Apoptosis of epithelial hepatocytes plays a pivotal role in acute as well as in chronic liver diseases. The cleavage of cytokeratin-18 (CK-18) by caspases is an early event in the apoptotic process. We therefore sought to investigate serum levels of CK-18 and 20S proteasome in patients with liver cirrhosis, primary graft dysfunction (PDF), and acute liver failure (ALF), and in healthy volunteers. Enzyme-linked immunosorbent assay (ELISA) was utilized to measure the concentration of M30, a fragment of CK-18 cleaved at Asp396 (M30 neoantigen), and the concentration of 20S proteasome. Serum levels of the CK-18 neoepitope M30 were significantly increased in ALF, primary graft dysfunction, and liver cirrhosis vs. healthy controls (1,993.6+/-124.7 U/L, 2,238.1+/-235.9 U/L, and 673.6+/-86.5 U/L vs. 66.8+/-29.1 U/L, respectively, P<0.001). Similar results were detected with the evaluation of 20S proteasome (124,014.5+/-13,235.6 ng/mL, 76,993.2+/-15,720.1 ng/mL, and 2,395.9+/-1,098.2 ng/mL vs. 1,074.5+/-259.4 ng/mL, respectively; P<0.001). Detection of CK-18 neoepitope M30 and 20S proteasome may represent a novel marker of tracing apoptotic epithelium, respectively mirroring degenerative liver processes in affected patient population.

In this paper we demonstrate that Generative Topographic Mapping (GTM), a machine learning method traditionally used for data visualisation, can be efficiently applied to QSAR modelling using probability distribution functions (PDF) computed in the latent 2-dimensional space. Several different scenarios of the activity assessment were considered: (i) the "activity landscape" approach based on direct use of PDF, (ii) QSAR models involving GTM-generated on descriptors derived from PDF, and, (iii) the k-Nearest Neighbours approach in 2D latent space. Benchmarking calculations were performed on five different datasets: stability constants of metal cations Ca(2+) , Gd(3+) and Lu(3+) complexes with organic ligands in water, aqueous solubility and activity of thrombin inhibitors. It has been shown that the performance of GTM-based regression models is similar to that obtained with some popular machine-learning methods (random forest, k-NN, M5P regression tree and PLS) and ISIDA fragment descriptors. By comparing GTM activity landscapes built both on predicted and experimental activities, we may visually assess the model's performance and identify the areas in the chemical space corresponding to reliable predictions. The applicability domain used in this work is based on data likelihood. Its application has significantly improved the model performances for 4 out of 5 datasets.

SemanticEye, an ontology with associated tools, improves the classification and open accessibility of chemical information in electronic publishing. In a manner analogous to digital music management, RDF metadata encoded as Adobe XMP can be extracted from a variety of document formats, such as PDF, and managed in an RDF repository called Sesame. Users upload electronic documents containing XMP to a central server by "dropping" them into WebDAV folders. The documents can then be navigated in a Web browser via their metadata, and multiple documents containing identical metadata can then be aggregated. SemanticEye does not actually store any documents. By including unique identifiers within the XMP, such as the DOI, associated documents can be retrieved from the Web with the help of resolving agents. The power of this metadata driven approach is illustrated by including, within the XMP, InChI identifiers for molecular structures and finding relationships between articles based on their InChIs. SemanticEye will become increasingly more comprehensive as usage becomes more widespread. Furthermore, following the Semantic Web architecture enables the reuse of open software tools, provides a "semantically intuitive" alternative to search engines, and fosters a greater sense of trust in Web-based scientific information.

