten to prolong the COVID-19 pandemic. Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. Here, we develop deep mutational learning (DML), a machine-learning-guided protein engineering technology, which is used to investigate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as Omicron, thus guiding the development of therapeutic antibody treatments and vaccines for COVID-19.


More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains.
While the lateral organization of plasma membrane components has been shown to control binding of Wnt ligands to their receptors preferentially in the ordered membrane domains, the role of posttranslational lipid modification of Wnt on this selective binding is unknown. Here, we identify that the canonical Wnt is presumably acylated by palmitic acid, a saturated 16-carbon fatty acid, at a conserved serine residue. Acylation of Wnt3 is dispensable for its secretion and binding to Fz8 while it is essential for Wnt3's proper binding and domain-like diffusion in the ordered membrane domains. We further unravel that non-palmitoylated Wnt3 is unable to activate Wnt/β-catenin signaling either in zebrafish embryos or in mammalian cells. Based on these results, we propose that the lipidation of canonical Wnt, presumably by a saturated fatty acid, determines its competence in interacting with the receptors in the appropriate domains of the plasma membrane, ultimately keeping the signaling activity under control.


Stylized and abstract painterly rendering system using a multiscale segmented sphere hierarchy.
This paper presents a novel system framework for interactive, three-dimensional, stylized, abstract painterly rendering. In this framework, the input models are first represented using 3D point sets and then this point-based representation is used to build a multiresolution bounding sphere hierarchy. From the leaf to root nodes, spheres of various sizes are rendered into multiple-size strokes on the canvas. The proposed sphere hierarchy is developed using multiscale region segmentation. This segmentation task assembles spheres with similar attribute regularities into a meaningful region hierarchy. These attributes include colors, positions, and curvatures. This hierarchy is very useful in the following respects: 1) it ensures the screen-space stroke density, 2) controls different input model abstractions, 3) maintains region structures such as the edges/boundaries at different scales, and 4) renders models interactively. By choosing suitable abstractions, brush stroke, and lighting parameters, we can interactively generate various painterly styles. We also propose a novel scheme that reduces the popping effect in animation sequences. Many different stylized images can be generated using the proposed framework.


Fine-needle aspiration biopsy of the thyroid. The problem of suspicious cytologic findings.
Cases in which thyroid nodules yielded suspicious cytologic findings on fine-needle aspiration biopsy were prospectively studied during a 3-year period. Of 1970 patients, 333 (17%) had suspicious cytologic findings; from this group, the cases of 253 patients were studied. The cytologic diagnoses were 96 (38%) H urthle cell neoplasms, 84 (33%) follicular cell neoplasms, and 73 (29%) nonspecific diagnoses. A thyroid scan was obtained in 123 of 203 (61%) patients with a solitary nodule, and the nodules were hypofunctional in 102 (83%). Malignant lesions were found in 60 (24%) of the 253 patients. Our findings are consistent with reports that 20% of patients who have a fine-needle aspiration biopsy will have suspicious cytologic findings and that of these, 20% may have a malignant lesion. Thyroid scanning will not distinguish between benign and malignant thyroid lesions that are suspicious on cytologic examination. Surgical excision of all suspicious lesions seems reasonable.


The Use of Targeted Next Generation Sequencing to Explore Candidate Regulators of TGF-β1's Impact on Kidney Cells.
Aims/Hypothesis: Transforming growth factor-beta (TGF-β1) plays an important regulatory role in the progression of chronic kidney failure. Further, damage to kidney glomerular mesangial cells is central to the progression of diabetic nephropathy. The aim of this study was to explore the genetic associations between mRNA, microRNA, and epigenetics in mesangial cells in response to TGF-β1. Methods: The regulatory effects of TGF-β1 on mesangial cells were investigated at different molecular levels by treating mesangial cells with TGF-β1 for 3 days followed by genome-wide miRNA, RNA, DNA methylation, and H3K27me3 expression profiling using next generation sequencing (NGS). Results: Our results provide the first comprehensive, computationally integrated report of RNA-Seq, miRNA-Seq, and epigenomic analyses across all genetic variations, confirming the occurrence of DNA methylation and H3K27me3 in response to TGF-β1. Our findings show that the expression of KLF7 and Gja4 are involved in TGF-β1 regulated DNA methylation. Our data also provide evidence of the association between epigenetic changes and the expression of genes closely related to TGF-β1 regulation. Conclusion: This study has advanced our current knowledge of mechanisms that contribute to the expression of TGF-β1-regulated genes involved in the pathogenesis of kidney disease. The molecular underpinnings of TGF-β1 stimulation of kidney cells was determined, thereby providing a robust platform for further target exploration.


