RBP-Jkappa/SHARP recruits CtIP/CtBP corepressors to silence Notch target genes.
Notch is a transmembrane receptor that determines cell fates and pattern formation in all animal species. After ligand binding, proteolytic cleavage steps occur and the intracellular part of Notch translocates to the nucleus, where it targets the DNA-binding protein RBP-Jkappa/CBF1. In the absence of Notch, RBP-Jkappa represses Notch target genes through the recruitment of a corepressor complex. We and others have identified SHARP as a component of this complex. Here, we functionally demonstrate that the SHARP repression domain is necessary and sufficient to repress transcription and that the absence of this domain causes a dominant negative Notch-like phenotype. We identify the CtIP and CtBP corepressors as novel components of the human RBP-Jkappa/SHARP-corepressor complex and show that CtIP binds directly to the SHARP repression domain. Functionally, CtIP and CtBP augment SHARP-mediated repression. Transcriptional repression of the Notch target gene Hey1 is abolished in CtBP-deficient cells or after the functional knockout of CtBP. Furthermore, the endogenous Hey1 promoter is derepressed in CtBP-deficient cells. We propose that a corepressor complex containing CtIP/CtBP facilitates RBP-Jkappa/SHARP-mediated repression of Notch target genes.


Early postoperative feeding with elemental diet.
The value of early postoperative feeding with an elemental diet was assessed in 30 patients after major gastrointestinal operations. The patients were allocated at random to conventional treatment (control group) or feeding with the elemental diet (ED group). The clinical and metabolic course of the 15 patients in the ED group was significantly better than that of the controls. Patients in the ED group lost less weight and had a shorter stay in hospital. Negative nitrogen balance was more pronounced in the control group throughout the seven postoperative days. Energy intake was higher in the ED group. Provided elemental feeding is used with caution, it may be given from the first postoperative day. Patients do better metabolically and require shorter stays in hospital.


Multiple steps in the localization of bicoid RNA to the anterior pole of the Drosophila oocyte.
The anterior region of the Drosophila embryonic pattern is determined by a gradient of the bicoid (bcd) protein. The correct formation of this gradient requires the localization of bcd RNA to the anterior pole of the egg. Here we use a wholemount in situ technique to examine the process of bcd RNA localization during oogenesis and embryogenesis. While bcd protein becomes distributed in a gradient that extends throughout the anterior two thirds of the early embryo, bcd RNA remains restricted to a much smaller region at the anterior pole. The difference between these distributions indicates that the shape of the protein gradient must depend to some extent on the posterior movement of the protein after it has been synthesized. Four distinct phases of bcd RNA localization can be distinguished during oogenesis. Between stages 6 and 9 of oogenesis, the RNA accumulates in a ring at the anterior end of the oocyte. During the second phase, in stage 9-10a follicles, the RNA also localizes to the apical regions of the nurse cells, demonstrating that the nurse cells possess an intrinsic polarity. As the nurse cells contract during stages 10b-11, all of the bcd RNA becomes localized to the cortex at the anterior end of the oocyte. During a final phase that must occur between stage 12 of oogenesis and egg deposition, the RNA becomes localized to a spherical region that occupies a slightly dorsal position at the anterior pole.(ABSTRACT TRUNCATED AT 250 WORDS)


Phase coupling in a cerebro-cerebellar network at 8-13 Hz during reading.
Words forming a continuous story were presented to 9 subjects at frequencies ranging from 5 to 30 Hz, determined individually to render comprehension easy, effortful, or practically impossible. We identified a left-hemisphere neural network sensitive to reading performance directly from the time courses of activation in the brain, derived from magnetoencephalography data. Regardless of the stimulus rate, communication within the long-range neural network occurred at a frequency of 8-13 Hz. Our coherence-based detection of interconnected nodes reproduced several brain regions that have been previously reported as active in reading tasks, based on traditional contrast estimates. Intriguingly, the face motor cortex and the cerebellum, typically associated with speech production, and the orbitofrontal cortex, linked to visual recognition and working memory, additionally emerged as densely connected components of the network. The left inferior occipitotemporal cortex, involved in early letter-string or word-specific processing, and the cerebellum turned out to be the main forward driving nodes of the network. Synchronization within a subset of nodes formed by the left occipitotemporal, the left superior temporal, and orbitofrontal cortex was increased with the subjects' effort to comprehend the text. Our results link long-range neural synchronization and directionality with cognitive performance.


Does physical exercise improve quality of life of advanced cancer patients?
We discuss the principal issues about physical activity in advanced cancer patients through the analyses of the last articles and our experience in this field. The efficacy of exercise training intervention could improve quality of life (QOL), fatigue and well being in advanced cancer patients. Several published studies have included, nevertheless, patients with early stage of disease and more recently, populations of patients with local advanced tumors of the breast, rectum and lung, who are undergoing neoadjuvant therapy. Despite the insufficient sample of patients in these studies, physical exercise is considered to improve both cardiopulmonary function and physical muscle fitness. Cancer-related fatigue is a devastating symptom in advanced cancer patients that implies loss of mobility and independence. Physical exercise could be a treatment to increase skeletal muscle endurance and improve well being. In palliative medicine, physical activity could be applied to medical assistance or to design prospective and controlled trials so as to evaluate possible usefulness.


Maternal disturbance in activated sphingolipid metabolism causes pregnancy loss in mice.
Uterine decidualization, a process that occurs in response to embryo implantation, is critical for embryonic survival and thus is a key event for successful pregnancy. Here we show that the sphingolipid metabolic pathway is highly activated in the deciduum during pregnancy and disturbance of the pathway by disruption of sphingosine kinase (Sphk) genes causes defective decidualization with severely compromised uterine blood vessels, leading to early pregnancy loss. Sphk-deficient female mice (Sphk1(-/-)Sphk2(+/-)) exhibited both an enormous accumulation of dihydrosphingosine and sphingosine and a reduction in phosphatidylethanolamine levels in pregnant uteri. These mice also revealed increased cell death in decidual cells, decreased cell proliferation in undifferentiated stromal cells, and massive breakage of decidual blood vessels, leading to uterine hemorrhage and early embryonic lethality. Thus, sphingolipid metabolism regulates proper uterine decidualization and blood vessel stability. Our findings also suggest that disturbance in sphingolipid metabolism may be considered as a cause of pregnancy loss in humans.


Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants.
Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.


Gene-expression profiles in hereditary breast cancer.
Many cases of hereditary breast cancer are due to mutations in either the BRCA1 or the BRCA2 gene. The histopathological changes in these cancers are often characteristic of the mutant gene. We hypothesized that the genes expressed by these two types of tumors are also distinctive, perhaps allowing us to identify cases of hereditary breast cancer on the basis of gene-expression profiles. RNA from samples of primary tumor from seven carriers of the BRCA1 mutation, seven carriers of the BRCA2 mutation, and seven patients with sporadic cases of breast cancer was compared with a microarray of 6512 complementary DNA clones of 5361 genes. Statistical analyses were used to identify a set of genes that could distinguish the BRCA1 genotype from the BRCA2 genotype. Permutation analysis of multivariate classification functions established that the gene-expression profiles of tumors with BRCA1 mutations, tumors with BRCA2 mutations, and sporadic tumors differed significantly from each other. An analysis of variance between the levels of gene expression and the genotype of the samples identified 176 genes that were differentially expressed in tumors with BRCA1 mutations and tumors with BRCA2 mutations. Given the known properties of some of the genes in this panel, our findings indicate that there are functional differences between breast tumors with BRCA1 mutations and those with BRCA2 mutations. Significantly different groups of genes are expressed by breast cancers with BRCA1 mutations and breast cancers with BRCA2 mutations. Our results suggest that a heritable mutation influences the gene-expression profile of the cancer.


Crowdsourcing data collection of the retail tobacco environment: case study comparing data from crowdsourced workers to trained data collectors.
To assess whether crowdsourcing is a viable option for conducting surveillance of point of sale (POS) tobacco marketing practices. We posted jobs to an online crowdsourcing platform to audit 194 Florida licensed tobacco retailers over a 3-week period. During the same period, trained data collectors conducted audits at the same retail locations. Data were collected on cigarette advertising, cigarette promotions and product availability (electronic cigarettes, snus and dissolvables). We compared data collected by crowdsourced workers and trained staff and computed frequencies, percent agreement and inter-rater reliability. Photographs of e-cigarettes and exterior cigarette advertisements submitted by crowdsourced workers were used to validate responses. Inter-rater reliability between crowdsourced and trained data collectors was moderate to high for coding exterior cigarette advertisements, product availability and some tobacco promotions, but poor to fair when coding presence of sales and interior cigarette advertisements. Photos submitted by crowdsourced workers confirmed e-cigarette availability that was missed by trained data collectors in three stores. Crowdsourcing may be a promising form of data collection for some POS tobacco measures. Future studies should examine the cost-effectiveness of crowdsourcing compared with traditional trained data collectors and assess which POS measures are most amenable to crowdsourcing.


Familial factors in bladder carcinoma.
Surprisingly, little is known about host factors in cases of bladder carcinoma. We investigated 2 families prone to transitional cell carcinoma of the bladder. A high degree of pathology verification of cancer of all anatomic sites and a meticulous recording of genealogy, associated diseases and environmental exposures, when known, have allowed a more cogent appraisal of cancer etiology. It is reasonable to assume that members of the subject families may be more susceptible to variable carcinogenic exposures, a concept that is in accord with a genetic-environmental interaction hypothesis for cancer etiology. In addition to increased surveillance of high risk patients for earlier detection of bladder cancer, cancer control measures also should take into consideration preventive programs directed toward the avoidance of known carcinogenic exposures, such as cigarette smoking in high risk relatives of cancer-affected probands. We propose that the etiology of familial bladder cancer may be complex, involving possible other associated malignant neoplasms and/or certain non-neoplastic disorders, in addition to specific carcinogenic exposures. There is a serious need for the detailed reporting of families prone to bladder cancer wherein all of these potentially important associated factors are considered, so that a fuller appraisal of etiology might be achieved.