Histamine and its two receptors, histamine-gated chloride channel subunit 1 (HisCl1) and ora transientless (Ort), are known to control photoreception and temperature sensing in Drosophila. However, histamine signaling in the context of neural circuitry for sleep-wake behaviors has not yet been examined in detail. Here, we obtained mutant flies with compromised or enhanced histamine signaling and tested their baseline sleep. Hypomorphic mutations in histidine decarboxylase (HDC), an enzyme catalyzing the conversion from histidine to histamine, caused an increase in sleep duration. Interestingly, hisCl1 mutants but not ort mutants showed long-sleep phenotypes similar to those in hdc mutants. Increased sleep duration in hisCl1 mutants was rescued by overexpressing hisCl1 in circadian pacemaker neurons expressing a neuropeptide pigment dispersing factor (PDF). Consistently, RNA interference (RNAi)-mediated depletion of hisCl1 in PDF neurons was sufficient to mimic hisCl1 mutant phenotypes, suggesting that PDF neurons are crucial for sleep regulation by the histamine-HisCl1 signaling. Finally, either hisCl1 mutation or genetic ablation of PDF neurons dampened wake-promoting effects of elevated histamine signaling via direct histamine administration. Taken together, these data clearly demonstrate that the histamine-HisCl1 receptor axis can activate and maintain the wake state in Drosophila and that wake-activating signals may travel via the PDF neurons.

The neural mechanisms of early vision can be explained in terms of an information-theoretic optimization of the neural processing with respect to the statistical properties of the natural environment. Recent applications of this approach have been successful in the prediction of the linear filtering properties of ganglion cells and simple cells, but the relations between the environmental statistics and cortical nonlinearities, like those of end-stopped or complex cells, are not yet fully understood. Here we present extensions of our previous investigations of the exploitation of higher-order statistics by nonlinear neurons. We use multivariate wavelet statistics to demonstrate that a strictly linear processing would inevitably leave substantial statistical dependencies between the outputs of the units. We then consider how the basic nonlinearities of cortical neurons--gain control and ON/OFF half-wave rectification--can exploit these higher-order statistical dependencies. We first show that gain control provides an adaptation to the polar separability of the multivariate probability density function (PDF), and, together with an output nonlinearity, enables an overcomplete sparse coding. We then consider how the remaining higher-order dependencies between different units can be exploited by a combination of basic ON/OFF point nonlinearities and subsequent weighted linear combinations. We consider two statistical optimization schemes for the computation of the optimal weights: principal component analysis (PCA) and independent component analysis (ICA). Since the intermediate nonlinearities transform some of the higher-order dependencies into second-order dependencies even the basic PCA approach is able to exploit part of the redundancies. ICA ignores this second-order structure, but can exploit higher-order dependencies. Both schemes yield a variety of nonlinear units which comprise the typical nonlinear processing properties, such as end-stopping, side-stopping, complex-cell properties and extra-classical receptive field properties, but the 'ideal' complex cells seem only to occur with PCA. Thus, a combination of ON/OFF nonlinearities with an integrated PCA-ICA strategy seems necessary to exploit the statistical properties of natural images.

The metalloenzyme peptide deformylase (PDF) represents one of the most promising bacterial targets in the search for novel mode of action antibiotics that lack cross-resistance to existing drugs. Initial research and clinical development has focused on anti-pneumococcal applications. During optimization, peptide analogs were developed containing either a hydroxamate or formyl-hydroxylamine as metal interacting group, yielding inhibitors with in vitro activity against a broad spectrum of organisms. Preclinical studies revealed potent antibacterial activity in vivo that is paired with good pharmacokinetic properties and excellent tolerability in different species. BB-83698, a potent PDF inhibitor with i.v. and oral efficacy in preclinical animal models, represents the first class-representative compound evaluated in man. The inhibitor was administered by i.v. infusion and was shown to exhibit generally dose-proportional pharmacokinetics. It was well tolerated up to doses providing predicted therapeutic exposures. These human results, combined with the preclinical information, clearly support the potential of PDF inhibitors for development as a novel class of antibacterial therapeutics.

OBJECTIVE

Adapting health technology assessment (HTA) reports for different contexts could reduce the need for multiple reports on the same health technology with resultant saving of time and resources. This article describes an instrument, the adaptation toolkit, which has been developed to aid in the process of adaptation of HTA reports.

METHODS

The toolkit was developed by a partnership of HTA agencies and networks from across Europe. The role of the toolkit is to guide the user through the process of selecting possible relevant material from these report(s), assessing the relevance, reliability, and transferability of the material, and adapting it for the desired context.