A livelihood in a risky environment: Farmers' preferences for irrigation with wastewater in Hyderabad, India.
Most cities in developing countries fail to treat their wastewater comprehensively. Consequently, farmers downstream use poor-quality water for irrigation. This practice implies risks for farmers, consumers and the environment. Conversely, this water supply supports the livelihood of these farmers and other stakeholders along the value chains. Linking safer options for wastewater management with irrigation could therefore be a win-win solution: removing the risks for society and maintaining the benefits for farmers. However, in developing countries, the high investment costs for the required treatment are problematic and the willingness of farmers to pay for the water (cost recovery) is often questionable. Using a choice experiment, this paper gives insight into farmers' preferences for wastewater use scenarios, quantifying their willingness to pay. The case study is Hyderabad, India. Farmers there prefer water treatment and are prepared to pay a surplus for this. Considering the cost-recovery challenge, this information could be valuable for planning small on site wastewater treatment systems.


Sequential steps in DNA replication are inhibited to ensure reduction of ploidy in meiosis.
Meiosis involves two successive rounds of chromosome segregation without an intervening S phase. Exit from meiosis I is distinct from mitotic exit, in that replication origins are not licensed by Mcm2-7 chromatin binding, but spindle disassembly occurs during a transient interphase-like state before meiosis II. The absence of licensing is assumed to explain the block to DNA replication, but this has not been formally tested. Here we attempt to subvert this block by expressing the licensing control factors Cdc18 and Cdt1 during the interval between meiotic nuclear divisions. Surprisingly, this leads only to a partial round of DNA replication, even when these factors are overexpressed and effect clear Mcm2-7 chromatin binding. Combining Cdc18 and Cdt1 expression with modulation of cyclin-dependent kinase activity, activation of Dbf4-dependent kinase, or deletion of the Spd1 inhibitor of ribonucleotide reductase has little additional effect on the extent of DNA replication. Single-molecule analysis indicates this partial round of replication results from inefficient progression of replication forks, and thus both initiation and elongation replication steps may be inhibited in late meiosis. In addition, DNA replication or damage during the meiosis I-II interval fails to arrest meiotic progress, suggesting absence of checkpoint regulation of meiosis II entry.


Effect of troglitazone on body fat distribution in type 2 diabetic patients.
Troglitazone was recently reported to specifically promote the differentiation of pre-adipocytes into adipocytes in vitro in subcutaneous fat only, indicating a relation to insulin-resistance-improving action of troglitazone. To expand on this finding, we investigated at the clinical level how long-term administration of troglitazone influences the body fat distribution in type 2 diabetic patients. Troglitazone (400 mg/day) was administered for 6 months to 30 type 2 diabetic patients whose glycemic control was poor. A total of 18 patients received diet therapy alone (in the single-treatment group, BMI 26.0 +/- 4.6, HbA1c 8.2 +/- 1.7%), and 12 patients concomitantly received glibenclamide (1.25-7.5 mg/day) (in the concomitant sulfonylurea group, BMI 25.4 +/- 4.7, HbA1c 9.2 +/- 1.2%). BMI, HbA1c, serum lipid level, and body fat distribution, which were determined by computed tomography (CT) scan at the umbilical level, were measured and compared before and after troglitazone treatment. During the 6-month troglitazone treatment, HbA1c levels decreased and BMI increased in both groups. As for body fat distribution in the single-treatment group, visceral fat area (VFA) decreased (from 118.3 +/- 54.3 to 101.1 +/- 50.8 cm2; P < 0.001), and subcutaneous fat area (SFA) increased (from 189.7 +/- 93.3 to 221.6 +/- 101.6 cm2; P < 0.001), resulting in a decrease in visceral/subcutaneous (V/S) ratio (from 0.74 +/- 0.48 to 0.50 +/- 0.32; P < 0.001). In the concomitant sulfonylurea group, VFA was unchanged (from 108.1 +/- 53.5 to 112.5 +/- 59.9 cm2), while SFA increased (from 144.6 +/- 122.0 to 180.5 +/- 143.5 cm2; P < 0.01), thereby decreasing the V/S ratio (from 0.91 +/- 0.46 to 0.77 +/- 0.44; P < 0.01). The serum triglyceride level and the area under glucose curve during the 75-g oral glucose tolerance test decreased significantly in the single-treatment group. According to our data, troglitazone appears to promote fat accumulation in the subcutaneous adipose tissue rather than in the visceral adipose tissue in mildly obese Japanese people with type 2 diabetes. This shift of energy accumulation from the visceral to subcutaneous adipose tissue may greatly contribute to the troglitazone-mediated amelioration of insulin resistance.