Invasion and fixation of sex-reversal genes.
We simulated a meta-population with random dispersal among demes but local mating within demes to investigate conditions under which a dominant female-determining gene W, with no individual selection advantage, can invade and become fixed in females, changing the population from male to female heterogamety. Starting with one mutant W in a single deme, the interaction of sex ratio selection and random genetic drift causes W to be fixed among females more often than a comparable neutral mutation with no influence on sex determination, even when YY males have slightly reduced viability. Meta-population structure and interdeme selection can also favour the fixation of W. The reverse transition from female to male heterogamety can also occur with higher probability than for a comparable neutral mutation. These results help to explain the involvement of sex-determining genes in the evolution of sex chromosomes and in sexual selection and speciation.


Magneto-optical effects in temperature-sensitive ferrofluids.
A temperature-dependent magneto-optical study of three different temperature-sensitive fluids was carried out. The changes in transmitted intensity as a function of applied magnetic field and temperature are recorded. The study provides an alternative technique for determining the Curie temperature of such fluids, and it is also feasible for the monitoring of temperature changes of such fluids optically within a limited time span.


Dynamic Cerebrospinal Fluid Flow on MRI in Cortical Cerebellar Atrophy and Multiple System Atrophy-cerebellar Type.
The purpose of this study was to examine a new MRI technology, dynamic cerebrospinal fluid (CSF) flow, to examine sporadic cerebellar ataxia patients with cortical cerebellar atrophy (CCA) and multiple system atrophy-cerebellar type (MSA-C). Nine CCA patients (3 men and 6 women; mean age: 64.2±6.9 years) and 31 MSA-C patients (13 men and 18 women; mean age: 62.7±6.8 years) were examined by a dynamic CSF flow analysis. All CSF flow data were evaluated by phase contrast-MRI using a 1.5T MRI scanner. The CSF flow was calculated by 15 images in the equidistant MRI sequence which was taken through a cardiac cycle. Compared with the CCA patients, the absolute values of the mean velocity of the MSA-C patients were significantly reduced at time points 5 (CCA, 0.24±0.14 cm/s; MSA-C, 0.13±0.11 cm/s; (*) p<0.05) and 13 (CCA, -0.60±0.37 cm/s; MSA-C, -0.31±0.17 cm/s; (**) p<0.01). Significant correlations in Spearman's rank correlation coefficient were also found in MSA-C patients between the disease duration and the difference between the maximum and minimum velocities (Vheight) (r=-0.429, (*) p<0.05), the minimum velocity of the CSF (Vmin) (r=0.486, (**) p<0.01) or the length of the minor axis of the pons (r=-0.529, (**) p<0.01). The linear regressions between the disease duration and Vheight or Vmin revealed a significant strong correlation only in the MSA-C patients. The present CSF flow study showed for the first time that Vheight and Vmin revealed good correlations with the disease duration in the MSA-C patients. Furthermore, the velocity of the prepontine CSF flow tended to decrease in the MSA-C patients compared with the CCA patients, suggesting that this particular CSF flow analysis may be a new surrogate marker for differentiating both types of cerebellar ataxia.


Salt loads attenuate potassium-induced vasodilation of forearm vasculature in humans.
To evaluate the role of the sodium pump in resistance control in vivo, we studied vascular responses to potassium, which produces vasodilation by the activation of vascular Na+, K(+)-ATPase, in normotensive volunteers receiving a high salt diet compared with volume-depleted subjects receiving diuretic treatment. Forearm blood flow was measured by strain-gauge plethysmography during small increments in local concentrations of potassium with intrabrachial arterial infusions of KCl. Infusions of 0.12 and 0.24 mEq/min KCl increased forearm blood flow and decreased forearm vascular resistance in a dose-dependent fashion. But the simultaneous intrabrachial arterial infusion of 2 micrograms/min ouabain, a Na+,K(+)-ATPase inhibitor, could blunt the decremental response of vascular resistance to 0.12 mEq/min KCl. The decrements of vascular resistance with KCl infusions divided by the initial resistance were significantly less with ouabain compared with those without ouabain (43 +/- 4% versus 57 +/- 3%, p < 0.01). This suggests that potassium produces vasodilation by the activation of vascular Na+,K(+)-ATPase activity. Similarly, salt loading (180 mEq NaCl for 7 days) after treatment with diuretics could attenuate percent decrements of resistance with KCl infusions (39 +/- 3% versus 53 +/- 2%, p < 0.01), whereas vascular resistance responses to sodium nitroprusside, a nonspecific vasodilator, and to verapamil, a calcium antagonist, did not change with salt loading after volume depletion. Therefore, salt loading could attenuate forearm vascular response to potassium specifically, as did the administration of ouabain.(ABSTRACT TRUNCATED AT 250 WORDS)


Identification of potential candidate genes controlling pea aphid tolerance in a Pisum fulvum high-density integrated DArTseq SNP-based genetic map.
Pea (Pisum sativum) is one of the most important temperate grain legumes in the world, and its production is severely constrained by the pea aphid (Acyrthosiphon pisum). Wild relatives, such as P. fulvum, are valuable sources of allelic diversity to improve the genetic resistance of cultivated pea species against A. pisum attack. To unravel the genetic control underlying resistance to the pea aphid attack, a quantitative trait loci (QTL) analysis was performed using the previously developed high density integrated genetic linkage map originated from an intraspecific recombinant inbred line (RIL) population (P. fulvum: IFPI3260 × IFPI3251). We accurately evaluated specific resistance responses to pea aphid that allowed the identification, for the first time, of genomic regions that control plant damage and aphid reproduction. Eight QTLs associated with tolerance to pea aphid were identified in LGs I, II, III, IV and V, which individually explained from 17.0% to 51.2% of the phenotypic variation depending on the trait scored, and as a whole from 17.0% to 88.6%. The high density integrated genetic linkage map also allowed the identification of potential candidate genes co-located with the QTLs identified. Our work shows how the survival of P. fulvum after the pea aphid attack depends on the triggering of a multi-component protection strategy that implies a quantitative tolerance. The genomic regions associated with the tolerance responses of P. fulvum during A. pisum infestation have provided six potential candidate genes that could be useful in marker-assisted selection (MAS) and genomic assisted breeding (GAB) after functional validation in the future. © 2019 Society of Chemical Industry.


Melatonin combined with chondroitin sulfate ABC promotes nerve regeneration after root-avulsion brachial plexus injury.
After nerve-root avulsion injury of the brachial plexus, oxidative damage, inflammatory reaction, and glial scar formation can affect nerve regeneration and functional recovery. Melatonin (MT) has been shown to have good anti-inflammatory, antioxidant, and neuroprotective effects. Chondroitin sulfate ABC (ChABC) has been shown to metabolize chondroitin sulfate proteoglycans and can reduce colloidal scar formation. However, the effect of any of these drugs alone in the recovery of nerve function after injury is not completely satisfactory. Therefore, this experiment aimed to explore the effect and mechanism of combined application of melatonin and chondroitin sulfate ABC on nerve regeneration and functional recovery after nerve-root avulsion of the brachial plexus. Fifty-two Sprague-Dawley rats were selected and their C5-7 nerve roots were avulsed. Then, the C6 nerve roots were replanted to construct the brachial plexus nerve-root avulsion model. After successful modeling, the injured rats were randomly divided into four groups. The first group (injury) did not receive any drug treatment, but was treated with a pure gel-sponge carrier nerve-root implantation and an ethanol-saline solution via intraperitoneal (i.p.) injection. The second group (melatonin) was treated with melatonin via i.p. injection. The third group (chondroitin sulfate ABC) was treated with chondroitin sulfate ABC through local administration. The fourth group (melatonin + chondroitin sulfate ABC) was treated with melatonin through i.p. injection and chondroitin sulfate ABC through local administration. The upper limb Terzis grooming test was used 2-6 weeks after injury to evaluate motor function. Inflammation and oxidative damage within 24 hours of injury were evaluated by spectrophotometry. Immunofluorescence and neuroelectrophysiology were used to evaluate glial scar, neuronal protection, and nerve regeneration. The results showed that the Terzis grooming-test scores of the three groups that received treatment were better than those of the injury only group. Additionally, these three groups showed lower levels of C5-7 intramedullary peroxidase and malondialdehyde. Further, glial scar tissue in the C6 spinal segment was smaller and the number of motor neurons was greater. The endplate area of the biceps muscle was larger and the structure was clear. The latency of the compound potential of the myocutaneous nerve-biceps muscle was shorter. All these indexes were even greater in the melatonin + chondroitin sulfate ABC group than in the melatonin only or chondroitin sulfate ABC only groups. Thus, the results showed that melatonin combined with chondroitin sulfate ABC can promote nerve regeneration after nerve-root avulsion injury of the brachial plexus, which may be achieved by reducing oxidative damage and inflammatory reaction in the injury area and inhibiting glial scar formation.


Alternative splicing and cancer metastasis: prognostic and therapeutic applications.
Metastatic cells exhibit an extraordinary phenotypic plasticity, not only in adapting to unfamiliar microenvironments but also in surviving aggressive treatments and immune responses. A major source of phenotypic variability is alternative splicing (AS) of the pre-messenger RNA. This process is catalyzed by one of the most complex pieces of cellular molecular regulatory events, the spliceosome, which is composed of ribonucleoproteins and polypeptides termed spliceosome factors. With strong evidence indicating that AS affects nearly all genes encoded by the human genome, aberrant AS programs have a significant impact on cancer cell development and progression. In this review, we present insights about the genomic and epigenomic factors affecting AS, summarize the most recent findings linking aberrant AS to metastatic progression, and highlight potential prognostic and therapeutic applications.