RESULTS

The adaptation toolkit has been developed, it comprises a collection of resources that help the user assess whether data and information in existing HTA reports should and could be adapted for their own setting. The toolkit contains two sections: a preliminary speedy sifting section and the main toolkit. The main toolkit includes five domains: (i) technology use and development, (ii) safety, (iii) effectiveness (including efficacy), (iv) economic evaluation, and (v) organizational aspects. Legal, ethical, and social aspects are beyond the scope of the toolkit. The toolkit is designed for the adaptation of evidence synthesis rather than primary research.

CONCLUSIONS

The completed current version of the toolkit contains checklists and resources to aid in the adaptation of HTA reports. This collection of resources is available for use by all HTA agencies and can be accessed at: http://www.eunethta.net/upload/WP5/EUnetHTA_HTA_Adaptation_Toolkit_October08.pdf..

Alzheimer's disease (AD) is the most common cause of dementia, which is associated with an enormous personal, social and economic burden worldwide. However, there are few current treatments with none of them targeting the underlying causes of the disease. Sleep and circadian rhythm defects are not only distressing symptoms of AD and other tauopathies and are a leading cause of care home admission but are also thought to accelerate AD pathology. Despite this, little is understood about the underlying causes of these behavioural changes. Expression of the 0N4R isoform of tau has been associated with AD pathology and we show that expressing it in the Drosophila clock network gives rise to circadian and sleep phenotypes which closely match the behavioural changes seen in human AD patients. Tauopathic flies exhibited greater locomotor activity throughout the day and night and displayed a loss of sleep, particularly at night. Under constant darkness, the locomotor behaviour of tau-expressing flies was less rhythmic than controls indicating a defect in their intrinsic circadian rhythm. Current clamp recordings from wake-promoting, pigment dispersing factor (PDF)-positive large lateral ventral clock neurons (l-LNvs) revealed elevated spontaneous firing throughout the day and night which likely underlies the observed hyperactive circadian phenotype. Interestingly, expression of tau in only the PDF-positive pacemaker neurons, which are thought to be the most important for behaviour under constant conditions, was not sufficient or even necessary to affect circadian rhythmicity. This work establishes Drosophila as a model to investigate interactions between human pathological versions of tau and the machinery that controls neuronal excitability, allowing the identification of underlying mechanisms of disease that may reveal new therapeutic targets.

We quantify the impact of the Wuhan Covid-19 lockdown on concentrations of four air pollutants using a two-step approach. First, we use machine learning to remove the confounding effects of weather conditions on pollution concentrations. Second, we use a new augmented synthetic control method (Ben-Michael et al. in The augmented synthetic control method. University of California Berkeley, Mimeo, 2019. https://arxiv.org/<em>pdf</em>/1811.04170.<em>pdf</em>) to estimate the impact of the lockdown on weather normalised pollution relative to a control group of cities that were not in lockdown. We find NO <math><msub><mrow></mrow> <mn>2</mn></msub> </math> concentrations fell by as much as 24 <math><mi>μ</mi></math> g/m <math><msup><mrow></mrow> <mn>3</mn></msup> </math> during the lockdown (a reduction of 63% from the pre-lockdown level), while PM10 concentrations fell by a similar amount but for a shorter period. The lockdown had no discernible impact on concentrations of SO <math><msub><mrow></mrow> <mn>2</mn></msub> </math> or CO. We calculate that the reduction of NO <math><msub><mrow></mrow> <mn>2</mn></msub> </math> concentrations could have prevented as many as 496 deaths in Wuhan city, 3368 deaths in Hubei province and 10,822 deaths in China as a whole.

Keywords: Air pollution; Covid-19; Health; Machine learning; Synthetic control.

A retrospective study of the treatment and short- and long-term outcomes of tuberculous peritonitis (TBP) complicating continuous ambulatory peritoneal dialysis (CAPD) among our dialysis patients over a 6-year period was performed. Ten cases of TBP complicating CAPD were identified among 601 dialysis patients between January 1988 and December 1994. There were four male and six female patients. The most common clinical features were abdominal pain, fever, and cloudy peritoneal fluid (PDF). Two patients had concurrent bacterial peritonitis. Extraperitoneal tuberculosis was not observed. The majority of the patients showed neutrophil predominance in the PDF. Only one patient had a positive acid-fast bacilli smear of the PDF. The acid-fast bacilli culture of the PDF was positive in all patients. The patients were treated with isoniazid, rifampicin, and pyrazinamide for 9 to 12 months (mean, 11 months). Continuous ambulatory peritoneal dialysis was continued in all patients. Two patients died, one from multiorgan failure at 2 months and the other from sudden cardiac death at 9 months. Two patients were converted to hemodialysis at 3 months. Six patients continued to receive CAPD after completion of the antituberculous treatment. Four of these six patients were still alive 5 years after the TBP. Three patients were still undergoing CAPD with satisfactory ultrafiltration and solute clearance. None of the patients developed relapse of TBP. We concluded that (1) TBP is a rare but important complication of CAPD, (2) removal of the Tenckhoff catheter is not mandatory in the management of TBP complicating CAPD, and (3) long-term continuation of CAPD is possible after TBP.

The authors present a segment-based convolution method to account for the interplay effect between intrafraction organ motion and the multileaf collimator position for each particular segment in intensity modulated radiation therapy (IMRT) delivered in a step-and-shoot manner. In this method, the static dose distribution attributed to each segment is convolved with the probability density function (PDF) of motion during delivery of the segment, whereas in the conventional convolution method ("average-based convolution"), the static dose distribution is convolved with the PDF averaged over an entire fraction, an entire treatment course, or even an entire patient population. In the case of IMRT delivered in a step-and-shoot manner, the average-based convolution method assumes that in each segment the target volume experiences the same motion pattern (PDF) as that of population. In the segment-based convolution method, the dose during each segment is calculated by convolving the static dose with the motion PDF specific to that segment, allowing both intrafraction motion and the interplay effect to be accounted for in the dose calculation. Intrafraction prostate motion data from a population of 35 patients tracked using the Calypso system (Calypso Medical Technologies, Inc., Seattle, WA) was used to generate motion PDFs. These were then convolved with dose distributions from clinical prostate IMRT plans. For a single segment with a small number of monitor units, the interplay effect introduced errors of up to 25.9% in the mean CTV dose compared against the planned dose evaluated by using the PDF of the entire fraction. In contrast, the interplay effect reduced the minimum CTV dose by 4.4%, and the CTV generalized equivalent uniform dose by 1.3%, in single fraction plans. For entire treatment courses delivered in either a hypofractionated (five fractions) or conventional >> 30 fractions) regimen, the discrepancy in total dose due to interplay effect was negligible.

BACKGROUND

Long-term peritoneal dialysis (PD) is associated with peritoneal fibrosis and loss of function. It has been shown that activation of the adenosine A(2A) receptor (A(2A)R) promotes tissue repair, wound healing and extracellular matrix (ECM) production. We have previously shown that adenosine is a potent regulator of inflammation in the peritoneum. In the current study, we explored the role of adenosine and the A(2A)R in two experimental models.

METHODS

Collagen deposition was evaluated in primary peritoneal fibroblasts following treatment with an A(2A)R agonist and antagonist. In addition, peritoneal fibrosis was induced by i.p. injection of either chlorhexidine gluconate for 2 weeks or 4.25% glucose peritoneal dialysis fluid (PDF) for 1 month. The development of fibrosis was compared between wild-type (WT) and WT mice treated with caffeine (an A(2A)R antagonist) in drinking water or between (A(2A)R(+/+)) mice and A(2A)R-deficient mice (A(2A)R(-/-)).

RESULTS

Adenosine or the A(2A)R agonist CGS21680 stimulated collagen production by peritoneal fibroblasts in vitro and A(2A)R antagonists (ZM241385 and caffeine) blocked this effect. Consistent with these results, caffeine-treated WT or A(2A)R(-/-) mice had reduced submesothelial thickness, collagen deposition and mRNA levels of fibroblast-specific protein (FSP-1) and connective tissue growth factor (CTGF). In addition, treatment with caffeine in vitro and in vivo diminished A(2A)R and A(2B)R mRNA levels induced by CG or PDF while it upregulated A(1)R levels.

CONCLUSIONS

Our data suggest that adenosine through its A(2A)R promotes peritoneal fibrosis and therefore should be considered as a target for pharmacological intervention.

To circumvent the potentially negative consequences of long-term exposure to unphysiologic acidic lactate-buffered peritoneal dialysis fluids (PDF), neutral pH solutions buffered with bicarbonate/lactate have recently been introduced in phase 2 and 3 clinical trials. This study examines the longitudinal changes in peritoneal macrophage (PMØ) function in patients dialyzed continuously with either lactate (LPD; 40 mM lactate, pH 5.2)-buffered or bicarbonate/lactate (TBL; 25 mM/15 mM bicarbonate/lactate, pH 7.3)-buffered PDF. Before the study, during the run in period of a phase 3 clinical trial, all patients had been taking LPD for at least the previous 18 wk. At the beginning of the study (day 0), both constitutive and serum-treated zymosan (STZ) stimulated tumor necrosis factor alpha (TNF-alpha) synthesis were assessed in PMØ isolated from 12-h dwell effluent (with 1.36% glucose) in all patients. The patients were subsequently randomized to either continuous TBL or LPD therapy and PMØ function was assessed after further 3- and 6-mo periods in all patients. At all time points measured STZ induced a dose-dependent increase in PMØ TNF-alpha secretion (P = 0.043 versus control for doses greater than 100 microg/ml). In patients continuously dialyzed with LPD, constitutive PMØ TNF-alpha synthesis levels (mean +/- SEM, pg/10(6) PMØ per18 h, n = 5 patients) were 154 +/- 65, 261 +/- 60, and 101 +/- 99 at 0, 3, and 6 mo, respectively. Stimulated STZ (1000 microg/ml) levels were 1340 +/- 519, 1046 +/- 586, and 758 +/- 250 at 0, 3, and 6 mo, respectively. In patients dialyzed with TBL, constitutive PMØ TNF-alpha synthesis levels (pg/10(6) PMØ per 18 h, n = 5 patients) were 300 +/- 136, 106 +/- 35, and 213 +/- 62 at 0, 3, and 6 mo, respectively. Stimulated STZ (1000 microg/ml) levels were 1969 +/- 751, 1541 +/- 330, and 2670 +/- 671 at 0, 3, and 6 mo, respectively. At 6 mo, STZ-stimulated PMØ TNF-alpha synthesis was significantly higher in patients treated with TBL compared with those treated with LPD (P = 0.0035). These data suggest that in patients continuously dialyzed with a neutral pH solution, there is a long-term improvement in PMØ function compared with patients on conventional therapy. Better PMØ function suggests improved host defense status and may affect the peritoneum's susceptibility to infection and potentially reduce the negative consequences of repeated intraperitoneal inflammation on long-term membrane function.

Salmonella typhimurium, resistant only to trimethoprim and sulphamethoxazole, was isolated from the faeces and blood of a chronic alcoholic patient in acute renal failure. The isolates harboured an 18 Md non-conjugative plasmid. He was dialysed peritoneally and treated with ampicillin; four days later there was no clinical improvement and his peritoneal dialysis fluid (PDF) had become infected. Salm. typhimurium was isolated from faeces and PDF. Both isolates were additionally resistant to ampicillin and contained two plasmids (55 Md and 18 Md). Therapy was changed to chloramphenicol and gentamicin was added to the PDF. Two weeks later Salm. typhimurium was again isolated from PDF and faeces. The PDF isolate was unchanged but 4% of the colonies isolated from this faecal specimen were resistant to chloramphenicol and had acquired an additional 62 Md plasmid. From all PDF and faecal specimens two different strains of Escherichia coli and one strain of Klebsiella pneumoniae were isolated which contained plasmids indistinguishable, on the basis of molecular weight and transferable resistance markers, from those acquired by Salm. typhimurium. The transferability of these plasmids in vitro to E. coli K12 and to the patient's initial Salm. typhimurium was studied and the results discussed.

Bioincompatibility of peritoneal dialysis fluids (PDF) limits their use in renal replacement therapy. PDF exposure harms mesothelial cells but induces heat shock proteins (HSP), which are essential for repair and cytoprotection. We searched for cellular pathways that impair the heat shock response in mesothelial cells after PDF-exposure. In a dose-response experiment, increasing PDF-exposure times resulted in rapidly increasing mesothelial cell damage but decreasing HSP expression, confirming impaired heat shock response. Using proteomics and bioinformatics, simultaneously activated apoptosis-related and inflammation-related pathways were identified as candidate mechanisms. Testing the role of sterile inflammation, addition of necrotic cell material to mesothelial cells increased, whereas addition of the interleukin-1 receptor (IL-1R) antagonist anakinra to PDF decreased release of inflammatory cytokines. Addition of anakinra during PDF exposure resulted in cytoprotection and increased chaperone expression. Thus, activation of the IL-1R plays a pivotal role in impairment of the heat shock response of mesothelial cells to PDF. Danger signals from injured cells lead to an elevated level of cytokine release associated with sterile inflammation, which reduces expression of HSP and other cytoprotective chaperones and exacerbates PDF damage. Blocking the IL-1R pathway might be useful in limiting damage during peritoneal dialysis.

Breast cancer remains one of the most frequently diagnosed cancers today. In developed countries, one in eight women is expected to present with breast cancer within her lifetime and an estimated 1,000,000 cases are detected each year worldwide (Canadian Cancer Statistics, http://www.cancer.ca/vgn/images/ portal/cit_86751114/14/33/1959864 11niw_stats2004_en.pdf). For women with recurrent disease, the median time of survival is about 2 years. Despite optimal surgery, adjuvant irradiation, hormonal treatment, and chemotherapy, approximately 30% of patients with localized breast cancer finally develop distant metastases. Early detection, which enables intervention at a localized and potentially curable stage, remains a central goal in breast cancer treatment. Indeed, the 5-year survival rate for women with breast cancer has been shown to increase dramatically when the disease is diagnosed at an early stage: from less than 25% in women with disseminated cancer to about 75% in patients with regional disease and over 95% in women with a localized tumor (Breast Cancer Facts and Figures, 2001-2002, http://www.cancer.org/downloads/STT/BrCaFF 2001.pdf). Unfortunately, only 60% of all breast cancers are diagnosed at a local stage. Any improvement in early detection through identification of tumor biomarkers would have a significant impact on reducing overall breast cancer mortality.

BACKGROUND

Acidic pH and the presence of glucose degradation products (GDP) are believed to compromise the biocompatibility of peritoneal dialysis fluids (PDF). The present study examines the effects of long-term exposure to GDP and low pH by comparing conventional PDF and a new, neutral pH, low GDP solution.

METHODS

All experiments were performed using a chronic infusion model of dialysis in nonuremic rats. The animals were treated for 6 weeks with 2 daily injections of 4.25% glucose-containing PDF. The following PDF were tested: CAPD3 (single-chamber bag, low pH, high GDP), CAPD3 pH 7.4 (single-chamber bag, neutral pH, high GDP), CAPD3-Balance (double-chamber bag, neutral pH, low GDP). All test solutions were obtained from Fresenius Medical Care, Bad Homburg, Germany.

RESULTS

After 6 weeks of exposure, peritoneal permeability to water, urea, creatinine, glucose, and sodium, assessed by peritoneal equilibration test, was similar in all groups. However, compared to other PDF, dialysis with CAPD3-Balance was associated with reduced concentrations of protein and hyaluronan in the dialysate, decreased peritoneal eosinophilia, and reduced dialysate levels of chemokines CCL2/MCP-1 and CCL5/RANTES. Morphologic changes in the peritoneal membrane of CAPD3-Balance-treated animals were much less pronounced and included reduced vascular density, preservation of the mesothelial monolayer and intercellular junction, and no reduplication of the submesothelial basement membrane.

CONCLUSIONS

A new generation of PDF with physiologic pH and low GDP level produce less irritation to the peritoneal membrane and better preserve its structural integrity. This effect seems to be related predominantly to minimized GDP concentrations.

Virtual paleontology unites a variety of computational techniques and methods for the visualization and analysis of fossils. Due to their great potential and increasing availability, these methods have become immensely popular in the last decade. However, communicating the wealth of digital information and results produced by the various techniques is still exacerbated by traditional methods of publication. Transferring and processing three-dimensional information, such as interactive models or animations, into scientific publications still poses a challenge. Here, we present different methods and applications to communicate digital data in academia, outreach and education. Three-dimensional PDFs, QR codes, anaglyph stereo imaging, and rapid prototyping-methods routinely used in the engineering, entertainment, or medical industries-are outlined and evaluated for their potential in science publishing and public engagement. Although limitations remain, these are simple, mostly cost-effective, and powerful tools to create novel and innovative resources for education, public engagement, or outreach.

The crystal structure of At<em>PDF</em>1B [Arabidopsis thaliana <em>PDF</em> (peptide deformylase) 1B; EC 3.5.1.88], a plant specific deformylase, has been determined at a resolution of 2.4 A (1 A=0.1 nm). The overall fold of At<em>PDF</em>1B is similar to other peptide deformylases that have been reported. Evidence from the crystal structure and gel filtration chromatography indicates that At<em>PDF</em>1B exists as a symmetric dimer. <em>PDF</em>1B is essential in plants and has a preferred substrate specificity towards the PS II (photosystem II) D1 polypeptide. Comparative analysis of At<em>PDF</em>1B, At<em>PDF</em>1A, and the type 1B deformylase from Escherichia coli, identifies a number of differences in substrate binding subsites that might account for variations in sequence preference. A model of the N-terminal five amino acids from the D1 polypeptide bound in the active site of At<em>PDF</em>1B suggests an influence of Tyr(178) as a structural determinant for polypeptide substrate specificity through hydrogen bonding with Thr(2) in the D1 sequence. Kinetic analyses using a polypeptide mimic of the D1 N-terminus was performed on At<em>PDF</em>1B mutated at Tyr(178) to alanine, phenylalanine or arginine (equivalent residue in At<em>PDF</em>1A). The results suggest that, whereas Tyr(178) can influence catalytic activity, other residues contribute to the overall preference for the D1 polypeptide.

Prostate derived factor (PDF) is a member of transforming growth factor-beta (TGF-beta) superfamily proteins involved in differentiation of the prostate epithelium. Proprotein convertases (PCs) such as furin are thought to mediate the processing of TGF-beta superfamily. In the present study, we demonstrated for the first time that human prostate cancer cell lines differentially synthesize and secret prostate derived factor (PDF), and that PDF secreted by LNCaP is processed by PCs. Exposure of LNCaP cells to the decanoyl-Arg-Val-Lys-Arg-chloromethylketone (CMK), a synthetic furin-like protease inhibitor, inhibited PDF processing and resulted in the loss of luminal cell phenotype and induction of basal cell phenotype in LNCaP cells as demonstrated by alternations in the expression of cytokeratins 8, 14, 18, and 19, markers of prostate epithelial cell differentiation. These results suggest that proprotein convertases may be involved in the regulation of prostate epithelial cell differentiation, and may be an important target of prostate cancer therapy.

BACKGROUND

Bone marrow lesions (BMLs) are useful diagnostic and prognostic markers in knee osteoarthritis (OA), but what they represent at the tissue level remains unclear. The aim of this study was to provide comprehensive tissue characterization of BMLs detected using two specific MRI sequences.

METHODS

Tibial plateaus were obtained from 60 patients (29 females, 31 males), undergoing knee arthroplasty for OA. To identify BMLs, MRI was performed ex vivo using T1 and PDFS-weighted sequences. Multi-modal tissue level analyses of the osteochondral unit (OCU) were performed, including cartilage volume measurement, OARSI grading, micro-CT analysis of bone microstructure, routine histopathological assessment and quantitation of bone turnover indices.

RESULTS

BMLs were detected in 74 % of tibial plateaus, the remainder comprising a No BML group. Of all BMLs, 59 % were designated BML 1 (detected only by PDFS) and 41 % were designated BML 2 (detected by both PDFS + T1). The presence of a BML was related to degeneration of the OCU, particularly within BML 2. When compared to No BML, BML 2 showed reduced cartilage volume (p = 0.008), higher OARSI scores (p = 0.004), thicker subchondral plate (p = 0.002), increased trabecular bone volume and plate-like structure (p = 0.0004), increased osteoid volume (p = 0.002) and thickness (p = 0.003), more bone marrow oedema (p = 0.03), fibrosis (p = 0.002), necrosis (p = 0.01) and fibrovascular cysts (p = 0.04). For most measures, BML 1 was intermediate between No BML and BML 2.

CONCLUSIONS

BMLs detected by specific MRI sequences identify different degrees of degeneration in the OCU. This suggests that MRI characteristics of BMLs may enable identification of different BML phenotypes and help target novel approaches to treatment and prevention of OA.

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation's (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7-36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged.

Although critical analysis of survey research is limited when reviewers and readers cannot view a study's questionnaire, access to novel questionnaires used in published research has not been systematically examined. The authors identified publications reporting the results of novel questionnaires in three medical journals (JAMA, The New England Journal of Medicine, and The Lancet) in January 2000-May 2003 and searched portable document format (PDF) versions of the studies for the complete questionnaire or a Uniform Resource Locator (URL) providing access to the questionnaire. When the questionnaire was not provided in the publication or a published URL, the authors requested it from the corresponding author in writing up to three times over a 6-week period. Of 93 publications with novel questionnaires, four printed the questionnaire in the article and three provided online access. Corresponding authors failed to provide questionnaires for 37 of 81 (46%) studies. Novel questionnaires used in published research are frequently not available to readers or researchers. Policies that improve access to novel questionnaires will allow better assessment of study results, reduce duplicated efforts, and improve authorship attribution for questionnaire design.

Circadian clocks control many self-sustained rhythms in physiology and behavior with approximately 24-hour periodicity. In many organisms, oxidative stress and aging negatively impact the circadian system and sleep. Conversely, loss of the clock decreases resistance to oxidative stress, and may reduce lifespan and speed up brain aging and neurodegeneration. Here we examined the effects of clock disruptions on locomotor aging and longevity in Drosophila. We found that lifespan was similarly reduced in three arrhythmic mutants (ClkAR, cyc0 and tim0) and in wild-type flies under constant light, which stops the clock. In contrast, ClkAR mutants showed significantly faster age-related locomotor deficits (as monitored by startle-induced climbing) than cyc0 and tim0, or than control flies under constant light. Reactive oxygen species accumulated more with age in ClkAR mutant brains, but this did not appear to contribute to the accelerated locomotor decline of the mutant. Clk, but not Cyc, inactivation by RNA interference in the pigment-dispersing factor (PDF)-expressing central pacemaker neurons led to similar loss of climbing performance as ClkAR. Conversely, restoring Clk function in these cells was sufficient to rescue the ClkAR locomotor phenotype, independently of behavioral rhythmicity. Accelerated locomotor decline of the ClkAR mutant required expression of the PDF receptor and correlated to an apparent loss of dopaminergic neurons in the posterior protocerebral lateral 1 (PPL1) clusters. This neuronal loss was rescued when the ClkAR mutation was placed in an apoptosis-deficient background. Impairing dopamine synthesis in a single pair of PPL1 neurons that innervate the mushroom bodies accelerated locomotor decline in otherwise wild-type flies. Our results therefore reveal a novel circadian-independent requirement for Clk in brain circadian neurons to maintain a subset of dopaminergic cells and avoid premature locomotor aging in Drosophila.