Physicians married or partnered to physicians: a comparative study in the American College of Surgeons.
Dual-physician relationships are increasingly common. In this study, the authors explore how surgeons in dual-physician relationships differ from other partnered surgeons in their demographics, practice characteristics, family lives, distress, and job satisfaction. In 2008, members of the American College of Surgeons were asked to complete a survey that included questions on burnout, work-home conflict, and career satisfaction. Among 7,905 responding surgeons (a 32% response rate), 7,120 (90%) had a domestic partner (DP). Half (3,471 of 7,120 [48.8%]) of DPs did not work outside the home, 16.4% (1,165) were physicians, and 34.9% (2,484) were working nonphysicians. Surgeons whose DP was a physician were younger, newer to practice, were more likely to delay having children and to believe childrearing had slowed their career advancement, and were less likely to believe that they had enough time for their personal and family life compared with their colleagues whose DP was a working nonphysician or stayed at home (all p < 0.05). Surgeons in dual-physician relationships more often experienced a recent career conflict with their DP and a work-home conflict than surgeons whose DPs were working nonphysicians (all p < 0.0001). Surgeons whose DP is another surgeon face even greater challenges in these areas. Physicians married or partnered to another physician were more likely to have depressive symptoms and low mental quality of life than surgeons whose DP stayed at home (all p < 0.05). Surgeons whose DP stayed at home appear to be more satisfied with their career (p = 0.0006). Surgeons whose DP is another physicians appear to experience greater challenges balancing personal and professional life than surgeons whose DP is a working nonphysicians or whose DP stays at home.


A double-blind, placebo-controlled study of the short term effects of a spring water supplemented with magnesium bicarbonate on acid/base balance, bone metabolism and cardiovascular risk factors in postmenopausal women.
A number of health benefits including improvements in acid/base balance, bone metabolism, and cardiovascular risk factors have been attributed to the intake of magnesium rich alkaline mineral water. This study was designed to investigate the effects of the regular consumption of magnesium bicarbonate supplemented spring water on pH, biochemical parameters of bone metabolism, lipid profile and blood pressure in postmenopausal women. In this double-blind, placebo-controlled, parallel-group, study, 67 postmenopausal women were randomised to receive between 1500 mL and 1800 mL daily of magnesium bicarbonate supplemented spring water (650 mg/L bicarbonate, 120 mg/L magnesium, pH 8.3-8.5) (supplemented water group) or spring water without supplements (control water group) over 84 days. Over this period biomarkers of bone turnover (serum parathyroid hormone (PTH), 1,25-dihydroxyvitamin D, osteocalcin, urinary telopeptides and hydroxyproline), serum lipids (total cholesterol, HDL-cholesterol, LDL-cholesterol and triglycerides), venous and urinary pH were measured together with measurements of standard biochemistry, haematology and urine examinations.Serum magnesium concentrations and urinary pH in subjects consuming the magnesium bicarbonate supplemented water increased significantly at Day 84 compared to subjects consuming the spring water control (magnesium - p = 0.03; pH - p = 0.018). The consumption of spring water led to a trend for an increase in parathyroid hormone (PTH) concentrations while the PTH concentrations remained stable with the intake of the supplemented spring water. However there were no significant effects of magnesium bicarbonate supplementation in changes to biomarkers of bone mineral metabolism (n-telopeptides, hydroxyproline, osteocalcin and 1,25-dihydroxyvitamin D) or serum lipids or blood pressure in postmenopausal women from Day 0 to Day 84. Short term regular ingestion of magnesium bicarbonate supplemented water provides a source of orally available magnesium. Long term clinical studies are required to investigate any health benefits. ACTRN12609000863235.