Central memory CD4+ T cells are preferential targets of double infection by HIV-1.
Template switching between two distinct HIV-1 RNA genomes during reverse transcription gives rise to recombinant viruses that greatly expand the genetic diversity of HIV-1 and have adverse implications for drug resistance, immune escape, and vaccine design. Virions with two distinct genomes are produced exclusively from cells infected with two or more viruses, or 'doubly infected' cells. Previous studies have revealed higher than expected frequencies of doubly infected cells compared to frequencies based on chance alone, suggesting non-random enhancement of double infection. We investigated double infection of unstimulated primary CD4+ T cells using reporter viruses carrying genes for different fluorescent proteins, EGFP and mCherry, combined with sophisticated modeling techniques based on Poisson distribution. Additionally, through the use of multiparameter flow cytometry we examined the susceptibility of naïve and memory subsets of CD4+ T cells to double infection by HIV. Using our double infection system, we confirm non-random enhancement of multiple infection events. Double infection of CD4+ T cells was not found to be a consequence of suboptimal provirus expression rescued by Tat in trans-as has been reported in cell lines-but rather due to a heterogeneous cell population in which only a fraction of primary peripheral blood CD4+ T cells are susceptible to HIV infection regardless of viral titer. Intriguingly, double infection of CD4+ T cells occurred preferentially in memory CD4+ T cells-particularly the central memory (TCM) subset-but was not a consequence of SAMHD1-mediated restriction of HIV infection in naïve cells. These findings reveal that double infection in primary CD4+ T cells is primarily a consequences of cellular heterogeneity and not rescue of suboptimal provirus expression by Tat in trans. Additionally, we report a previously unappreciated phenomenon of enhanced double infection within primary TCM cells and suggest that these long-lived cells may serve as an archive that drive ongoing viral recombination events in vivo.


Differential recognition of snake venom proteins expressing specific Arg-Gly-Asp (RGD) sequence motifs by wild-type and variant integrin alphaIIbbeta3: further evidence for distinct sites of RGD ligand recognition exhibiting negative allostery.
Several studies have demonstrated that the amino acid residues flanking the Arg-Gly-Asp (RGD) sequence of high-affinity ligands modulate their specificity of interaction with integrin complexes. Because of the absence of structural data for integrin complexes with bound ligand, the molecular basis for this specificity modulation remains obscure. In a previous paper [Rahman, Lu, Kakkar and Authi (1995) Biochem. J. 312, 223-232] we demonstrated that two genetically distinct venom-derived RGD proteins, kistrin and dendroaspin (both containing the sequence PRGDMP), were simple competitors, indicating the recognition of an identical binding site on the alpha(IIb)beta(3) complex. Furthermore, both kistrin and dendroaspin inhibited the binding of the disintegrin elegantin (containing the sequence ARGDNP) via a non-competitive mechanism, suggesting that the binding of elegantin to the alpha(IIb)beta(3) complex was at a remote site and down-regulated via an allosteric mechanism. Here we present further evidence for distinct RGD ligand recognition sites on the alpha(IIb)beta(3) complex that exhibit a negative allosteric relationship. A panel of well-characterized recombinant dendroaspin and elegantin derivatives were employed for this study. These recombinant molecules were constructed as glutathione S-transferase fusion proteins with either an Ala or Pro residue N-terminal to the RGD sequence in combination with either a Met or an Asn residue immediately C-terminal. Equilibrium competition experiments showed that elegantin binding to ADP-treated platelets was inhibited by derivatives Eleg. AM (ARGDMP) and Eleg. PM (PRGDMP) via an allosteric competitive mechanism, providing direct evidence that modulation of the RGD motif can alter competitive behaviour. In addition, recombinant kistrin and dendroaspin both inhibited elegantin binding via a non-competitive mechanism, confirming our previous observations. Further evidence for distinct binding sites employing an independent approach was obtained by analysing the binding of the panel of venom proteins to the functionally defective heterodimer alpha(IIb)beta(3) Ser(123)-->Ala expressed on Chinese hamster ovary cells. These studies demonstrated that simple competitors kistrin and dendroaspin bound with high affinity to the variant integrin complex. In contrast, the binding of elegantin and most significantly, recombinant Dendro. PN (PRGDNP) and Dendro. AN (ARGDNP) were abolished. These observations, taken together, are consistent with a model depicting the presence of distinct sites of RGD ligand recognition on the alpha(IIb)beta(3) complex that show the preferential recognition of specific RGD motifs. Competition experiments demonstrate a negative allosteric relationship between these RGD recognition sites.


Echocardiographic variables after left ventricular assist device implantation associated with adverse outcome.
Operative mortality after left ventricular assist device (LVAD) implantation is heavily influenced by patient selection and the technical difficulty of surgery. However, how we treat our patients and LVAD setting may affect the patient outcome beyond this period. We postulated that the presence of echocardiographic variables 1 month after surgery suggesting appropriate degree of LV unloading and an adequate forward flow would be important in determining clinical outcomes after the initial successful LVAD implantation. We retrospectively analyzed various variables in echocardiographic examinations performed 30 days after LVAD implant in 76 consecutive patients receiving continuous flow device for their association with a compound end point (90-day mortality, readmission for heart failure, or New York Heart Association class III or higher at the end of the 90-day period). The echocardiographic associations examined included estimated LVAD flow, with and without native LV contribution, interventricular septal position, the status of aortic valve opening, an estimated left atrial pressure (ELAP), the mitral flow E-wave deceleration time, and the ratio of deceleration time to E-wave velocity (mitral deceleration index [MDI]). Four patients died during the 30- to 90-day period, 6 patients were readmitted for heart failure, and 25 patients were considered to have New York Heart Association class III or higher at the end of the 90-day period. Variables associated with adverse outcome included increased ELAP (odds ratio, 1.30 [1.16-1.48]; P<0.0001), MDI <2 ms/[cm/s] (odds ratio, 4.4 implantation [1.22-18]; P=0.02) and decreased tricuspid lateral annulus velocity (odds ratio, 0.70 implantation [0.48-0.95]; P=0.02). A leftward deviation of interventricular septum was associated with a worse outcome (odds ratio, 3.03 implantation [1.21-13.3]; P=0.01). Mortality and heart failure after LVAD surgery appear to be predominantly determined by echocardiographic evidence of inefficient unloading of the left ventricle and persistence of right ventricular dysfunction. Increased estimated LA pressure and short MDI are associated with worse mid term outcome. Leftward deviation of the septum is associated with worse outcome as well.


RNA-Seq of the xylose-fermenting yeast Scheffersomyces stipitis cultivated in glucose or xylose.
Xylose is the second most abundant lignocellulosic component besides glucose, but it cannot be fermented by the widely used ethanol-producing yeast Saccharomyces cerevisiae. The yeast Scheffersomyces stipitis, however, is well known for its high native capacity to ferment xylose. Here, we applied next-generation sequencing technology for RNA (RNA-Seq) to generate two high-resolution transcriptional maps of the S. stipitis genome when this yeast was grown using glucose or xylose as the sole carbon source. RNA-Seq revealed that 5,176 of 5,816 annotated open reading frames had a uniform transcription and that 214 open reading frames were differentially transcribed. Differential expression analysis showed that, compared with other biological processes, carbohydrate metabolism and oxidation-reduction reactions were highly enhanced in yeast grown on xylose. Measurement of metabolic indicators of fermentation showed that, in yeast grown on xylose, the concentrations of cysteine and ornithine were twofold higher and the concentrations of unsaturated fatty acids were also increased. Analysis of metabolic profiles coincided with analysis of certain differentially expressed genes involved in metabolisms of amino acid and fatty acid. In addition, we predicted protein-protein interactions of S. stipitis through integration of gene orthology and gene expression. Further analysis of metabolic and protein-protein interactions networks through integration of transcriptional and metabolic profiles predicted correlations of genes involved in glycolysis, the tricarboxylic acid cycle, gluconeogenesis, sugar uptake, amino acid metabolism, and fatty acid β-oxidation. Our study reveals potential target genes for xylose fermentation improvement and provides insights into the mechanisms underlying xylose fermentation in S. stipitis.


Uptake and implementation of Advance Care Planning in Australia: findings of key informant interviews.
Advance Care Planning (ACP) has an important role in enhancing patient autonomy and guiding end-of-life care. However, there is low uptake of ACP and evidence that advance care plans are often not implemented. We explored these issues in interviews with expert clinicians and representatives of key stakeholder organisations with interest in end-of-life care. Qualitative descriptive study of semi-structured telephone interviews with 23 participants. Participants thought that the low uptake of ACP in Australia is a result of inadequate awareness, societal reluctance to discuss end-of-life issues, and lack of health professionals' involvement in ACP. Problems in implementation of advance care plans were thought to be a result of problems in accessing ACP documents; interpreting written documents; making binding decisions for future unpredictable situations; and paternalistic attitudes of health professionals and families. Participants had different perspectives on how advance care plans should be implemented, with some believing in strict implementation, whereas others believed in a more flexible approach. Low uptake and poor implementation of advance care plans may be addressed by (1) increasing community awareness; (2) encouraging health professional involvement; and (3) system-wide implementation of multi-faceted interventions. A patient-centred approach to ACP is required to resolve the differences in views on how advance care plans should be implemented.


Intein-mediated cyclization of a soluble and a membrane protein in vivo: function and stability.
Cyclized subunits of the E. coli glucose transporter were produced in vivo by intein mediated trans-splicing. IIA(Glc) is a beta-sandwich protein, IICB(Glc) spans the membrane eight times. Genes encoding the circularly permuted precursors U(Cdelta)-IIA(Glc)-U(Ndelta) and U(Cdelta)-IICB(Glc)-U(Ndelta) were assembled from DNA fragments encoding the 3' and 5' segments of the recA intein of M. tuberculosis and crr and ptsG of E. coli, respectively. A 20-residues long, Ala-Pro rich linker peptide and/or a histidine tag were used to join the native N- and C-termini in the cyclized proteins. The cyclized proteins complemented growth of glucose auxotrophic strains. Purified, cyclized IIA(Glc) and IICB(Glc) had 100 and 25%, respectively, of wild-type glucose phosphotransferase activity. They had an increased electrophoretic mobility, which decreased upon linearization of the proteins with chymotrypsin. Cyclized IIA(Glc) displayed increased stability against temperature and GuHCl-induced unfolding (75 vs. 70 degrees C; 1.52 vs. 1.05 M).


A phase 2 study of patupilone in patients with metastatic castration-resistant prostate cancer previously treated with docetaxel: Canadian Urologic Oncology Group study P07a.
The purpose of this study was to determine the clinical activity of patupilone in patients with metastatic castration-resistant prostate cancer previously treated with docetaxel. Eligible patients had progressive disease within 6 months of receiving docetaxel. Patupilone was administered 10 mg/m2 i.v. every 3 weeks. The primary end point was the proportion of patients with a confirmed≥50% prostate-specific antigen (PSA) decline. Eighty-three patients were enrolled. At baseline, the median time to progression after prior docetaxel was 1.4 months (range 0-5.7). Gastrointestinal serious adverse events occurred in four of the six initial patients leading to a reduction of the starting dose of patupilone to 8 mg/m2 for subsequent patients. Grade 3-4 toxicity at this dose included diarrhea (22%), fatigue (21%), and anorexia (10%). One patient experienced grade 3-4 hematologic toxicity. A PSA decline of ≥50% occurred in 47% of patients. A partial measurable disease response occurred in 24% of assessable patients. A patient-reported pain response was observed in 59% of assessable patients. Median time to PSA progression was 6.1 months [95% confidence interval (CI) 4.7-8.0] and median overall survival was 11.3 months (95% CI 9.8-15.4). Patupilone at 8 mg/m2 was tolerable, had antitumor activity, and was associated with symptomatic improvement in patients previously treated with docetaxel.


StCDPK5 confers resistance to late blight pathogen but increases susceptibility to early blight pathogen in potato via reactive oxygen species burst.
• Potato (Solanum tuberosum) calcium-dependent protein kinase (StCDPK5) has been shown to phosphorylate the N-terminal region of plasma membrane RBOH (respiratory burst oxidase homolog) proteins, and participate in StRBOHB-mediated reactive oxygen species (ROS) burst. The constitutively active form, StCDPK5VK, provides a useful tool for gain-of-function analysis of RBOH in defense responses. • StCDPK5- and StCDPK5VK-green fluorescent protein fusion proteins were predominantly targeted to the plasma membrane, and conditional expression of StCDPK5VK activated StRBOHA-D. The interaction was confirmed by bimolecular fluorescence complementation assay. We generated transgenic potato plants containing StCDPK5VK under the control of a pathogen-inducible promoter to investigate the role of ROS burst on defense responses to blight pathogens. • Virulent isolates of the late blight pathogen Phytophthora infestans and the early blight pathogen Alternaria solani induced hypersensitive response-like cell death accompanied by ROS production at the infection sites of transgenic plants. Transgenic plants showed resistance to the near-obligate hemibiotrophic pathogen P. infestans and, by contrast, increased susceptibility to the necrotrophic pathogen A. solani. • These results indicate that RBOH-dependent ROS contribute to basal defense against near-obligate pathogens, but have a negative role in resistance or have a positive role in expansion of disease lesions caused by necrotrophic pathogens.


Correlations between Janus kinase 2 V617F allele burdens and clinicohematologic parameters in myeloproliferative neoplasms.
This study evaluated potential correlations between the allele burden of the Janus kinase 2 (JAK2) V617F mutation and clinicohematologic characteristics in patients with myeloproliferative neoplasms (MPN). Clinical and hematologic features were reviewed for 103 MPN patients, including patients with polycythemia vera (PV, 22 patients), essential thrombocythemia (ET, 64 patients), and primary myelofibrosis (PMF, 17 patients). JAK2 V617F allele status and allele burdens were measured by allele-specific PCR and pyrosequencing, respectively. The JAK2 V617F mutation was detected in 95.5%, 68.8%, and 52.9% of PV, ET, and PMF patients, respectively. JAK2 V617F-positive ET patients were significantly older and exhibited higher neutrophil fractions, a higher frequency of thrombotic events, and a higher myelofibrosis rate than JAK2 V617F-negative patients (P <0.05). PV patients carried the highest mean T allele burden (66.0%±24.9%) compared with ET (40.5%±25.2%) and PMF patients (31.5%±37.0%) (P =0.00). No significant correlations were detected between V617F allele burden and patient age, white blood cell count, Hb, Hct, or the platelet count for PV, ET, or PMF patients. ET patients with organomegaly had a higher JAK2 V617F allele burden (53.4%±23.7%) than patients without organomegaly (35.6%±24.3%) (P =0.03). The JAK2 V617F mutational status and its allele burden correlate with the clinicohematologic phenotypes of ET patients, including older age, higher neutrophil count, and greater rates of organomegaly, thrombotic events, and myelofibrosis. For PV and PMF patients, larger-scale studies involving more MPN patients are needed.


[Cysteine proteinases and their inhibitors in the development of mouse HA-1 hepatoma and antineoplastic therapy].
Development of murine HA-1 hepatoma was accompanied by increased activity of cathepsin B (in ascitic cells), cathepsin D (in ascitic fluid) and increased activity of procathepsin B. There were some changes of cysteine proteinases in liver and spleen, not involved directly into tumor growth. The most prominent changes included the decreased level of cysteine proteinase inhibitors cystatin C and stefin A in ascitic cells (and to a lesser degree in liver tissue). During tumor development serum cystatin C concentration decreased by 3-times compared to intact mice. Treatment by antitumor drug Ukraine increased life span of mice with HA-1 hepatoma (transplanted intravenously), decreased the increment of tumor weight. In ascite such treatment caused a decrease of number of tumor cells and an increase of number of macrophages. Ukraie (administered once or 5-times in a dose of 0.5 mg per mice) increased cystatin C level, revealing protective mechanism of action.


Multiprotein interactions during surface adsorption: a molecular dynamics study of lysozyme aggregation at a charged solid surface.
Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein-protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein-protein and protein-surface), and gives an insight into processes to be considered in the development of new functionalized material systems.


Prognostic significance of Cyclin A in epidermoid anal cancer.
Ultimately aiming at a more individualized therapeutic approach in epidermoid anal cancer, this study explored the prognostic and predictive impact of a set of tumour markers. From a population-based cohort of 276 patients with epidermoid anal cancer, treated according to prospective protocols, 215 pre-treatment biopsies were investigated using immunohistochemistry. The expression of p53, p21, Cyclin A and CD31 was measured semi-quantitatively. The expression rate was classified as high when immunostaining was seen in > 5% of the tumour cells for p53 and p21, > 20% in Cyclin A and, above median vessel count for CD31. Marker expression was correlated to survival and treatment response. A high Cyclin A expression correlated significantly with improved overall (77% vs 59%, p = 0.005) and tumour-specific (81% vs 64%, p = 0.009) survival at 5 years. Also, the locoregional failure rate was significantly lower in patients with a high Cyclin A expression (12% vs 24%, p < 0.05). In a multivariate Cox analysis Cyclin A was an independent prognostic factor. A low p21 expression correlated with a reduced rate of locoregional failure (14% vs 27%, p < 0.05) but no impact on survival was found. For p53 and CD31 no significant correlations were obtained. Cyclin A may be an indicator of radiosensitivity and a valuable prognostic marker in epidermoid anal cancer.


Allele loss, replication errors and loss of expression of E-cadherin in colorectal cancers.
Loss of E-cadherin expression has been implicated in the development of invasive characteristics in colorectal carcinomas. Failure to express E-cadherin may result from mutations of the E-cadherin gene (HSECAD). To examine the correlation between E-cadherin expression and genetic changes at HSECAD; and to examine differences in E-cadherin expression and genetic changes at HSECAD between three different groups of colorectal cancer--replication error positive (RER+) sporadic cancers, RER--sporadic cancers and ulcerative colitis associated cancers. Sixty eight colorectal cancers (22 RER+ sporadic cancers, 32 RER- sporadic cancers and 14 ulcerative colitis associated cancers) were studied using immunohistochemistry and for allele loss at the HSECAD locus. Exon 16 of HSECAD contains several mononucleotide repeat tracts which are very similar to microsatellite repeats and which may be susceptible to replication errors (manifest as new alleles). All cases were also examined for new alleles in exon 16. Absent or decreased E-cadherin protein expression was found in 27 (38%) of 68 colorectal cancers and the pattern of expression did not differ significantly among the three tumour groups. Allele loss occurred at HSECAD in four (10%) of 40 informative cancers and there were no differences between the three subgroups. New alleles at exon 16 were detected in three (14%) of 22 RER+ tumours; no new alleles were detected in RER- or ulcerative colitis associated cancers. Overall, there was no correlation between allelic loss or exon 16 replication errors and immunohistochemical E-cadherin expression. (1) Loss of E-cadherin expression probably does not occur as a result of mutation at the HSECAD locus in colorectal cancers. (2) There is no difference in the frequency of loss of heterozygosity at HSECAD among RER+, RER- and ulcerative colitis associated colorectal cancers.


Body mass index, waist circumference, and chronic disease risk factors in Australian adolescents.
To determine the association between measures of adiposity (body mass index and waist circumference) and risk factors for heart disease, type 2 diabetes, fatty liver disease, and the clustering of risk factors in middle adolescence. Cross-sectional study. Secondary schools in Sydney. Grade 10 students (N = 496; 58.4% boys; mean [SD] age, 15.4 [0.4] years). Height, weight, waist circumference, blood pressure, and fasting blood samples. Participants were categorized as overweight or obese using the International Obesity Task Force cut points and the UK waist circumference cut points. Blood was analyzed for high- and low-density lipoprotein cholesterol, triglycerides, insulin, glucose, alanine aminotransferase, gamma-glutamyltransferase, and high-sensitivity C-reactive protein levels, and the results were categorized as normal or abnormal according to published guidelines where possible. Associations between overweight and obesity and risk factors were explored using logistic regression. Clustering of risk factors within individuals was also explored. Insulin (P < .001), alanine aminotransferase (P < .001), gamma-glutamyltransferase (P = .005), high-density lipoprotein cholesterol (P < .001), high-sensitivity C-reactive protein (P < .001), and blood pressure (P < .001) were significantly associated with overweight and obesity in adolescent boys. In adolescent girls, insulin, high-density lipoprotein cholesterol (P < .001), and high-sensitivity C-reactive protein (P < .001) were significantly associated with overweight and obesity. Obese adolescent boys and girls were significantly more likely to have 2 or more risk factors (boys: 73.5% vs 7.6%; girls: 44.4% vs 5.4%; P < .001 for both) than nonoverweight adolescents. Overweight and obese adolescents, especially boys, are at substantial risk for chronic conditions. Waist circumference is not a better predictor of metabolic risk factors than is body mass index.


Towards onset prevention of cognition decline in adults with Down syndrome (The TOP-COG study): A pilot randomised controlled trial.
Dementia is very common in Down syndrome (trisomy 21) adults. Statins may slow brain amyloid β (Aβ, coded on chromosome 21) deposition and, therefore, delay Alzheimer disease onset. One prospective cohort study with Down syndrome adults found participants on statins had reduced risk of incident dementia, but there are no randomised controlled trials (RCTs) on this issue. Evidence is sparse on the best instruments to detect longitudinal cognitive decline in older Down syndrome adults. TOP-COG was a feasibility/pilot, double-blind RCT of 12 months simvastatin 40 mg versus placebo for the primary prevention of dementia in Alzheimer disease in Down syndrome adults aged 50 years or older. Group allocation was stratified by age, apolipoprotein E (APOE) ε4 allele status, and cholesterol level. Recruitment was from multiple general community sources over 12 months. Adults with dementia, or simvastatin contraindications, were excluded. Main outcomes were recruitment and retention rates. Cognitive decline was measured with a battery of tests; secondary measures were adaptive behaviour skills, general health, and quality of life. Assessments were conducted pre randomisation and at 12 months post randomisation. Blood Aβ40/Aβ42 levels were investigated as a putative biomarker. Results were analysed on an intention-to-treat basis. A qualitative sub-study was conducted and analysed using the Framework Approach to determine recruitment motivators/barriers, and participation experience. We identified 181 (78 %) of the likely eligible Down syndrome population, and recruited 21 (11.6 %), from an area with a general population size of 3,135,974. Recruitment was highly labour-intensive. Thirteen (62 %) participants completed the full year. Results favoured the simvastatin group. The most appropriate cognitive instrument (regarding ease of completion and detecting change over time) was the Memory for Objects test from the Neuropsychological Assessment of Dementia in Individuals with Intellectual Disabilities battery. Cognitive testing appeared more sensitive than proxy-rated adaptive behaviour, quality of life, or general health scores. Aβ40 levels changed less for the simvastatin group (not statistically significant). People mostly declined to participate because of not wanting to take medication, and not knowing if they would receive simvastatin or placebo. Participants reported enjoying taking part. A full-scale RCT is feasible. It will need 37 % UK population coverage to recruit the required 160 participants. Information/education about the importance of RCT participation is needed for this population. ISRCTN67338640 .


Immunotherapy response assessment in neuro-oncology: a report of the RANO working group.
Immunotherapy is a promising area of therapy in patients with neuro-oncological malignancies. However, early-phase studies show unique challenges associated with the assessment of radiological changes in response to immunotherapy reflecting delayed responses or therapy-induced inflammation. Clinical benefit, including long-term survival and tumour regression, can still occur after initial disease progression or after the appearance of new lesions. Refinement of the response assessment criteria for patients with neuro-oncological malignancies undergoing immunotherapy is therefore warranted. Herein, a multinational and multidisciplinary panel of neuro-oncology immunotherapy experts describe immunotherapy Response Assessment for Neuro-Oncology (iRANO) criteria based on guidance for the determination of tumour progression outlined by the immune-related response criteria and the RANO working group. Among patients who demonstrate imaging findings meeting RANO criteria for progressive disease within 6 months of initiating immunotherapy, including the development of new lesions, confirmation of radiographic progression on follow-up imaging is recommended provided that the patient is not significantly worse clinically. The proposed criteria also include guidelines for the use of corticosteroids. We review the role of advanced imaging techniques and the role of measurement of clinical benefit endpoints including neurological and immunological functions. The iRANO guidelines put forth in this Review will evolve successively to improve their usefulness as further experience from immunotherapy trials in neuro-oncology accumulate.


Incidence and severity of acute complications after spinal cord injury.
The aim of this multicenter, prospective study was to determine the spectrum, incidence, and severity of complications during the initial hospitalization of patients with spinal cord injury. The study was conducted at 9 university-affiliated hospitals that comprise the clinical centers of the North American Clinical Trials Network (NACTN) for Treatment of Spinal Cord Injury. The study population comprised 315 patients admitted to NACTN clinical centers between June 25, 2005, and November 2, 2010, who had American Spinal Injury Association (ASIA) Impairment Scale grades of A-D and were 18 years of age or older. Patients were managed according to a standardized protocol. The study population was 79% male with a median age of 44 years. The leading causes of injury were falls (37%) and motor vehicle accidents (28%). The distribution of initial ASIA grades were A (40%), B (16%), C (15%), and D (29%). Fifty-eight percent of patients sustained 1 or more severe, moderate, or mild complications. Complications were associated with more severe ASIA grade: 84% of patients with Grade A and 25% of patients with Grade D had at least 1 complication. Seventy-eight percent of complications occurred within 14 days of injury. The most frequent types of severe and moderate complications were respiratory failure, pneumonia, pleural effusion, anemia, cardiac dysrhythmia, and severe bradycardia. The mortality rate was 3.5% and was associated with increased age and preexisting morbidity. Knowledge of the type, frequency, time of occurrence, and severity of specific complications that occur after spinal cord injury can aid in their early detection, treatment, and prevention. The data are of importance in evaluating and selecting therapy for clinical trials.


Binding STAT2 by the acidic domain of human cytomegalovirus IE1 promotes viral growth and is negatively regulated by SUMO.
The human cytomegalovirus (HCMV) 72-kDa immediate-early 1 (IE1) protein is thought to modulate cellular antiviral functions impacting on promyelocytic leukemia (PML) nuclear bodies and signal transducer and activator of transcription (STAT) signaling. IE1 consists of four distinct regions: an amino-terminal region required for nuclear localization, a large central hydrophobic region responsible for PML targeting and transactivation activity, an acidic domain, and a carboxyl-terminal chromatin tethering domain. We found that the acidic domain of IE1 is required for binding to STAT2. A mutant HCMV encoding IE1(Delta421-475) with the acidic domain deleted was generated. In mutant virus-infected cells, IE1(Delta421-475) failed to bind to STAT2. The growth of mutant virus was only slightly delayed at a high multiplicity of infection (MOI) but was severely impaired at a low MOI with low-level accumulation of viral proteins. When cells were pretreated with beta interferon, the mutant virus showed an additional 1,000-fold reduction in viral growth, even at a high MOI, compared to the wild type. The inhibition of STAT2 loading on the target promoter upon infection was markedly reduced with mutant virus. Furthermore, sumoylation of IE1 at this acidic domain was found to abolish the activity of IE1 to bind to STAT2 and repress the interferon-stimulated genes. Our results provide genetic evidence that IE1 binding to STAT2 requires the 55-amino-acid acidic domain and promotes viral growth by interfering with interferon signaling and demonstrate that this viral activity is negatively regulated by a cellular sumoylation pathway.


Reliance on head versus eyes in the gaze following of great apes and human infants: the cooperative eye hypothesis.
As compared with other primates, humans have especially visible eyes (e.g., white sclera). One hypothesis is that this feature of human eyes evolved to make it easier for conspecifics to follow an individual's gaze direction in close-range joint attentional and communicative interactions, which would seem to imply especially cooperative (mututalistic) conspecifics. In the current study, we tested one aspect of this cooperative eye hypothesis by comparing the gaze following behavior of great apes to that of human infants. A human experimenter "looked" to the ceiling either with his eyes only, head only (eyes closed), both head and eyes, or neither. Great apes followed gaze to the ceiling based mainly on the human's head direction (although eye direction played some role as well). In contrast, human infants relied almost exclusively on eye direction in these same situations. These results demonstrate that humans are especially reliant on eyes in gaze following situations, and thus, suggest that eyes evolved a new social function in human evolution, most likely to support cooperative (mututalistic) social interactions.


Results from the multi-species benchmark problem (BM3) using one-dimensional models.
The IWA's Biofilm Modeling Task Group created a multi-species benchmark problem in which heterotrophic bacteria, nitrifying bacteria, and inert biomass coexist in a biofilm. Members of the Task Group submitted solutions from nine different one-dimensional models. The most important distinctions among the models were (1) whether the model required a full numerical solution or was solved with a spreadsheet, and (2) the way the biomass types were distributed in the biofilm. The models that protected the slow-growing species by having them accumulate away from the outer surface always had the largest surface coverage by nitrifiers and inerts, but the heterotroph coverage declined to compensate. Coverage by heterotrophs and removal of substrate COD were most strongly affected by dilution from nitrifiers and inerts near the outer surface. Models that did not allow the nitrifiers and inerts to dilute the heterotrophs significantly in the outer layer predicted more removal of COD than did the other models. The choice of the model to use depends on the user's needs and the relative importance of including protection of slow-growing species and/or dilution of fast-growing species.


Complete genome sequencing of exopolysaccharide-producing Lactobacillus plantarum K25 provides genetic evidence for the probiotic functionality and cold endurance capacity of the strain.
Lactobacillus plantarum (L. plantarum) K25 is a probiotic strain isolated from Tibetan kefir. Previous studies showed that this exopolysaccharide (EPS)-producing strain was antimicrobial active and cold tolerant. These functional traits were evidenced by complete genome sequencing of strain K25 with a circular 3,175,846-bp chromosome and six circular plasmids, encoding 3365 CDSs, 16 rRNA genes and 70 tRNA genes. Genomic analysis of L. plantarum K25 illustrates that this strain contains the previous reported mechanisms of probiotic functionality and cold tolerance, involving plantaricins, lysozyme, bile salt hydrolase, chaperone proteins, osmoprotectant, oxidoreductase, EPSs and terpenes. Interestingly, strain K25 harbors more genes that function in defense mechanisms, and lipid transport and metabolism, in comparison with other L. plantarum strains reported. The present study demonstrates the comprehensive analysis of genes related to probiotic functionalities of an EPS-producing L. plantarum strain based on whole genome sequencing.


The importance of the location of antibody binding on the M6 protein for opsonization and phagocytosis of group A M6 streptococci.
One of 19 mAbs against the native group A streptococcal M6 protein proved opsonic for type 6 organisms in a bactericidal assay. The opsonic and three nonopsonic antibodies were selected for isotype and complement fixation studies based on previous knowledge of their epitope site on the M6 molecule. While mAb 3B8 (IgG3), whose epitope is in the NH2-terminal hypervariable region of the molecule (distal from the cell), and mAbs 10B6 (IgG2a) and 10F5 (IgG2b), both located in the conserved central region of the molecule, all fix complement, 10A11 (IgG1) did not. Only mAb 3B8 was opsonic despite the fact that mAbs 10B6 and 10F5 both exhibited similar complement-fixing capacity, binding titer, and surface exposure of epitopes. Analysis of antibodies raised against synthetic peptides representing various regions of the M6 protein showed that only the amino-terminal peptide (residues 1-21) was capable of eliciting opsonic antibodies, despite the fact that peptides from other areas produced antibodies with high-binding titers to the native M6 protein and also with the ability to bind to intact streptococcal cells. These results not only support the observed type specificity of opsonic antibodies, but also clearly point to the importance of the location of antibody binding on the M molecule relative to the actual functional capacity of the antibody with respect to the opsonization and phagocytosis of M6 streptococci. These results may underscore the recently observed role of complement Factor H in the antiphagocytic activity of the M protein.


Dendritic cell mediated delivery of plasmid DNA encoding LAMP/HIV-1 Gag fusion immunogen enhances T cell epitope responses in HLA DR4 transgenic mice.
This report describes the identification and bioinformatics analysis of HLA-DR4-restricted HIV-1 Gag epitope peptides, and the application of dendritic cell mediated immunization of DNA plasmid constructs. BALB/c (H-2d) and HLA-DR4 (DRA1*0101, DRB1*0401) transgenic mice were immunized with immature dendritic cells transfected by a recombinant DNA plasmid encoding the lysosome-associated membrane protein-1/HIV-1 Gag (pLAMP/gag) chimera antigen. Three immunization protocols were compared: 1) primary subcutaneous immunization with 1x10(5) immature dendritic cells transfected by electroporation with the pLAMP/gag DNA plasmid, and a second subcutaneous immunization with the naked pLAMP/gag DNA plasmid; 2) primary immunization as above, and a second subcutaneous immunization with a pool of overlapping peptides spanning the HIV-1 Gag sequence; and 3) immunization twice by subcutaneous injection of the pLAMP/gag DNA plasmid. Primary immunization with pLAMP/gag-transfected dendritic cells elicited the greatest number of peptide specific T-cell responses, as measured by ex vivo IFN-gamma ELISpot assay, both in BALB/c and HLA-DR4 transgenic mice. The pLAMP/gag-transfected dendritic cells prime and naked DNA boost immunization protocol also resulted in an increased apparent avidity of peptide in the ELISpot assay. Strikingly, 20 of 25 peptide-specific T-cell responses in the HLA-DR4 transgenic mice contained sequences that corresponded, entirely or partially to 18 of the 19 human HLA-DR4 epitopes listed in the HIV molecular immunology database. Selection of the most conserved epitope peptides as vaccine targets was facilitated by analysis of their representation and variability in all reported sequences. These data provide a model system that demonstrates a) the superiority of immunization with dendritic cells transfected with LAMP/gag plasmid DNA, as compared to naked DNA, b) the value of HLA transgenic mice as a model system for the identification and evaluation of epitope-based vaccine strategies, and c) the application of variability analysis across reported sequences in public databases for selection of historically conserved HIV epitopes as vaccine targets.


Comparison of the Transcriptional Profiles of Melanocytes from Dark and Light Skinned Individuals under Basal Conditions and Following Ultraviolet-B Irradiation.
We analysed the whole-genome transcriptional profile of 6 cell lines of dark melanocytes (DM) and 6 of light melanocytes (LM) at basal conditions and after ultraviolet-B (UVB) radiation at different time points to investigate the mechanisms by which melanocytes protect human skin from the damaging effects of UVB. Further, we assessed the effect of different keratinocyte-conditioned media (KCM+ and KCM-) on melanocytes. Our results suggest that an interaction between ribosomal proteins and the P53 signaling pathway may occur in response to UVB in both DM and LM. We also observed that DM and LM show differentially expressed genes after irradiation, in particular at the first 6h after UVB. These are mainly associated with inflammatory reactions, cell survival or melanoma. Furthermore, the culture with KCM+ compared with KCM- had a noticeable effect on LM. This effect includes the activation of various signaling pathways such as the mTOR pathway, involved in the regulation of cell metabolism, growth, proliferation and survival. Finally, the comparison of the transcriptional profiles between LM and DM under basal conditions, and the application of natural selection tests in human populations allowed us to support the significant evolutionary role of MIF and ATP6V0B in the pigmentary phenotype.


The presence of accessory cusps in chimpanzee lower molars is consistent with a patterning cascade model of development.
Tooth crown morphology is of primary importance in fossil primate systematics and understanding the developmental basis of its variation facilitates phenotypic analyses of fossil teeth. Lower molars of species in the chimp/human clade (including fossil hominins) possess between four and seven cusps and this variability has been implicated in alpha taxonomy and phylogenetic systematics. What is known about the developmental basis of variation in cusp number - based primarily on experimental studies of rodent molars - suggests that cusps form under a morphodynamic, patterning cascade model involving the iterative formation of enamel knots. In this study we test whether variation in cusp 6 (C6) presence in common chimpanzee and bonobo lower molars (n = 55) is consistent with predictions derived from the patterning cascade model. Using microcomputed tomography we imaged the enamel-dentine junction of lower molars and used geometric morphometrics to examine shape variation in the molar crown correlated with variation in C6 presence (in particular the size and spacing of the dentine horns). Results indicate that C6 presence is consistent with predictions of a patterning cascade model, with larger molars exhibiting a higher frequency of C6 and with the location and size of later-forming cusps correlated with C6 variation. These results demonstrate that a patterning cascade model is appropriate for interpreting cusp variation in Pan and have implications for cusp nomenclature and the use of accessory cusp morphology in primate systematics.


Challenging Global Waste Management - Bioremediation to Detoxify Asbestos.
As the 21st century uncovers ever-increasing volumes of asbestos and asbestos-contaminated waste, we need a new way to stop 'grandfather's problem' from becoming that of our future generations. The production of inexpensive, mechanically strong, heat resistant building materials containing asbestos has inevitably led to its use in many public and residential buildings globally. It is therefore not surprising that since the asbestos boom in the 1970s, some 30 years later, the true extent of this hidden danger was exposed. Yet, this severely toxic material continues to be produced and used in some countries, and in others the disposal options for historic uses - generally landfill - are at best unwieldy and at worst insecure. We illustrate the global scale of the asbestos problem via three case studies which describe various removal and/or end disposal issues. These case studies from both industrialised and island nations demonstrate the potential for the generation of massive amounts of asbestos contaminated soil. In each case, the final outcome of the project was influenced by factors such as cost and land availability, both increasing issues, worldwide. The reduction in the generation of asbestos containing materials will not absolve us from the necessity of handling and disposal of contaminated land. Waste treatment which relies on physico-chemical processes is expensive and does not contribute to a circular model economy ideal. Although asbestos is a mineral substance, there are naturally occurring biological-mediated processes capable of degradation (such as bioweathering). Therefore, low energy options, such as bioremediation, for the treatment for asbestos contaminated soils are worth exploring. We outline evidence pointing to the ability of microbe and plant communities to remove from asbestos the iron that contributes to its carcinogenicity. Finally, we describe the potential for a novel concept of creating ecosystems over asbestos landfills ('activated landfills') that utilize nature's chelating ability to degrade this toxic product effectively.


Fitness of Enterohemorrhagic Escherichia coli (EHEC)/Enteroaggregative E. coli O104:H4 in Comparison to That of EHEC O157: Survival Studies in Food and In Vitro.
In 2011, one of the world's largest outbreaks of hemolytic-uremic syndrome (HUS) occurred, caused by a rare Escherichia coli serotype, O104:H4, that shared the virulence profiles of Shiga toxin-producing E. coli (STEC)/enterohemorrhagic E. coli (EHEC) and enteroaggregative E. coli (EAEC). The persistence and fitness factors of the highly virulent EHEC/EAEC O104:H4 strain, grown either in food or in vitro, were compared with those of E. coli O157 outbreak-associated strains. The log reduction rates of the different EHEC strains during the maturation of fermented sausages were not significantly different. Both the O157:NM and O104:H4 serotypes could be shown by qualitative enrichment to be present after 60 days of sausage storage. Moreover, the EHEC/EAEC O104:H4 strain appeared to be more viable than E. coli O157:H7 under conditions of decreased pH and in the presence of sodium nitrite. Analysis of specific EHEC strains in experiments with an EHEC inoculation cocktail showed a dominance of EHEC/EAEC O104:H4, which could be isolated from fermented sausages for 60 days. Inhibitory activities of EHEC/EAEC O104:H4 toward several E. coli strains, including serotype O157 strains, could be determined. Our study suggests that EHEC/EAEC O104:H4 is well adapted to the multiple adverse conditions occurring in fermented raw sausages. Therefore, it is strongly recommended that STEC strain cocktails composed of several serotypes, instead of E. coli O157:H7 alone, be used in food risk assessments. The enhanced persistence of EHEC/EAEC O104:H4 as a result of its robustness, as well as the production of bacteriocins, may account for its extraordinary virulence potential. In 2011, a severe outbreak caused by an EHEC/EAEC serovar O104:H4 strain led to many HUS sequelae. In this study, the persistence of the O104:H4 strain was compared with those of other outbreak-relevant STEC strains under conditions of fermented raw sausage production. Both O157:NM and O104:H4 strains could survive longer during the production of fermented sausages than E. coli O157:H7 strains. E. coli O104:H4 was also shown to be well adapted to the multiple adverse conditions encountered in fermented sausages, and the secretion of a bacteriocin may explain the competitive advantage of this strain in an EHEC strain cocktail. Consequently, this study strongly suggests that enhanced survival and persistence, and the presumptive production of a bacteriocin, may explain the increased virulence of the O104:H4 outbreak strain. Furthermore, this strain appears to be capable of surviving in a meat product, suggesting that meat should not be excluded as a source of potential E. coli O104:H4 infection.


Impact of the Opioid Safety Initiative on opioid-related prescribing in veterans.
The Veterans Health Administration (VHA) designed the Opioid Safety Initiative (OSI) to help decrease opioid prescribing practices associated with adverse outcomes. Key components included disseminating a dashboard tool that aggregates electronic medical record data to audit real-time opioid-related prescribing and identifying a clinical leader at each facility to implement the tool and promote safer prescribing. This study examines changes associated with OSI implementation in October 2013 among all adult VHA patients who filled outpatient opioid prescriptions. Interrupted time series analyses controlled for baseline trends and examined data from October 2012 to September 2014 to determine the changes after OSI implementation in prescribing of high-dosage opioid regimens (total daily dosages >100 morphine equivalents [MEQ] and >200 MEQ) and concurrent benzodiazepines. Across VHA facilities nationwide, there was a decreasing trend in high-dosage opioid prescribing with 55,722 patients receiving daily opioid dosages >100 MEQ in October 2012, which decreased to 46,780 in September 2014 (16% reduction). The OSI was associated with an additional decrease, compared to pre-OSI trends, of 331 patients per month (95% confidence interval [CI] -378 to -284) receiving opioids >100 MEQ, a decrease of 164 patients per month (95% CI -186 to -142) receiving opioids >200 MEQ, and a decrease of 781 patients per month (95% CI -969 to -593) receiving concurrent benzodiazepines. Implementation of a national health care system-wide initiative was associated with reductions in outpatient prescribing of risky opioid regimens. These findings provide evidence for the potential utility of large-scale interventions to promote safer opioid prescribing.


Early Prescription Opioid Use for Musculoskeletal Disorders and Work Outcomes: A Systematic Review of the Literature.
Musculoskeletal disorders (MSDs) are a common source of work disability. Opioid prescribing for MSDs has been on the rise, despite a lack of data on effectiveness. The objective of this study was to conduct a systematic review to determine whether early receipt of opioids is associated with future work outcomes among workers with MSDs compared with other analgesics, no analgesics, or placebo. MEDLINE, EMBASE, CINAHL, and CENTRAL were searched from inception to 2014 and reference lists were scanned. Studies were included if opioids were prescribed within 12 weeks of MSD onset. Eligible outcomes included absenteeism, work status, receiving disability payments, and functional status. Two reviewers independently reviewed articles for relevance, risk of bias, and data extraction using standardized forms. Data synthesis using best evidence synthesis methods was planned. Five historical cohort studies met the inclusion criteria, all including workers filing wage compensation claims. Four studies demonstrated a significant association between early opioids and prolonged work disability. One study found a shorter time between prescriptions to be associated with shorter work disability. However, all studies were found to be at a high risk of bias and a best evidence synthesis could not be conducted. The main limitations identified were with exposure measurement and control of confounding. Current literature suggests that opioids provided within the first 12 weeks of onset of an MSD are associated with prolonged work disability. However, the conclusions of these studies need testing in a high-quality study that addresses the methodological shortcomings identified in the current review.


Characterization of biominerals in species of Canna (Cannaceae).
Plant biominerals are not always well characterized, although this information is important for plant physiology and can be useful for taxonomic purposes. In this work, fresh plant material of seven wild neotropical species of genus Canna, C. ascendens, C. coccinea, C. indica, C. glauca, C. plurituberosa, C. variegatifolia and C. fuchsina sp. ined., taken from different habitats, were studied to characterize the biominerals in their internal tissues. For the first time, samples from primary and secondary veins of leaves were investigated by means of infrared spectroscopy, complemented with X-ray powder diffractometry and scanning electron microscopy. The spectroscopic results, supported by X-ray powder diffractometry, suggest that the calcium oxalate is present in the form of whewellite (CaC2O4 x H2O) in all the investigated samples. It is interesting to emphasize that all IR spectra obtained were strongly similar in all species studied, thus indicating an identical chemical composition in terms of the biominerals found. In this sense, the results suggest that the species of Canna show similar ability to produce biogenic silica and produce an identical type of calcium oxalate within their tissues. These results can be an additional trait to support the relationship among the families of Zingiberales.


Enhanced peak growth of global vegetation and its key mechanisms.
The annual peak growth of vegetation is critical in characterizing the capacity of terrestrial ecosystem productivity and shaping the seasonality of atmospheric CO2 concentrations. The recent greening of global lands suggests an increasing trend of terrestrial vegetation growth, but whether or not the peak growth has been globally enhanced still remains unclear. Here, we use two global datasets of gross primary productivity (GPP) and a satellite-derived Normalized Difference Vegetation Index (NDVI) to characterize recent changes in annual peak vegetation growth (that is, GPPmax and NDVImax). We demonstrate that the peak in the growth of global vegetation has been linearly increasing during the past three decades. About 65% of the NDVImax variation is evenly explained by expanding croplands (21%), rising CO2 (22%) and intensifying nitrogen deposition (22%). The contribution of expanding croplands to the peak growth trend is substantiated by measurements from eddy-flux towers, sun-induced chlorophyll fluorescence and a global database of plant traits, all of which demonstrate that croplands have a higher photosynthetic capacity than other vegetation types. The large contribution of CO2 is also supported by a meta-analysis of 466 manipulative experiments and 15 terrestrial biosphere models. Furthermore, we show that the contribution of GPPmax to the change in annual GPP is less in the tropics than in other regions. These multiple lines of evidence reveal an increasing trend in the peak growth of global vegetation. The findings highlight the important roles of agricultural intensification and atmospheric changes in reshaping the seasonality of global vegetation growth.


Acute administration of buprenorphine in humans: partial agonist and blockade effects.
Buprenorphine, a mixed opioid agonist-antagonist, is being investigated as a treatment for opioid dependence. This study compared the acute subjective and physiological effects of sublingual buprenorphine to those of p.o. methadone over a wide range of doses and compared the ability of both drugs to alter the effects of an opioid challenge. Male inpatient volunteers (n = 9) with histories of opioid abuse participated in this double-blind, double-dummy study. Sublingual buprenorphine (0, 0.5, 2, 8, 16 and 32 mg) and p.o. methadone (3.75, 15 and 60 mg) were administered once weekly according to a Latin-square design, and subjects were monitored on a variety of physiological and subjective measures. Twenty-four hours later, subjects were tested with ascending doses of i.m. hydromorphone (0, 1 and 4 mg) given 45 min apart. Buprenorphine and methadone produced typical opioid agonist effects of long duration, including pupillary constriction, respiratory depression and elevations on subject-rated and observer-rated indices of euphoria, sedation and opioid-like symptoms. The buprenorphine dose-effect curves were nonlinear and maximal effects for most physiological and subjective measures were observed between 4 and 8 mg, with no greater effects observed at higher doses. The methadone dose-effect curves were linear across the range of doses tested. High doses of buprenorphine and methadone both attenuated the response to hydromorphone challenge 24 hr later. These data indicate that there is a ceiling on the effects of buprenorphine in humans that may reduce its abuse liability and increase its safety, and indicate that opioid blockade occurs after acute administration of buprenorphine or methadone.


A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site.
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic-site density distributions. Furthermore, we assess the quality of the resulting solvation thermodynamics density distributions by analyzing the binding site of coagulation Factor Xa with both GIST and 3D-RISM. We find good qualitative agreement between the methods for oxygen and hydrogen densities as well as direct solute-solvent energetic interactions. However, 3D-RISM predicts lower energetic and entropic penalties for moving water from the bulk to the binding site.


On the long-run sensitivity of probabilistic Boolean networks.
Boolean networks and, more generally, probabilistic Boolean networks, as one class of gene regulatory networks, model biological processes with the network dynamics determined by the logic-rule regulatory functions in conjunction with probabilistic parameters involved in network transitions. While there has been significant research on applying different control policies to alter network dynamics as future gene therapeutic intervention, we have seen less work on understanding the sensitivity of network dynamics with respect to perturbations to networks, including regulatory rules and the involved parameters, which is particularly critical for the design of intervention strategies. This paper studies this less investigated issue of network sensitivity in the long run. As the underlying model of probabilistic Boolean networks is a finite Markov chain, we define the network sensitivity based on the steady-state distributions of probabilistic Boolean networks and call it long-run sensitivity. The steady-state distribution reflects the long-run behavior of the network and it can give insight into the dynamics or momentum existing in a system. The change of steady-state distribution caused by possible perturbations is the key measure for intervention. This newly defined long-run sensitivity can provide insight on both network inference and intervention. We show the results for probabilistic Boolean networks generated from random Boolean networks and the results from two real biological networks illustrate preliminary applications of sensitivity in intervention for practical problems.


Predator-prey dynamics of bald eagles and glaucous-winged gulls at Protection Island, Washington, USA.
Bald eagle (Haliaeetus leucocephalus) populations in North America rebounded in the latter part of the twentieth century, the result of tightened protection and outlawing of pesticides such as DDT. An unintended consequence of recovery may be a negative impact on seabirds. During the 1980s, few bald eagles disturbed a large glaucous-winged gull (Larus glaucescens) colony on Protection Island, Washington, USA, in the Salish Sea. Breeding gull numbers in this colony rose nearly 50% during the 1980s and early 1990s. Beginning in the 1990s, a dramatic increase in bald eagle activity ensued within the colony, after which began a significant decline in gull numbers.To examine whether trends in the gull colony could be explained by eagle activity, we fit a Lotka-Volterra-type predator-prey model to gull nest count data and Washington State eagle territory data collected in most years between 1980 and 2016. Both species were assumed to grow logistically in the absence of the other.The model fits the data with generalized R 2 = 0.82, supporting the hypothesis that gull dynamics were due largely to eagle population dynamics.Point estimates of the model parameters indicated approach to stable coexistence. Within the 95% confidence intervals for the parameters, however, 11.0% of bootstrapped parameter vectors predicted gull colony extinction.Our results suggest that the effects of bald eagle activity on the dynamics of a large gull colony were explained by a predator-prey relationship that included the possibility of coexistence but also the possibility of gull colony extinction. This study serves as a cautionary exploration of the future, not only for gulls on Protection Island, but for other seabirds in the Salish Sea. Managers should monitor numbers of nests in seabird colonies as well as eagle activity within colonies to document trends that may lead to colony extinction.


Impaired Insulin Clearance as the Initial Regulator of Obesity-Associated Hyperinsulinemia: Novel Insight Into the Underlying Mechanism Based on Serum Bile Acid Profiles.
To investigate the roles of insulin clearance and insulin secretion in the development of hyperinsulinemia in obese subjects and to reveal the association between insulin clearance and bile acids (BAs). In cohort 1, insulin secretion, sensitivity, and endogenous insulin clearance were evaluated with an oral glucose tolerance test in 460 recruited participants. In cohort 2, 81 participants underwent an intravenous glucose tolerance test and a hyperinsulinemic-euglycemic clamp to assess insulin secretion, endogenous and exogenous insulin clearance, and insulin sensitivity. Based on insulin resistance levels ranging from mild to severe, obese participants without diabetes were further divided into 10 quantiles in cohort 1 and into tertiles in cohort 2. Forty serum BAs were measured in cohort 2 to examine the association between BAs and insulin clearance. All obese participants had impaired insulin clearance, and it worsened with additional insulin resistance in obese subjects without diabetes. However, insulin secretion was unchanged from quantile 1 to 3 in cohort 1, and no difference was found in cohort 2. After adjustments for all confounding factors, serum-conjugated BAs, especially glycodeoxycholic acid (GDCA; β = -0.335, P = 0.004) and taurodeoxycholic acid (TDCA; β = -0.333, P = 0.003), were negatively correlated with insulin clearance. The ratio of unconjugated to conjugated BAs (β = 0.335, P = 0.002) was positively correlated with insulin clearance. Hyperinsulinemia in obese subjects might be primarily induced by decreased insulin clearance rather than increased insulin secretion. Changes in circulating conjugated BAs, especially GDCA and TDCA, might play an important role in regulating insulin clearance.


Hurricane Harvey Impacts on Water Quality and Microbial Communities in Houston, TX Waterbodies.
Extreme weather events can temporarily alter the structure of coastal systems and generate floodwaters that are contaminated with fecal indicator bacteria (FIB); however, every coastal system is unique, so identification of trends and commonalities in these episodic events is challenging. To improve our understanding of the resilience of coastal systems to the disturbance of extreme weather events, we monitored water quality, FIB at three stations within Clear Lake, an estuary between Houston and Galveston, and three stations in bayous that feed into the estuary. Water samples were collected immediately before and after Hurricane Harvey (HH) and then throughout the fall of 2017. FIB levels were monitored by culturing E. coli and Enterococci. Microbial community structure was profiled by high throughput sequencing of PCR-amplified 16S rRNA gene fragments. Water quality and FIB data were also compared to historical data for these water body segments. Before HH, salinity within Clear Lake ranged from 9 to 11 practical salinity units (PSU). Immediately after the storm, salinity dropped to < 1 PSU and then gradually increased to historical levels over 2 months. Dissolved inorganic nutrient levels were also relatively low immediately after HH and returned, within a couple of months, to historical levels. FIB levels were elevated immediately after the storm; however, after 1 week, E. coli levels had decreased to what would be acceptable levels for freshwater. Enterococci levels collected several weeks after the storm were within the range of historical levels. Microbial community structure shifted from a system dominated by Cyanobacteria sp. before HH to a system dominated by Proteobacteria and Bacteroidetes immediately after. Several sequences observed only in floodwater showed similarity to sequences previously reported for samples collected following Hurricane Irene. These changes in beta diversity corresponded to salinity and nitrate/nitrite concentrations. Differential abundance analysis of metabolic pathways, predicted from 16S sequences, suggested that pathways associated with virulence and antibiotic resistance were elevated in floodwater. Overall, these results suggest that floodwater generated from these extreme events may have high levels of fecal contamination, antibiotic resistant bacteria and bacteria rarely observed in other systems.


Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis.
Invasive lobular and ductal breast tumors have distinct histologies and clinical presentation. Other than altered expression of E-cadherin, little is known about the underlying biology that distinguishes the tumor subtypes. We used cDNA microarrays to identify genes differentially expressed between lobular and ductal tumors. Unsupervised clustering of tumors failed to distinguish between the two subtypes. Prediction analysis for microarrays (PAM) was able to predict tumor type with an accuracy of 93.7%. Genes that were significantly differentially expressed between the two groups were identified by MaxT permutation analysis using t tests (20 cDNA clones and 10 unique genes), significance analysis for microarrays (33 cDNA clones and 15 genes, at an estimated false discovery rate of 2%), and PAM (31 cDNAs and 15 genes). There were 8 genes identified by all three of these related methods (E-cadherin, survivin, cathepsin B, TPI1, SPRY1, SCYA14, TFAP2B, and thrombospondin 4), and an additional 3 that were identified by significance analysis for microarrays and PAM (osteopontin, HLA-G, and CHC1). To validate the differential expression of these genes, 7 of them were tested by real-time quantitative PCR, which verified that they were differentially expressed in lobular versus ductal tumors. In conclusion, specific changes in gene expression distinguish lobular from ductal breast carcinomas. These genes may be important in understanding the basis of phenotypic differences among breast cancers.


Anabolic steroids and Norwegian weightlifters.
The mean bodyweight, in kilograms, and mean weightlifting result, in points, for the ten best weightlifters at the annual Norwegian championships 1962-82 have been studied. During the 21 years, the mean bodyweight for these ten increased by 18 kg, probably due to the effect of androgens. The weightlifting results improved rapidly from 1968 onwards, probably reflecting an increasingly widespread use of anabolic steroids by Norwegian weightlifters. In 1977 doping tests were introduced, and from then on, rate of improvement has increased much more slowly. The annual sale of anabolic steroids 1963-81 and testosterone 1974-81, in Norway have been recorded. The sale of anabolic steroids increased irregularly until 1974-75, and has since shown a 42% decrease. The sale of testosterone 1974-81 showed a slight reduction, thus giving no support to the suggestion that doping tests for anabolic steroids would lead to a transfer to testosterone abuse.


The Composer's Program Note for Newly Written Classical Music: Content and Intentions.
In concerts of western classical music the provision of a program note is a widespread practice dating back to the 18th century and still commonly in use. Program notes tend to inform listeners and performers about historical context, composer biographical details, and compositional thinking. However, the scant program note research conducted to date reveals that program notes may not foster understanding or enhance listener enjoyment as previously assumed. In the case of canonic works, performers and listeners may already be familiar with much of the program note information. This is not so in the case of newly composed works, which formed the basis of the exploratory study reported here. This article reports the views of 17 living contemporary composers on their writing of program notes for their own works. In particular, the study sought to understand the intended recipient, role and the content of composer-written program notes. Participating composers identified three main roles for their program notes: to shape a performer's interpretation of the work; to guide, engage or direct the listener and/or performer; and as collaborative mode of communication between the composer, performer, and listener. For some composers, this collaboration was intended to result in "performative listening" in which listeners were actively engaged in bringing each composition to life. This was also described as a form of empathy that results in the co-construction of the musical experience. Overall, composers avoided giving too much personal information and they provided performers with more structural information. However, composers did not agree on whether the same information should be provided to both performers and listeners. Composers' responses problematize the view of a program note as a simple statement from writer to recipient, indicating instead a more complex set of relations at play between composer, performer, listener, and the work itself. These relations are illustrated in a model. There are implications for program note writers and readers, and for educators. Future research might seek to enhance understanding of program notes, including whether the written program note is the most effective format for communications about music.


Mg(2+)-induced conformational changes in the btuB riboswitch from E. coli.
Mg(2+) has been shown to modulate the function of riboswitches by facilitating the ligand-riboswitch interactions. The btuB riboswitch from Escherichia coli undergoes a conformational change upon binding to its ligand, coenzyme B12 (adenosyl-cobalamine, AdoCbl), and down-regulates the expression of the B12 transporter protein BtuB in order to control the cellular levels of AdoCbl. Here, we discuss the structural folding attained by the btuB riboswitch from E. coli in response to Mg(2+) and how it affects the ligand binding competent conformation of the RNA. The btuB riboswitch notably adopts different conformational states depending upon the concentration of Mg(2+). With the help of in-line probing, we show the existence of at least two specific conformations, one being achieved in the complete absence of Mg(2+) (or low Mg(2+) concentration) and the other appearing above ∼0.5 mM Mg(2+). Distinct regions of the riboswitch exhibit different dissociation constants toward Mg(2+), indicating a stepwise folding of the btuB RNA. Increasing the Mg(2+) concentration drives the transition from one conformation toward the other. The conformational state existing above 0.5 mM Mg(2+) defines the binding competent conformation of the btuB riboswitch which can productively interact with the ligand, coenzyme B12, and switch the RNA conformation. Moreover, raising the Mg(2+) concentration enhances the ratio of switched RNA in the presence of AdoCbl. The lack of a AdoCbl-induced conformational switch experienced by the btuB riboswitch in the absence of Mg(2+) indicates a crucial role played by Mg(2+) for defining an active conformation of the riboswitch.


CPAS: the UK's national machine learning-based hospital capacity planning system for COVID-19.
The coronavirus disease 2019 (COVID-19) global pandemic poses the threat of overwhelming healthcare systems with unprecedented demands for intensive care resources. Managing these demands cannot be effectively conducted without a nationwide collective effort that relies on data to forecast hospital demands on the national, regional, hospital and individual levels. To this end, we developed the COVID-19 Capacity Planning and Analysis System (CPAS)-a machine learning-based system for hospital resource planning that we have successfully deployed at individual hospitals and across regions in the UK in coordination with NHS Digital. In this paper, we discuss the main challenges of deploying a machine learning-based decision support system at national scale, and explain how CPAS addresses these challenges by (1) defining the appropriate learning problem, (2) combining bottom-up and top-down analytical approaches, (3) using state-of-the-art machine learning algorithms, (4) integrating heterogeneous data sources, and (5) presenting the result with an interactive and transparent interface. CPAS is one of the first machine learning-based systems to be deployed in hospitals on a national scale to address the COVID-19 pandemic-we conclude the paper with a summary of the lessons learned from this experience.