Jumonji domain containing 1A is a novel prognostic marker for colorectal cancer: in vivo identification from hypoxic tumor cells.
This study aimed to identify novel hypoxia-inducible and prognostic markers in vivo from hypoxic tumor cells. Using carbonic anhydrase 9 and CD34 as a guide for hypoxic tumor cells, laser capture microdissection was used to isolate colorectal cancer (CRC) liver metastases. The samples were analyzed by microarray analysis, in parallel with five CRC cell lines cultured under hypoxic conditions. To evaluate the prognostic impact of the expression of certain genes, samples from a total of 356 CRC patients were analyzed by microarray or quantitative reverse transcription-PCR. In vitro mechanistic studies and in vivo therapeutic experiments were also done about a histone H3 Lys(9) demethylase, Jumonji domain containing 1A (JMJD1A). Several candidate genes were identified by microarray analysis of liver metastases and culturing of CRC cells under hypoxic conditions. Among them, we found that JMJD1A was a novel independent prognostic factor for CRC (P = 0.013). In vitro assays revealed that loss of JMJD1A by small interfering RNA treatment was associated with a reduction of proliferative activity and decrease in invasion of CRC cell lines. Furthermore, treatment with an adenovirus system for antisense JMJD1A construct displayed prominent therapeutic effects when injected into established tumor xenografts of the CRC cell lines HCT116 and DLD1. JMJD1A is a useful biomarker for hypoxic tumor cells and a prognostic marker that could be a promising therapeutic target against CRC.


Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells.
Hematopoietic stem cell renewal and differentiation are regulated through epigenetic processes. The conversion of 5-methylcytosine into 5-hydroxymethylcytosine (5hmC) by ten-eleven-translocation enzymes provides new insights into the epigenetic regulation of gene expression during development. Here, we studied the potential gene regulatory role of 5hmC during human hematopoiesis. We used reduced representation of 5-hydroxymethylcytosine profiling (RRHP) to characterize 5hmC distribution in CD34+ cells, CD4+ T cells, CD19+ B cells, CD14+ monocytes and granulocytes. In all analyzed blood cell types, the presence of 5hmC at gene bodies correlates positively with gene expression, and highest 5hmC levels are found around transcription start sites of highly expressed genes. In CD34+ cells, 5hmC primes for the expression of genes regulating myeloid and lymphoid lineage commitment. Throughout blood cell differentiation, intragenic 5hmC is maintained at genes that are highly expressed and required for acquisition of the mature blood cell phenotype. Moreover, in CD34+ cells, the presence of 5hmC at enhancers associates with increased binding of RUNX1 and FLI1, transcription factors essential for hematopoiesis. Our study provides a comprehensive genome-wide overview of 5hmC distribution in human hematopoietic cells and new insights into the epigenetic regulation of gene expression during human hematopoiesis.


Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium.
Nontyphoidal salmonellae are among the leading causes of food-borne disease in the United States. Because of the importance of Salmonella enterica in food-borne disease, numerous typing methodologies have been developed. Among the several molecular typing methods, pulsed-field gel electrophoresis (PFGE) is currently considered the "gold standard" technique in typing Salmonella. The aim of this study was to compare the discriminatory power of PFGE to multilocus sequence typing (MLST) in typing Salmonella enterica serovar Typhimurium clinical isolates. A total of 85 Salmonella Typhimurium clinical isolates from cattle were used in this study. PFGE using XbaI was performed on the 85 isolates by the Centers for Disease Control and Prevention method, and data were analyzed using the BioNumerics software package. Fifty PFGE profiles were observed among the isolates, and these grouped into three major clusters. For the MLST analysis, the manB, pduF, glnA, and spaM genes were amplified by PCR from the same 85 isolates. DNA sequencing of these four genes, manB, pduF, glnA, and spaM, showed no genetic diversity among the isolates tested, with a 100% identity in nucleotide sequence. Moreover, the DNA sequences of the aforementioned genes showed 100% identity to the sequence reported in GenBank for the S. enterica serovar Typhimurium LT2 strain. Therefore, MLST, using these genes, lacks the discriminatory power of PFGE for typing Salmonella enterica serovar Typhimurium.


Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids.
Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids. We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations. Sequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs.