Inflammatory Pathways in Parkinson's Disease; A BNE Microarray Study.
The aetiology of Parkinson's disease (PD) is yet to be fully understood but it is becoming more and more evident that neuronal cell death may be multifactorial in essence. The main focus of PD research is to better understand substantia nigra homeostasis disruption, particularly in relation to the wide-spread deposition of the aberrant protein α-synuclein. Microarray technology contributed towards PD research with several studies to date and one gene, ALDH1A1 (Aldehyde dehydrogenase 1 family, member A1), consistently reappeared across studies including the present study, highlighting dopamine (DA) metabolism dysfunction resulting in oxidative stress and most probably leading to neuronal cell death. Neuronal cell death leads to increased inflammation through the activation of astrocytes and microglia. Using our dataset, we aimed to isolate some of these pathways so to offer potential novel neuroprotective therapeutic avenues. To that effect our study has focused on the upregulation of P2X7 (purinergic receptor P2X, ligand-gated ion channel, 7) receptor pathway (microglial activation) and on the NOS3 (nitric oxide synthase 3) pathway (angiogenesis). In summary, although the exact initiator of striatal DA neuronal cell death remains to be determined, based on our analysis, this event does not remain without consequence. Extracellular ATP and reactive astrocytes appear to be responsible for the activation of microglia which in turn release proinflammatory cytokines contributing further to the parkinsonian condition. In addition to tackling oxidative stress pathways we also suggest to reduce microglial and endothelial activation to support neuronal outgrowth.


Runx2 is required for early stages of endochondral bone formation but delays final stages of bone repair in Axin2-deficient mice.
Runx2 and Axin2 regulate skeletal development. We recently determined that Axin2 and Runx2 molecularly interact in differentiating osteoblasts to regulate intramembranous bone formation, but the relationship between these factors in endochondral bone formation was unresolved. To address this, we examined the effects of Axin2 deficiency on the cleidocranial dysplasia (CCD) phenotype of Runx2(+/-) mice, focusing on skeletal defects attributed to improper endochondral bone formation. Axin2 deficiency unexpectedly exacerbated calvarial components of the CCD phenotype in the Runx2(+/-) mice; the endocranial layer of the frontal suture, which develops by endochondral bone formation, failed to mineralize in Axin2(-/-):Runx2(+/-) mice, resulting in a cartilaginous, fibrotic and larger fontanel than observed in Runx2(+/-) mice. Transcripts associated with cartilage development (e.g., Acan, miR140) were expressed at higher levels, whereas blood vessel morphogenesis transcripts (e.g., Slit2) were suppressed in Axin2(-/-):Runx2(+/-) calvaria. Cartilage maturation was impaired, as primary chondrocytes from double mutant mice demonstrated delayed differentiation and produced less calcified matrix in vitro. The genetic dominance of Runx2 was also reflected during endochondral fracture repair, as both Runx2(+/-) and double mutant Axin2(-/-):Runx2(+/-) mice had enlarged fracture calluses at early stages of healing. However, by the end stages of fracture healing, double mutant animals diverged from the Runx2(+/-) mice, showing smaller calluses and increased torsional strength indicative of more rapid end stage bone formation as seen in the Axin2(-/-) mice. Taken together, our data demonstrate a dominant role for Runx2 in chondrocyte maturation, but implicate Axin2 as an important modulator of the terminal stages of endochondral bone formation.


Functional Genomics Uncover the Biology behind the Responsiveness of Head and Neck Squamous Cell Cancer Patients to Cetuximab.
To identify the tumor portrait of the minority of head and neck squamous cell carcinoma (HNSCC) patients with recurrent-metastatic (RM) disease who upon treatment with platinum-based chemotherapy plus cetuximab present a long-lasting response. The gene expression of pretreatment samples from 40 HNSCC-RM patients, divided in two groups [14 long-progression-free survival (PFS) and 26 short-PFS (median = 19 and 3 months, respectively)], was associated with PFS and was challenged against a dataset from metastatic colon cancer patients treated with cetuximab. For biologic analysis, we performed functional and subtype association using gene set enrichment analysis, associated biology across all currently available HNSCC signatures, and inferred drug sensitivity using data from the Cancer Genomic Project. The identified genomic profile exhibited a significant predictive value that was essentially confirmed in the single publicly available dataset of cetuximab-treated patients. The main divergence between long- and short-PFS groups was based on developmental/differentiation status. The long-PFS patients are characterized by basal subtype traits such as strong EGFR signaling phenotype and hypoxic differentiation, further validated by the significantly higher association with the hypoxia metagene. The short-PFS patients presented a strong activation of RAS signaling confirmed in an in vitro model of two isogenic HNSCC cell lines sensitive or resistant to cetuximab. The predicted drug sensitivity for all four EGFR inhibitors was higher in long- versus short-PFS patients (P range: <0.0022-1e-07). Our data uncover the biology behind response to platinum-based chemotherapy plus cetuximab in RM-HNSCC cancer and may have translational implications improving treatment selection. Clin Cancer Res; 22(15); 3961-70. ©2016 AACRSee related commentary by Chau and Hammerman, p. 3710.


PAS-cal: a generic recombinant peptide calibration standard for mass spectrometry.
We describe the design, preparation, and mass-spectrometric characterization of a new recombinant peptide calibration standard with uniform biophysical and ionization characteristics for mass spectrometry. "PAS-cal" is an artificial polypeptide concatamer of peptide cassettes with varying lengths, each composed of the three small, chemically stable amino acids Pro, Ala, and Ser, which are interspersed by Arg residues to allow site-specific cleavage with trypsin. PAS-cal is expressed at high yields in Escherichia coli as a Small Ubiquitin-like MOdifier (SUMO) fusion protein, which is easily purified and allows isolation of the PAS-cal moiety after SUMO protease cleavage. Upon subsequent in situ treatment with trypsin, the PAS-cal polypeptide yields a set of four defined homogeneous peptides in the range from 2 to 8 kDa with equal mass spacing. ESI-MS analysis revealed a conveniently interpretable raw spectrum, which after deconvolution resulted in a very simple pattern of four peaks with similar ionization signals. MALDI-MS analysis of a PAS-cal peptide mixture comprising both the intact polypeptide and its tryptic fragments revealed not only the four standard peptides but also the singly and doubly charged states of the intact concatamer as well as di- and trimeric adduct ion species between the peptides, thus augmenting the observable m/z range. The advantageous properties of PAS-cal are most likely a result of the strongly hydrophilic and conformationally disordered PEG-like properties of the PAS sequences. Therefore, PAS-cal offers an inexpensive and versatile recombinant peptide calibration standard for mass spectrometry in protein/peptide bioanalytics and proteomics research, the composition of which may be further adapted to fit individual needs.


The leading role of pathology in assessing the somatic molecular alterations of cancer: Position Paper of the European Society of Pathology.
Molecular pathology is an essential part of pathology complementing conventional morphological tools to obtain a correct integrated diagnosis with appropriate assessment of prognosis and prediction of response to therapy, particularly in cancer. There is a concern about the situation of molecular pathology in some areas of Europe, namely, regarding the central role of pathologists in assessing somatic genomic alterations in cancer. In some countries, there are attempts that other laboratory medicine specialists perform the molecular analysis of somatic alterations in cancer, particularly now when next generation sequencing (NGS) is incorporated into clinical practice. In this scenario, pathologists may play just the role of "tissue providers," and other specialists may take the lead in molecular analysis. Geneticists and laboratory medicine specialists have all background and skills to perform genetic analysis of germline alterations in hereditary disorders, including familial forms of cancers. However, interpretation of somatic alterations of cancer belongs to the specific scientific domain of pathology. Pathologists are necessary to guarantee the quality of the results, for several reasons: (1) The identified molecular alterations should be interpreted in the appropriate morphologic context, since most of them are context-specific; (2) pre-analytical issues must be taken into consideration; (3) it is crucial to check the proportion of tumor cells in the sample subjected to analysis and presence of inflammatory infiltrate and necrosis should be monitored; and 4) the role of pathologists is crucial to select the most appropriate methods and to control the turnaround time in which the molecular results are delivered in the context of an integrated diagnosis. Obviously, there is the possibility of having core facilities for NGS in a hospital to perform the sequence analysis that are open to other specialties (microbiologists, geneticists), but also in this scenario, pathologists should have the lead in assessing somatic alterations of cancer. In this article, we emphasize the importance of interpreting somatic molecular alterations of the tumors in the context of morphology. In this Position Paper of the European Society of Pathology, we strongly support a central role of pathology departments in the process of analysis and interpretation of somatic molecular alterations in cancer.


Endoscopic management of complex hydrocephalus.
The management of complex hydrocephalus is challenging. There is no consensus of the best treatment for isolated fourth ventricles, arachnoid cysts, and multiloculated hydrocephalus, although the avoidance of multiple shunts is desirable. We reviewed our experience with the use of endoscopic techniques to simplify complex multicompartmental hydrocephalus to determine its efficacy and safety. We performed a retrospective study of 114 consecutive adults and children undergoing endoscopic management of hydrocephalus by a single surgeon. The type of hydrocephalus and endoscopic procedure performed were recorded. The management algorithm for simplification of complex hydrocephalus is reviewed. All patients were followed up in the office or by telephone. A total of 143 endoscopic procedures were performed on 114 patients with a mean age of 4.4 years (4 weeks to 32 years). The endoscopic procedures performed included cyst fenestration, septum pellucidotomy, endoscopic third ventriculostomy, aqueductal plasty with and without stent, and removal of cystercicotic cysts. Twenty-two (19.3%) patients had planned staged endoscopic procedures. Mean follow up was 65 months (range 33-122 months). Eighty-two (72%) patients were reduced to 1 shunt, shunt independence was achieved in 32 (28%) patients, and only 8 (11%) patients required shunt revision in the follow-up period. Endoscopic simplification of complex hydrocephalus enables dependence on only a single shunt in the majority of patients, and a significant proportion achieve shunt independence. Endoscopic management should be considered before the placement of a second shunt, and some cases require staged endoscopic procedures to adequately communicate multicompartmental hydrocephalus.


The effects of therapeutic x-ray doses on mechanical, chemical and physical properties of poly methyl methacrylate.
The aim of this study was to investigate the effect of radiation doses very close to the human dose for oral cancers on mechanical, chemical and physical properties for poly methyl-methacrylate (PMMA). PMMA samples were divided into four different groups: no irradiated group, 25-Gy irradiated group, 50-Gy irradiated group and 75-Gy irradiated group. Each group contained nine samples. After 24 h, a three-point loading test was applied to each PMMA groups. The transverse strength and the elastic modulus were calculated using the test results. The results were analyzed statistically by using one-way analysis of variance. The structural characterizations of the PMMA samples were carried out by a Fourier Transform Infrared (FTIR) spectrophotometer to evaluate the chemical structure differences. The transverse strength values of 25-Gy, 50-Gy and 75-Gy radiation groups were significantly higher than that of the no radiation group (p < 0.05). There was no significant difference among the elastic modulus values of the study groups (p > 0.05). The FTIR findings demonstrated that the irradiation process did not change the chemical structure of the PMMA polymeric materials. The therapeutic radiation doses increase the mechanical properties of the PMMA; however, the chemical and structural properties have no effect. When the findings of this study are taken into account, it can be said that patients can wear dentures during the radiotherapy.


Nutrition and diet in the clinical management of multiple sclerosis.
For many years, medical interest in the relationship between nutrition and multiple sclerosis (MS) has focused largely on aetiology and the influence of dietary fat on the rate and severity of disease. While the cause of MS remains unknown and the influence of dietary fat is unclear, recent studies on antioxidant intake and oxidative stress in MS are strengthening the rationale in support of a healthy eating regime following diagnosis. Dietary intake in MS and the influence of advanced disease on nutritional status are less well researched and documented. Both obesity and malnutrition may occur with detrimental consequences to functional abilities. Cognitive difficulties, dysphagia and the side-effects of drug treatment may further contribute to deterioration in nutritional status. This paper aims to provide a practical overview of dietary management in MS. It reviews the available evidence relating nutrition to MS and discusses dietary management, with particular emphasis on the identification and alleviation of factors affecting nutritional status.


A multi-institutional study of brainstem gliomas in children with neurofibromatosis type 1.
To define the clinical and radiologic features of brainstem gliomas (BSGs) in children with neurofibromatosis type 1 (NF1). We performed a retrospective cross-sectional study of 133 children with NF1 and concurrent BSGs cared for at 4 NF1 referral centers. BSG was determined using radiographic criteria. Age at diagnosis, tumor location and appearance, clinical symptoms, treatment, and presence of a concurrent optic pathway glioma were assessed. The average age at BSG diagnosis was 7.2 years, and tumors occurred most often in the midbrain and medulla (66%). The majority of children with NF1-BSGs were asymptomatic (54%) and were not treated (88%). Only 9 of the 72 asymptomatic children received treatment because of progressive tumor enlargement. In contrast, 61 children presented with clinical signs/symptoms attributable to their BSG; these individuals were older and more often had focal lesions. Thirty-one patients underwent treatment for their tumor, and 14 received CSF diversion only. Progression-free survival was ∼3 years shorter for children receiving tumor-directed therapy relative to those who had either no treatment or CSF diversion only. Overall survival was 85% for the tumor-directed therapy group, whereas no deaths were reported in the untreated or CSF diversion groups. Unlike children with sporadically occurring BSGs, most children with NF1-BSGs were asymptomatic, and few individuals died from complications of their tumor. Those requiring tumor-directed treatment tended to be older children with focal lesions, and had clinically more aggressive disease relative to those who were not treated or underwent CSF diversion only.


An efficient moments-based inference method for within-host bacterial infection dynamics.
Over the last ten years, isogenic tagging (IT) has revolutionised the study of bacterial infection dynamics in laboratory animal models. However, quantitative analysis of IT data has been hindered by the piecemeal development of relevant statistical models. The most promising approach relies on stochastic Markovian models of bacterial population dynamics within and among organs. Here we present an efficient numerical method to fit such stochastic dynamic models to in vivo experimental IT data. A common approach to statistical inference with stochastic dynamic models relies on producing large numbers of simulations, but this remains a slow and inefficient method for all but simple problems, especially when tracking bacteria in multiple locations simultaneously. Instead, we derive and solve the systems of ordinary differential equations for the two lower-order moments of the stochastic variables (mean, variance and covariance). For any given model structure, and assuming linear dynamic rates, we demonstrate how the model parameters can be efficiently and accurately estimated by divergence minimisation. We then apply our method to an experimental dataset and compare the estimates and goodness-of-fit to those obtained by maximum likelihood estimation. While both sets of parameter estimates had overlapping confidence regions, the new method produced lower values for the division and death rates of bacteria: these improved the goodness-of-fit at the second time point at the expense of that of the first time point. This flexible framework can easily be applied to a range of experimental systems. Its computational efficiency paves the way for model comparison and optimal experimental design.


Depth perception--a major issue in medical AR: evaluation study by twenty surgeons.
The idea of in-situ visualization for surgical procedures has been widely discussed in the community. While the tracking technology offers nowadays a sufficient accuracy and visualization devices have been developed that fit seamlessly into the operational workflow [1, 3], one crucial problem remains, which has been discussed already in the first paper on medical augmented reality. Even though the data is presented at the correct place, the physician often perceives the spatial position of the visualization to be closer or further because of virtual/real overlay. This paper describes and evaluates novel visualization techniques that are designed to overcome misleading depth perception of trivially superimposed virtual images on the real view. We have invited 20 surgeons to evaluate seven different visualization techniques using a head mounted display (HMD). The evaluation has been divided into two parts. In the first part, the depth perception of each kind of visualization is evaluated quantitatively. In the second part, the visualizations are evaluated qualitatively in regard to user friendliness and intuitiveness. This evaluation with a relevant number of surgeons using a state-of-the-art system is meant to guide future research and development on medical augmented reality.


A "win-win" nanoplatform: TiO2:Yb,Ho,F for NIR light-induced synergistic therapy and imaging.
To avoid the defect of low energy transfer efficiency in core-shell UCNP-TiO2 NPs, doping rare earth into TiO2 and improving the photocatalytic activity of TiO2 itself under Vis-NIR light might be a more direct and efficient strategy for high 1O2 production. Here, we designed a TiO2:Yb,Ho,F-β-CD@DTX/HA nanoplatform using TiO2:Yb,Ho,F as the core, β-CD as the drug carrier, hyaluronic acid (HA) as the capping agent and target, and then applied it for 808 nm induced photodynamic-chemotherapy and 980 nm upconversion fluorescence/MR imaging. The results were as follows: (i) for TiO2 as a photosensitizer, after doping Yb, Ho, F into TiO2, it could directly generate reactive oxygen species under an 808 nm laser; the dopants enhanced the absorption under the UV-Vis-NIR region and increased the electron-hole pair separation. (ii) For TiO2 as the upconversion host, F and Ho also endowed TiO2:Yb,Ho,F with enhanced upconversion fluorescence under a 980 nm laser and T2-MRI contrast performance (r2 = 30.71 mM-1 s-1), respectively, thus, facilitating imaging for deep tissues. (iii) The HA shell outside of β-CD prevented the unexpected leaking of DTX, which improved the target abilities and achieved the enzyme-responsive drug release. The in vitro and in vivo studies also demonstrated the nanosystem could efficiently suppress tumor growth by combination therapy and had excellent imaging (UCL/MR) ability. Particularly, our work was the first example that utilized TiO2 simultaneously as a photosensitizer and upconversion host, which simplified the core-shell UCNP-TiO2 nanocomposites and reached a "win-win" cooperation in NIR-induced photodynamic therapy and UCL imaging.


Effect of body mass index on outcome after aneurysmal subarachnoid hemorrhage treated with clipping versus coiling.
OBJECTIVE It has been suggested that increased body mass index (BMI) may confer a protective effect on patients who suffer from aneurysmal subarachnoid hemorrhage (aSAH). Whether the modality of aneurysm occlusion influences the effect of BMI on patient outcomes is not well understood. The authors aimed to compare the effect of BMI on outcomes for patients with aSAH treated with surgical clipping versus endovascular coiling. METHODS The authors retrospectively reviewed the outcomes for patients admitted to their institution for the management of aSAH treated with either clipping or coiling. BMI at the time of admission was recorded and used to assign patients to a group according to low or high BMI. Cutoff values for BMI were determined by classification and regression tree analysis. Predictors of poor functional outcome (defined as modified Rankin Scale score > 2 measured ≥ 90 days after the ictus) and posttreatment cerebral hypodensities detected during admission were then determined separately for patients treated with clipping or coiling using stepwise multivariate logistic regression analysis. RESULTS Of the 469 patients admitted to the authors' institution with aSAH who met the study's inclusion criteria, 144 were treated with clipping and 325 were treated with coiling. In the clipping group, the frequency of poor functional outcome was higher in patients with BMI ≥ 32.3 kg/m2 (47.6% vs 19.0%; p = 0.007). In contrast, in the coiling group, patients with BMI ≥ 32.3 kg/m2 had a lower frequency of poor functional outcome at ≥ 90 days (5.8% vs 30.9%; p < 0.001). On multivariate analysis, high BMI was independently associated with an increased (OR 3.92, 95% CI 1.20-13.41; p = 0.024) and decreased (OR 0.13, 95% CI 0.03-0.40; p < 0.001) likelihood of poor functional outcome for patients treated with clipping and coiling, respectively. For patients in the surgical group, BMI ≥ 28.4 kg/m2 was independently associated with incidence of cerebral hypodensities during admission (OR 2.44, 95% CI 1.16-5.25; p = 0.018) on multivariate analysis. For patients treated with coiling, BMI ≥ 33.2 kg/m2 was independently associated with reduced odds of hypodensities (OR 0.45, 95% CI 0.21-0.89; p = 0.021). CONCLUSIONS The results of this study suggest that BMI may differentially affect functional outcomes after aSAH, depending on treatment modality. These findings may aid in treatment selection for patients with aSAH.


Automatic airway-artery analysis on lung CT to quantify airway wall thickening and bronchiectasis.
Bronchiectasis and airway wall thickening are commonly assessed in computed tomography (CT) by comparing the airway size with the size of the accompanying artery. Thus, in order to automate the quantification of bronchiectasis and wall thickening following a similar principle, there is a need for methods that automatically segment the airway and vascular trees, measure their size, and pair each airway branch with its accompanying artery. This paper combines and extends existing techniques to present a fully automated pipeline that, given a thoracic chest CT, segments, measures, and pairs airway branches with the accompanying artery, then quantifies airway wall thickening and bronchiectasis by measuring the wall-artery ratio (WAR) and lumen and outer wall airway-artery ratio (AAR). Measurements that do not use the artery size for normalization are also extracted, including wall area percentage (WAP), wall thickness ratio (WTR), and airway diameters. The method was thoroughly evaluated using 8000 manual annotations of airway-artery pairs from 24 full-inspiration pediatric CT scans (12 diseased and 12 controls). Limits of agreement between the automatically and manually measured diameters were comparable to interobserver limits of agreement. Differences in automatically obtained WAR, AAR, WAP, and WTR between bronchiectatic subjects and controls were similar as when manual annotations were used: WAR and outer AAR were significantly higher in the bronchiectatic subjects (p < 0.05), but lumen AAR, WAP, and WTR were not. Only measurements that use artery size for normalization led to significant differences between groups, highlighting the importance of airway-artery pairing. The fully automatic method presented in this paper could replace time-consuming manual annotations and visual scoring methods to quantify abnormal widening and thickening of airways.


The role of EZH2 in the regulation of the activity of matrix metalloproteinases in prostate cancer cells.
Degradation of the extracellular matrix (ECM), a critical step in cancer metastasis, is determined by the balance between MMPs (matrix metalloproteinases) and their inhibitors TIMPs (tissue inhibitors of metalloproteinases). In cancer cells, this balance is shifted towards MMPs, promoting ECM degradation. Here, we show that EZH2 plays an active role in this process by repressing the expression of TIMP2 and TIMP3 in prostate cancer cells. The TIMP genes are derepressed by knockdown of EZH2 expression in human prostate cancer cells but repressed by overexpression of EZH2 in benign human prostate epithelial cells. EZH2 catalyzes H3K27 trimethylation and subsequent DNA methylation of the TIMP gene promoters. Overexpression of EZH2 confers an invasive phenotype on benign prostate epithelial cells; however, this phenotype is suppressed by cooverexpression of TIMP3. EZH2 knockdown markedly reduces the proteolytic activity of MMP-9, thereby decreasing the invasive activity of prostate cancer cells. These results suggest that the transcriptional repression of the TIMP genes by EZH2 may be a major mechanism to shift the MMPs/TIMPs balance in favor of MMP activity and thus to promote ECM degradation and subsequent invasion of prostate cancer cells.


Transmission blocking immunity in Plasmodium vivax malaria: antibodies raised against a peptide block parasite development in the mosquito vector.
One approach towards the development of a vaccine against malaria is to immunize against the parasite sexual stages that mediate transmission of the parasite from man to mosquito. Antibodies against these stages, ingested with the blood meal, inhibit the parasite development in the mosquito vector, constituting "transmission blocking immunity." Most epitopes involved in transmission-blocking immunity depend on the tertiary conformational structure of surface antigens. However, one of the transmission-blocking monoclonal antibodies we have raised against Plasmodium vivax reacts with a linear epitope on both asexual stages and gametes. This monoclonal antibody (A12) is capable of totally blocking development of the parasite in the mosquito host when tested in membrane feeding assays with gametocytes from P. vivax-infected patients. Immune screening of a P. vivax lambda gt11 genomic expression library with A12 led to the isolation of a clone to which was mapped the six-amino acid epitope recognized by A12. Antisera raised in mice against a 12-mer synthetic peptide containing this epitope coupled to bovine serum albumin not only had high titers of antipeptide antibodies as measured by enzyme-linked immunosorbent assay, but in addition recognized the same 24- and 57-kD parasite components as A12 on Western blots and reacted with the parasite by immunofluorescence. When tested in membrane feeding assays, these antibodies have significant suppressive effects on parasite development in the mosquito.


An examination of the diversity of a novel Campylobacter reservoir.
The diversity of eukaryotic populations, in particular protozoa, in the water supplies of intensively reared broilers has not been previously studied. This important food-rearing environment was screened for the molecular diversity of eukaryotes by the analysis of PCR-amplified 18S rRNA. DNA was extracted from filtered water samples that were collected from the poultry drinking water systems of five farms. The total genomic DNA was used to produce rRNA-PCR amplicons, which, with the application of TTGE, provided an overview of the eukaryotic population diversity. The rRNA-PCR amplicons were then used to generate 34 random clones that were subject to comparative sequence analysis. Twenty-five of the clones (73.5%) showed high similarity with yeasts and fungi (>92%) and 9 clones demonstrated similarity (>86%) with certain protozoan groups, including flagellates and alveolates. Further studies of the microbial diversity in the previously ignored niche of intensively reared poultry drinking water systems are required, along with subsequent in vitro co-culture assays of the detected protozoa and bacterial strains.


CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.
Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats. In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(n) in space and O(nm/l) in time.


Mx1-based resistance to thogoto virus in A2G mice is bypassed in tick-mediated virus delivery.
The interferon-induced mouse Mx1 protein has intrinsic antiviral activity against orthomyxoviruses, including Thogoto virus. Thus, Mx1(+) A2G mice are apparently resistant to infection following needle- or tick-borne virus challenge. However, tick-borne challenge and, to a lesser degree, injection of virus mixed with tick salivary gland extract resulted in virus transmission to uninfected ticks feeding on the A2G mice. The data indicate that immunomodulatory components in tick saliva can overcome a natural antiviral mechanism.


Tumor necrosis factor-alpha-mutant mice exhibit high frequency hearing loss.
Exogenous tumor necrosis factor-alpha (TNF-α) plays a role in auditory hair cell death by altering the expression of apoptosis-related genes in response to noxious stimuli. Little is known, however, about the function of TNF-α in normal hair cell physiology. We, therefore, investigated the cochlear morphology and auditory function of TNF-α-deficient mice. Auditory evoked brainstem response showed significantly higher thresholds, especially at higher frequencies, in 1-month-old TNF-α(-/-) mice as compared to TNF-α(+/-) and wild type (WT); hearing loss did not progress further from 1 to 4 months of age. There was no difference in the gross morphology of the organ of Corti, lateral wall, and spiral ganglion cells in TNF-α(-/-) mice compared to WT mice at 4 months of age, nor were there differences in the anatomy of the auditory ossicles. Outer hair cells were completely intact in surface preparations of the organ of Corti of TNF-α(-/-) mice, and synaptic ribbon counts of TNF-α(-/-) and WT mice at 4 months of age were similar. Reduced amplitudes of distortion product otoacoustic emissions, however, indicated dysfunction of outer hair cells in TNF-α(-/-) mice. Scanning electron microscopy revealed that stereocilia were sporadically absent in the basal turn and distorted in the middle turn. In summary, our results demonstrate that TNF-α-mutant mice exhibit early hearing loss, especially at higher frequencies, and that loss or malformation of the stereocilia of outer hair cells appears to be a contributing factor.


Sperm motility inhibitor from human seminal plasma: association with semen coagulum.
Human seminal plasma contains a sperm motility inhibitor (SPMI) originating from the seminal vesicles as a 52 kDa precursor form that is rapidly degraded by prostatic proteases after ejaculation. In this study, the distribution of SPMI biological activity and antigens was analysed in chemically induced, as well as naturally occurring, arrest of semen liquefaction. SPMI activity was detected exclusively in the coagulated semen fraction at 2200 +/- 560 IU, whereas total seminal plasma proteins separated more evenly between soluble and coagulated components (91 +/- 19 and 65 +/- 18 mg, respectively). An SPMI antiserum recognized different forms of SPMI precursors at 52, 38, 35, 33 and 20 kDa in the coagulum while the soluble protein fraction contained only one major immunoreactive band at 15 kDa. High levels of SPMI activity (1500 +/- 180 IU/ml) together with high molecular mass forms of SPMI precursor and low sperm motility (26%) were detected in semen samples that failed to liquefy spontaneously at room temperature. Addition of prostatic secretions to the non-liquefying samples caused a decrease of SPMI activity (330 +/- 17 IU/ml) and transformed the SPMI precursor into low molecular mass forms (14-22 kDa) with a concomitant increase in sperm motility to 49%. The results suggest that SPMI is highly associated with the seminal coagulum components as very active forms that may adversely affect sperm motility when not properly processed after ejaculation.


Pharmacological potentiation of the efferent vagus nerve attenuates blood pressure and renal injury in a murine model of systemic lupus erythematosus.
Recent evidence suggests hypertension may be secondary to chronic inflammation that results from hypoactive neuro-immune regulatory mechanisms. To further understand this association, we used systemic lupus erythematosus (SLE) as a model of inflammation-induced hypertension. In addition to prevalent inflammatory kidney disease and hypertension, SLE patients suffer from dysautonomia in the form of decreased efferent vagal tone. Based on this, the cholinergic anti-inflammatory pathway, an endogenous vagus-to-spleen mechanism that, when activated results in decreases in systemic inflammation, may be compromised in SLE. We hypothesized that stimulation of the cholinergic anti-inflammatory pathway via pharmacological potentiation of the efferent vagus nerve would reduce inflammation and halt the development of hypertension and renal injury in SLE. Female NZBWF1 mice, an established model of murine SLE, and female control mice were treated with galantamine (4 mg/kg daily ip), an acetylcholinesterase inhibitor, or saline for 14 days. At the end of therapy, carotid catheters were surgically implanted and were used to measure mean arterial pressure before the animals were euthanized. Chronic galantamine administration attenuated both splenic and renal cortical inflammation, which likely explains why the hypertension and renal injury (i.e., glomerulosclerosis and fibrosis) typically observed in murine SLE was attenuated following therapy. Based on this, the anti-inflammatory, antihypertensive, and renoprotective effects of galantamine may be mediated through activation of the cholinergic anti-inflammatory pathway. It is possible that dysfunction of the cholinergic anti-inflammatory pathway exists in SLE at the level of the efferent vagus nerve and promoting restoration of its activity through central cholinergic receptor activation may be beneficial.


Concepts in sumoylation: a decade on.
A decade has passed since SUMO (small ubiquitin-related modifier) was discovered to be a reversible post-translational protein modifier. During this time many enzymes that participate in regulated SUMO-conjugation and -deconjugation pathways have been identified and characterized. In parallel, the search for SUMO substrates has produced a long list of targets, which appear to be involved in most cellular functions. Sumoylation is a highly dynamic process and its outcomes are extremely diverse, ranging from changes in localization to altered activity and, in some cases, stability of the modified protein. At first glance, these effects have nothing in common; however, it seems that they all result from changes in the molecular interactions of the sumoylated proteins.


Attenuated recombinant vaccinia virus expressing oncofetal antigen (tumor-associated antigen) 5T4 induces active therapy of established tumors.
The human oncofetal antigen 5T4 (h5T4) is a transmembrane glycoprotein overexpressed by a wide spectrum of cancers, including colorectal, ovarian, and gastric, but with a limited normal tissue expression. Such properties make 5T4 an excellent putative target for cancer immunotherapy. The murine homologue of 5T4 (m5T4) has been cloned and characterized, which allows for the evaluation of immune intervention strategies in "self-antigen" in vivo tumor models. We have constructed recombinant vaccinia viruses based on the highly attenuated and modified vaccinia virus ankara (MVA strain), expressing h5T4 (MVA-h5T4), m5T4 (MVA-m5T4), and Escherichia coli LacZ (MVA-LacZ). Immunization of BALB/c and C57BL/6 mice with MVA-h5T4 and MVA-m5T4 constructs induced antibody responses to human and mouse 5T4, respectively. C57BL/6 and BALB/c mice vaccinated with MVA-h5T4 were challenged with syngeneic tumor line transfectants, B16 melanoma, and CT26 colorectal cells that express h5T4. MVA-h5T4-vaccinated mice showed significant tumor retardation compared with mice vaccinated with MVA-LacZ or PBS. In active treatment studies, inoculation with MVA-h5T4 was able to treat established CT26-h5T4 lung tumor and to a lesser extent B16.h5T4 s.c. tumors. Additionally, when C57BL/6 mice vaccinated with MVA-m5T4 were challenged with B16 cells expressing m5T4, resulting growth of the tumors was significantly retarded compared with control animals. Furthermore, mice vaccinated with MVA-m5T4 showed no signs of autoimmune toxicity. These data support the use of MVA-5T4 for tumor immunotherapy.


Differential performance and parasitism of caterpillars on maize inbred lines with distinctly different herbivore-induced volatile emissions.
Plant volatiles induced by insect feeding are known to attract natural enemies of the herbivores. Six maize inbred lines that showed distinctly different patterns of volatile emission in laboratory assays were planted in randomized plots in the Central Mexican Highlands to test their ability to recruit parasitic wasps under field conditions. The plants were artificially infested with neonate larvae of the fall armyworm Spodoptera frugiperda, and two of its main endoparasitoids, Campoletis sonorensis and Cotesia marginiventris, were released in the plots. Volatiles were collected from equally treated reference plants in the neighbourhood of the experimental field. The cumulative amount of 36 quantified volatile compounds determined for each line was in good accordance with findings from the laboratory; there was an almost 15-fold difference in total emission between the two extreme lines. We found significant differences among the lines with respect to the numbers of armyworms recovered from the plants, their average weight gain and parasitism rates. Average weight of the caterpillars was negatively correlated with the average total amount of volatiles released by the six inbred lines. However, neither total volatile emission nor any specific single compound within the blend could explain the differential parasitism rates among the lines, with the possible exception of (E)-2-hexenal for Campoletis sonorensis and methyl salicylate for Cotesia marginiventris. Herbivore-induced plant volatiles and/or correlates thereof contribute to reducing insect damage of maize plants through direct plant defence and enhanced attraction of parasitoids, alleged indirect defence. The potential to exploit these volatiles for pest control deserves to be further evaluated.


The structure and function of proline recognition domains.
One particularly abundant group of modular recognition domains consists of those that bind proline-rich motifs. Such modules, including the SH3, WW, and EVH1 domains, play a critical role in the assembly and regulation of many intracellular signaling complexes. These domains use strikingly similar molecular mechanisms of proline recognition. We discuss some of the potential biological advantages conferred by proline recognition, which may explain its widespread use in signaling.


Killing me softly--future challenges in apoptosis research.
The induction of apoptosis, a highly regulated and clearly defined mode of cell dying, is a vital tenet of modern cancer therapy. In this review we focus on three aspects of apoptosis research which we believe are the most crucial and most exciting areas currently investigated and that will need to be better understood in order to enhance the efficacy of therapeutic measures. First, we discuss which target to select for cancer therapy and argue that not the cancer cell as such, but its interaction with the microenvironment is a more promising and genetically stable site of attack. Second, the complexity of combination therapy is elucidated using the PI3-K-mediated signaling network as a specific example. Here we show that the current clinical approach to sensitize malignancies to apoptosis by maximal, prolonged inhibition of so-called survival pathways can actually be counter productive. Third, we propose that under certain conditions which will need to be clearly defined in future, chronification of a tumor might be preferable to the attempt at a cure. Finally, we discuss further problems with utilizing apoptosis induction in cancer therapy and propose a novel potential therapeutic approach that combines the previously discussed features.


Occupational exposure to inhaled pollutants and risk of airflow obstruction: a large UK population-based UK Biobank cohort.
Although around 10% to 15% of COPD burden can be attributed to workplace exposures, little is known about the role of different airborne occupational pollutants (AOP). The main aim of the study was to assess the effect size of the relationship between various AOP, their level and duration of exposure with airflow obstruction (AFO). A cross-sectional analysis was conducted in 228 614 participants from the UK Biobank study who were assigned occupational exposure using a job exposure matrix blinded to health outcome. Adjusted prevalence ratios (PRs) and 95% CI for the risk of AFO for ever and years of exposure to AOPs were estimated using robust Poisson model. Sensitivity analyses were conducted for never-smokers, non-asthmatic and bi-pollutant model. Of 228 614 participants, 77 027 (33.7%) were exposed to at least one AOP form. 35.5% of the AFO cases were exposed to vapours, gases, dusts or fumes (VGDF) and 28.3% to dusts. High exposure to vapours increased the risk of occupational AFO by 26%. Exposure to dusts (adjusted PR=1.05; 95% CI 1.01 to 1.08), biological dusts (1.05; 1.01 to 1.10) and VGDF (1.04; 1.01 to 1.07) showed a significantly increased risk of AFO, however, statistically not significant following multiple testing. There was no significant increase in risk of AFO by duration (years) of exposure in current job. The results were null when restricted to never-smokers and when a bi-pollutant model was used. However, when data was analysed based on the level of exposure (low, medium and high) compared with no exposure, directionally there was increase in risk for those with high exposure to vapours, gases, fumes, mists and VGDF but statistically significant only for vapours. High exposure (in current job) to airborne occupational pollutants was suggestive of higher risk of AFO. Future studies should investigate the relationship between lifetime occupational exposures and COPD.


Management of Functional Somatic Syndromes and Bodily Distress.
Functional somatic syndromes (FSS), like irritable bowel syndrome or fibromyalgia and other symptoms reflecting bodily distress, are common in practically all areas of medicine worldwide. Diagnostic and therapeutic approaches to these symptoms and syndromes vary substantially across and within medical specialties from biomedicine to psychiatry. Patients may become frustrated with the lack of effective treatment, doctors may experience these disorders as difficult to treat, and this type of health problem forms an important component of the global burden of disease. This review intends to develop a unifying perspective on the understanding and management of FSS and bodily distress. Firstly, we present the clinical problem and review current concepts for classification. Secondly, we propose an integrated etiological model which encompasses a wide range of biopsychosocial vulnerability and triggering factors and considers consecutive aggravating and maintaining factors. Thirdly, we systematically scrutinize the current evidence base in terms of an umbrella review of systematic reviews from 2007 to 2017 and give recommendations for treatment for all levels of care, concentrating on developments over the last 10 years. We conclude that activating, patient-involving, and centrally acting therapies appear to be more effective than passive ones that primarily act on peripheral physiology, and we recommend stepped care approaches that translate a truly biopsychosocial approach into actual management of the patient.


Elastomer-glass micropump employing active throttles.
We report a reciprocating microfluidic pump, the Micro Throttle Pump (MTP), constructed in a relatively uncomplicated manner from glass and microstructured poly(dimethylsiloxane)(PDMS). Unconventionally, the MTP employs throttling of fluid flow as distinct from fully-closing valve structures. Accordingly, this technique offers the prospect of solid-phase suspension tolerance. The reported MTP employs piezoelectrically (PZT) actuated deformation of flow constrictions (throttles) fabricated from PDMS at the two ports of a central, PZT actuated pump chamber. By appropriate time-sequencing of the individual PZTs' actuation, pumping can be induced in either direction. PDMS' elasticity further facilitates throttle operation by virtue of allowing significant PZT flexure that is substantially independent of the underlying PDMS microstructure. In contrast, in a rigid substrate such as silicon, deformation is constrained to where underlying microstructured cavities exist and this restricts design options. We describe the construction and performance of a prototype MTP capable of pumping 300 microl min(-1) or alternatively generating a back-pressure of 5.5 kPa. Preliminary modelling of MTP operation is also presented.


Evaluation of a sleep education program for low-income preschool children and their families.
To evaluate a novel sleep education program for low-income preschool children and their families. Randomized trial of an educational intervention. Community-based. Head Start preschool families (n = 152) in greater Lansing and Detroit, Michigan. Classrooms or Head Start sites were randomized to an intervention group (prompt intervention) versus a control group (delayed intervention). Parents attended a one-time, 45-min sleep education program and preschoolers received 2 w (320 total min) of classroom sleep curriculum. Parent knowledge, attitudes, self-efficacy, and beliefs were assessed as the primary outcomes just before the 45-min sleep intervention, immediately postintervention, and approximately 1 mo postintervention. Parents reported their child's bedtimes and wake times on 7-day sleep diaries at baseline and at 1-mo follow-up. Average weeknight sleep durations and bedtimes served as secondary outcomes. Linear mixed models showed a time × treatment effect for parents' knowledge, attitudes, and self-efficacy (each P < 0.05) but not beliefs. These improvements were found immediately postintervention but were not retained at 1-mo follow-up. Children in the intervention group improved their weeknight sleep duration at 1-mo follow-up by 30 min (11.0 ± 0.9 h vs. 10.5 ± 1.0 hours at baseline) compared to controls (10.4 ± 0.9 h versus 10.5 ± 0.9 h at baseline) (P = 0.04 for difference between groups). Children did not show statistically significant improvements in bedtime. Educational interventions in early childhood can have an effect on parents' sleep knowledge, attitudes, and self-efficacy, and on children's sleep behavior. However, repeated exposure to the new information may be important for parents as well as their children.


Uncertainty of blank correction in isotope ratio measurement.
Blank correction for isotope ratio measurement on small amounts of substances is often limited by presence of a blank, with an apparent isotopic composition different from that of the sample. For isotope ratios, blank correction is commonly performed either by the regression method, which works without the need for estimation of the blank, or by the subtraction method. With the subtraction method, estimation of the amount and isotope delta of the blank is required, and these estimates could be obtained either by direct, semi-indirect, or indirect measurement. Previously given expressions for the standard uncertainties of indirectly measured blank amounts and blank isotope deltas did not account for covariance between input quantities. In the present work, a previously published data set was re-evaluated, with covariance terms properly included in the calculation of uncertainties. It was shown that covariance effects may yield a significant reduction in uncertainty estimates, both for blank quantities and for blank corrected results. For series measurements on a standard material, it was also shown that the distribution of individual corrected isotope delta values around the average value was approximately normal, with its standard deviation equal to the estimated standard uncertainty of the corrected values. In most cases, it was observed that the regression and subtraction methods yield approximately the same blank corrected average values and uncertainties, regardless of method selected for estimation of blank quantities.


The cumulative effect of unemployment on risks for acute myocardial infarction.
Employment instability is a major source of strain affecting an increasing number of adults in the United States. Little is known about the cumulative effect of multiple job losses and unemployment on the risks for acute myocardial infarction (AMI). We investigated the associations between different dimensions of unemployment and the risks for AMI in US adults in a prospective cohort study of adults (N = 13,451) aged 51 to 75 years in the Health and Retirement Study with biennial follow-up interviews from 1992 to 2010. Unadjusted rates of age-specific AMI were used to demonstrate observed differences by employment status, cumulative number of job losses, and cumulative time unemployed. Cox proportional hazards models were used to examine the multivariate effects of cumulative work histories on AMI while adjusting for sociodemographic background and confounding risk factors. The median age of the study cohort was 62 years, and 1061 AMI events (7.9%) occurred during the 165,169 person-years of observation. Among the sample, 14.0% of subjects were unemployed at baseline, 69.7% had 1 or more cumulative job losses, and 35.1% had spent time unemployed. Unadjusted plots showed that age-specific rates of AMI differed significantly for each dimension of work history. Multivariate models showed that AMI risks were significantly higher among the unemployed (hazard ratio, 1.35 [95% CI, 1.10-1.66]) and that risks increased incrementally from 1 job loss (1.22 [1.04-1.42]) to 4 or more cumulative job losses (1.63 [1.29-2.07]) compared with no job loss. Risks for AMI were particularly elevated within the first year of unemployment (hazard ratio, 1.27 [95% CI, 1.01-1.60]) but not thereafter. Results were robust after adjustments for multiple clinical, socioeconomic, and behavioral risk factors. Unemployment status, multiple job losses, and short periods without work are all significant risk factors for acute cardiovascular events.


Yeast-enhanced green fluorescent protein (yEGFP): a reporter of gene expression in Candida albicans.
The green fluorescent protein (GFP) of Aequorea victoria has been developed here as a reporter for gene expression and protein localization in Candida albicans. When wild-type (wt) GFP was expressed in C. albicans, it was not possible to detect fluorescence or a translation product for the wt protein. Since this was probably due in part to the presence of the non-canonical CTG serine codon in the Aequorea sequence, this codon was changed to the leucine codon TTG. C. albicans cells expressing this construct contained GFP mRNA but were non-fluorescent and contained no detectable translation product. Hence a codon-optimized GFP gene was constructed in which all of the 239 amino acids are encoded by optimal codons for C. albicans. In this gene were also incorporated two previously identified mutations in the chromophore that increase GFP fluorescence. C. albicans cells expressing this yeast-enhanced GFP gene (yEGFP3) are fluorescent and contain GFP protein. yEGFP3 can be used as a versatile reporter of gene expression in C. albicans and Saccharomyces cerevisiae and the optimized GFP described here should have broad applications in these and other fungal species.


Osteoclast stimulatory transmembrane protein (OC-STAMP), a novel protein induced by RANKL that promotes osteoclast differentiation.
Microarray and real-time RT-PCR were used to examine expression changes in primary bone marrow cells and RAW 264.7 cells in response to RANKL. In silico sequence analysis was performed on a novel gene which we designate OC-STAMP. Specific siRNA and antibodies were used to inhibit OC-STAMP RNA and protein, respectively, and tartrate-resistant acid phosphatase (TRAP)+ multinucleated osteoclasts were counted. Antibodies were used to probe bone tissues and western blots of RAW cell extracts +/- RANKL. cDNA overexpression constructs were transfected into RAW cells and the effect on RANKL-induced differentiation was studied. OC-STAMP was very strongly up-regulated during osteoclast differentiation. Northern blots and sequence analysis revealed two transcripts of 2 and 3.7 kb differing only in 3'UTR length, consistent with predictions from genome sequence. The mRNA encodes a 498 amino acid, multipass transmembrane protein that is highly conserved in mammals. It has little overall homology to other proteins. The carboxy-terminal 193 amino acids, however, are significantly similar to the DC-STAMP family consensus sequence. DC-STAMP is a transmembrane protein required for osteoclast precursor fusion. Knockdown of OC-STAMP mRNA by siRNA and protein inhibition by antibodies significantly suppressed the formation of TRAP+, multinucleated cells in differentiating osteoclast cultures, with many TRAP+ mononuclear cells present. Conversely, overexpression of OC-STAMP increased osteoclastic differentiation of RAW 264.7 cells. We conclude that OC-STAMP is a previously unknown, RANKL-induced, multipass transmembrane protein that promotes the formation of multinucleated osteoclasts.


Amyloid β synaptotoxicity is Wnt-PCP dependent and blocked by fasudil.
Synapse loss is the structural correlate of the cognitive decline indicative of dementia. In the brains of Alzheimer's disease sufferers, amyloid β (Aβ) peptides aggregate to form senile plaques but as soluble peptides are toxic to synapses. We previously demonstrated that Aβ induces Dickkopf-1 (Dkk1), which in turn activates the Wnt-planar cell polarity (Wnt-PCP) pathway to drive tau pathology and neuronal death. We compared the effects of Aβ and of Dkk1 on synapse morphology and memory impairment while inhibiting or silencing key elements of the Wnt-PCP pathway. We demonstrate that Aβ synaptotoxicity is also Dkk1 and Wnt-PCP dependent, mediated by the arm of Wnt-PCP regulating actin cytoskeletal dynamics via Daam1, RhoA and ROCK, and can be blocked by the drug fasudil. Our data add to the importance of aberrant Wnt signaling in Alzheimer's disease neuropathology and indicate that fasudil could be repurposed as a treatment for the disease.


Communication of Career Pathways Through Associate Degree Program Web Sites: A Baseline Assessment.
The American Association for Respiratory Care sponsored a series of conferences that addressed the competency of the future workforce of respiratory therapists (RTs). Based upon the findings from those conferences, several initiatives emerged that support RTs earning a baccalaureate (or bachelor's) degree. The objective of this study was to identify the ways that associate degree programs communicate career pathways toward a baccalaureate degree through their Web sites. This cross-sectional observational study used a random sample of 100 of the 362 associate degree programs approved by the Commission on Accreditation for Respiratory Care. Data were collected from 3 specific categories: demographic data, baccalaureate completion information, and the Web page location for the program. The presence of statements related to any pathway toward a bachelor's degree, transfer credits, articulation agreements, and links for baccalaureate completion were recorded. The descriptive statistics in this study were reported as total numbers and percentages. Of the 100 programs in the random sample, only 89 were included in the study. Only 39 (44%) programs had links on their program Web site that had any content related to bachelor's degrees, 16 (18%) identified college transfer courses toward a bachelor's degree, and 26 (29%) programs included baccalaureate articulation agreements on their Web site. A minority of associate degree programs communicated career pathway information to their prospective and current students through program Web sites. An informative Web site would make the path more transparent for entry-level students to meet their future educational needs as their careers progress.


CD40 expression in prostate cancer: a potential diagnostic and therapeutic molecule.
CD40, a member of the TNF receptor superfamily, is widely expressed on human immune cells. It is also frequently expressed on epithelial malignancies, suggesting that CD40 may contribute to the pathogenesis of some cancers. Activation of CD40 in cancer cells induces growth inhibition and sensitization to apoptotic stimuli. This study investigates CD40 expression in archival tissue from patients with prostate cancer. In all cases, normal prostatic acini expressed CD40, however, in 56 of 57 cases of prostate cancer no CD40 expression was detected. In the one other case, patchy CD40 expression was associated with prostatic in situ neoplasia. In conclusion, invasive prostate cancer is a CD40-negative tumour. These data may be relevant as a diagnostic tool; in providing insight into progression of cancer from normal epithelium; and in identifying novel therapeutic strategies for prostate cancer.


Antibiotics for the neurological complications of Lyme disease.
Various central nervous system-penetrant antibiotics are bactericidal in vitro and in vivo against the causative agent of Lyme neuroborreliosis (LNB), Borrelia burgdorferi. These antibiotics are routinely used clinically to treat LNB, but their relative efficacy is not clear. To assess the effects of antibiotics for the treatment of LNB. On 25 October 2016 we searched the Cochrane Neuromuscular Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, and Embase. We searched clinical trial registers on 26 October 2016. We reviewed the bibliographies of the randomized trials identified and contacted the authors and known experts in the field to identify additional published or unpublished data. There were no language restrictions when searching for studies. Randomized clinical trials of antibiotic treatment of LNB in adults and children that compared any antibiotic treatment, including combinations of treatments, versus any other treatment, placebo, or no treatment. We excluded studies of entities considered as post-Lyme syndrome. We used standard methodological procedures expected by Cochrane. We identified seven randomized studies involving 450 European participants with LNB for inclusion in this systematic review. We found no trials conducted in the United States. Marked heterogeneity among these studies prevented meta-analysis. None of the studies included a placebo control on the initial antibiotic treatment, and only one was blinded. None were delayed-start studies. All were active comparator studies, and most were not adequately powered for non-inferiority comparison. The trials investigated four antibiotics: penicillin G and ceftriaxone in four studies, doxycycline in three studies, and cefotaxime in two studies. One study tested a three-month course of oral amoxicillin versus placebo following initial treatment with intravenous ceftriaxone. One study was limited to children. The trials measured efficacy using heterogeneous physician- or patient-reported outcomes, or both. In some cases cerebrospinal fluid analysis was included as an indirect biomarker of disease and outcome. None of the studies reported on our proposed primary outcome, 'Improvement in a measure of overall disability in the long term (three or more months).' None of the trials revealed any between-group differences in symptom resolution in response to active treatment. In general, treatment was tolerated well. The quality of adverse event reporting, however, was low. There is mostly low- to very low-quality clinical evidence from a limited number of mostly small, heterogeneous trials with diverse outcome measures, comparing the relative efficacy of central nervous system-penetrant antibiotics for the treatment of LNB. The few existing randomized studies have limited power and lack consistent and well-defined entry criteria and efficacy endpoints. It is not possible to draw firm conclusions on the relative efficacy of accepted antibiotic drug regimens for the treatment of LNB. The majority of people are reported to have good outcomes, and symptoms resolve by 12 months regardless of the antibiotic used. A minority of participants did not improve sufficiently, and some were retreated. These randomized studies provide some evidence that doxycycline, penicillin G, ceftriaxone, and cefotaxime are efficacious in the treatment of European LNB. No evidence of additional efficacy was observed when, in one study, an initial antibiotic treatment with intravenous ceftriaxone was followed by additional longer treatment with oral amoxicillin. There is a lack of evidence identified through our high-quality search strategy on the efficacy of antibiotics for treatment of LNB in the United States.


Fe-N-Doped Carbon Capsules with Outstanding Electrochemical Performance and Stability for the Oxygen Reduction Reaction in Both Acid and Alkaline Conditions.
High surface area N-doped mesoporous carbon capsules with iron traces exhibit outstanding electrocatalytic activity for the oxygen reduction reaction in both alkaline and acidic media. In alkaline conditions, they exhibit more positive onset (0.94 V vs RHE) and half-wave potentials (0.83 V vs RHE) than commercial Pt/C, while in acidic media the onset potential is comparable to that of commercial Pt/C with a peroxide yield lower than 10%. The Fe-N-doped carbon catalyst combines high catalytic activity with remarkable performance stability (3500 cycles between 0.6 and 1.0 V vs RHE), which stems from the fact that iron is coordinated to nitrogen. Additionally, the newly developed electrocatalyst is unaffected by the methanol crossover effect in both acid and basic media, contrary to commercial Pt/C. The excellent catalytic behavior of the Fe-N-doped carbon, even in the more relevant acid medium, is attributable to the combination of chemical functions (N-pyridinic, N-quaternary, and Fe-N coordination sites) and structural properties (large surface area, open mesoporous structure, and short diffusion paths), which guarantees a large number of highly active and fully accessible catalytic sites and rapid mass-transfer kinetics. Thus, this catalyst represents an important step forward toward replacing Pt catalysts with cheaper alternatives. In this regard, an alkaline anion exchange membrane fuel cell was assembled with Fe-N-doped mesoporous carbon capsules as the cathode catalyst to provide current and power densities matching those of a commercial Pt/C, which indicates the practical applicability of the Fe-N-carbon catalyst.


The Phospholipid Linoleoylglycerophosphocholine as a Biomarker of Directly Measured Insulin Resistance.
Plasma concentrations of some lysophospholipids correlate with metabolic alterations in humans, but their potential as biomarkers of insulin resistance (IR) is insufficiently known. We aimed to explore the association between plasma linoleoylglycerophosphocholine (LGPC) and objective measures of IR in adults with different metabolic profiles. We studied 62 men and women, ages 30 to 69 years, (29% normal weight, 59% overweight, 12% obese). Participants underwent a 5-point oral glucose tolerance test (5p-OGTT) from which we calculated multiple indices of IR and insulin secretion. Fifteen participants additionally underwent a hyperinsulinemic-euglycemic clamp for estimation of insulin-stimulated glucose disposal. Plasma LGPC was determined using high performance liquid chromatography/time-of-flight mass spectrometry. Plasma LGPC was compared across quartiles defined by the IR indices. Mean LGPC was 15.4±7.6 ng/mL in women and 14.1±7.3 ng/mL in men. LGPC did not correlate with body mass in-dex, percent body fat, waist circumference, blood pressure, glycosylated hemoglobin, log-triglycerides, or high density lipoprotein cholesterol. Plasma LGPC concentrations was not systematically associated with any of the studied 5p-OGTT-derived IR indices. However, LGPC exhibited a significant negative correlation with glucose disposal in the clamp (Spearman r=-0.56, P=0.029). Despite not being diabetic, participants with higher plasma LGPC exhibited significantly higher post-challenge plasma glucose excursions in the 5p-OGTT (P trend=0.021 for the increase in glucose area under the curve across quartiles of plasma LGPC). In our sample of Latino adults without known diabetes, LGPC showed potential as a biomarker of IR and impaired glucose metabolism.


ALAIN01--Alemtuzumab in autoimmune inflammatory neurodegeneration: mechanisms of action and neuroprotective potential.
Alemtuzumab (Lemtrada®) is a newly approved therapeutic agent for relapsing-remitting multiple sclerosis (RRMS). In previous phase II and III clinical trials, alemtuzumab has proven superior efficacy to subcutaneous interferon beta-1a concerning relapse rate and disability progression with unprecedented durability and long-lasting freedom of disease activity. The humanized monoclonal antibody targets CD52, leading to a rapid and long-lasting depletion, especially of B and T cells. Arising from hematopoietic precursor cells a fundamental reprogramming of the immune system restores tolerogenic networks effectively suppressing autoimmune inflammatory responses in the central nervous system (CNS). Despite its favourable effects alemtuzumab holds a severe risk of side effects with secondary autoimmunity being the most considerable. Markers for risk stratification and treatment response improving patient selection and therapy guidance are a big unmet need for MS patients and health care providers. This is a mono center, single arm, explorative phase IV study including 15 patients with highly active RRMS designed for 3 years. Patients will be studied by a high-resolution analysis comprising a repertoire of various immunological assays for the detection of immune cells and their function in peripheral blood as well as the cerebrospinal fluid (CSF). These assays encompass a number of experiments investigating immune cell subset composition, activation status, cytokine secretion, migratory capacity, potential neuroprotective properties and cytolytic activity complemented by instrument-based diagnostics like MRI scans, evoked potentials and optical coherence tomography (OCT). Our study represents the first in-depth and longitudinal functional analysis of key immunological parameters in the periphery and the CNS compartment underlying the fundamental effects of alemtuzumab in MS patients. By combining clinical, experimental and MRI data our study will provide a deeper understanding of alemtuzumab's mechanisms of action (MOA) potentially identifying immune signatures associated with treatment response or the development of secondary autoimmunity. After validation in larger cohorts this might help to improve efficacy and safety of alemtuzumab therapy in RRMS patients. NCT02419378 (clinicaltrials.gov), registered 31 March 2015.


What has been the effect on trial outcome assessments of a decade of patient participation in OMERACT?
Since 2002, 58 patients have participated as collaborating partners in 6 Outcome Measures in Rheumatology (OMERACT) conferences. Little is known about how they engage with researchers and how they have influenced conference outcomes. A responsive evaluation was carried out, including a thematic document analysis of conference proceedings and gray literature, participant observation, and 38 interviews with patients and professionals representing research, industry, and regulators. Interview transcripts were subjected to an inductive content analysis. The role of patients has evolved from a single focus group in 2002 to full integration in all parts of the conference in 2012. Longterm engagement has made a significant change in the scope and conduct of rheumatology research. It has enriched the research agenda by identifying previously neglected outcome domains such as fatigue, sleep disturbances, and flares, and it has contributed to more patient-relevant outcomes in clinical trials. Facilitating factors have been a strong commitment of the leadership, adequate selection procedure, inclusive conference design, interactive and encouraging moderation style, and self-organized support. The intensity of the program and doubts regarding the representativeness of the patient group were still seen as challenges for the future. Making patient participation an integral part of the vision and procedures of OMERACT has significantly contributed to the success of OMERACT. It has changed the perceptions and beliefs of many participants. Full use of patients' experiential knowledge before and during the conference is still challenging.


Influence of a heptad repeat stutter on the pH-dependent conformational behavior of the central coiled-coil from influenza hemagglutinin HA2.
The coiled-coil is one of the most common protein structural motifs. Amino acid sequences of regions that participate in coiled-coils contain a heptad repeat in which every third then forth residue is occupied by a hydrophobic residue. Here we examine the consequences of a "stutter," a deviation of the idealized heptad repeat that is found in the central coiled-coil of influenza hemagluttinin HA2. Characterization of a peptide containing the native stutter-containing HA2 sequence, as well as several variants in which the stutter was engineered out to restore an idealized heptad repeat pattern, revealed that the stutter is important for allowing coiled-coil formation in the WT HA2 at both neutral and low pH (7.1 and 4.5). By contrast, all variants that contained idealized heptad repeats exhibited marked pH-dependent coiled-coil formation with structures forming much more stably at low pH. A crystal structure of one variant containing an idealized heptad repeat, and comparison to the WT HA2 structure, suggest that the stutter distorts the optimal interhelical core packing arrangement, resulting in unwinding of the coiled-coil superhelix. Interactions between acidic side chains, in particular E69 and E74 (present in all peptides studied), are suggested to play a role in mediating these pH-dependent conformational effects. This conclusion is partially supported by studies on HA2 variant peptides in which these positions were altered to aspartic acid. These results provide new insight into the structural role of the heptad repeat stutter in HA2.


Antimalarial-induced Cardiomyopathy in Systemic Lupus Erythematosus: As Rare as Considered?
Antimalarials (AM) are recommended for all systemic lupus erythematosus (SLE) patients without specific contraindications. Their main adverse effect is retinal damage; however, heart disease has been described in isolated cases. The aim of our study is to describe 8 patients with AM-induced cardiomyopathy (AMIC) in a defined SLE cohort. Patients attending the Toronto Lupus Clinic and diagnosed with definite (based on endomyocardial biopsy; EMB) and possible AMIC were included [based on cardiac magnetic resonance imaging (cMRI) and other investigations]. Eight female patients (median age 62.5 yrs, disease duration 35 yrs, AM use duration 22 yrs) were diagnosed with AMIC in the past 2 years. Diagnosis was based on EMB in 3 (extensive cardiomyocyte vacuolation, intracytoplasmic myelinoid, and curvilinear bodies). In 4 patients, cMRI was highly suggestive of AMIC (ventricular hypertrophy and/or atrial enlargement and late gadolinium enhancement in a nonvascular pattern). Another patient was diagnosed with complete atrioventricular block, left ventricular and septal hypertrophy, along with concomitant ocular toxicity. All patients had abnormal cardiac troponin I (cTnI) and brain natriuretic peptide (BNP), whereas 7/8 also had chronically elevated creatine phosphokinase. During followup, 1 patient died from refractory heart failure. In the remaining patients, hypertrophy regression and a steady decrease of heart biomarkers were observed after AM cessation. Once considered extremely rare, AMIC seems to be underrecognized, probably because of the false attribution of heart failure or hypertrophy to other causes. Certain biomarkers (cTnI, BNP) and imaging findings may lead to early diagnosis and enhance survival.


The Effect of Water Loading on Acute Weight Loss Following Fluid Restriction in Combat Sports Athletes.
Novel methods of acute weight loss practiced by combat sport athletes include "water loading," the consumption of large fluid volumes for several days prior to restriction. We examined claims that this technique increases total body water losses, while also assessing the risk of hyponatremia. Male athletes were separated into control (n = 10) and water loading (n = 11) groups and fed a standardized energy-matched diet for 6 days. Days 1-3 fluid intake was 40 and 100 ml/kg for control and water loading groups, respectively, with both groups consuming 15 ml/kg on Day 4 and following the same rehydration protocol on Days 5 and 6. We tracked body mass (BM), urine sodium, urine specific gravity and volume, training-related sweat losses and blood concentrations of renal hormones, and urea and electrolytes throughout. Physical performance was assessed preintervention and postintervention. Following fluid restriction, there were substantial differences between groups in the ratio of fluid input/output (39%, p < .01, effect size = 1.2) and BM loss (0.6% BM, p = .02, effect size = 0.82). Changes in urine specific gravity, urea and electrolytes, and renal hormones occurred over time (p < .05), with an interaction of time and intervention on blood sodium, potassium, chloride, urea, creatinine, urine specific gravity, and vasopressin (p < .05). Measurements of urea and electrolyte remained within reference ranges, and no differences in physical performance were detected over time or between groups. Water loading appears to be a safe and effective method of acute BM loss under the conditions of this study. Vasopressin-regulated changes in aquaporin channels may potentially partially explain the mechanism of increased body water loss with water loading.


Association of Physical Activity and Inflammation With All-Cause, Cardiovascular-Related, and Cancer-Related Mortality.
To investigate the association between physical activity (PA) and risk of mortality in a large middle-aged cohort stratified by inflammatory status. A total of 336,560 individuals (mean age, 39.7 years; 58% male) who underwent comprehensive health screenings were enrolled in this prospective cohort study. They were grouped according to self-reported PA level using a questionnaire: no regular PA with a sedentary lifestyle, regular but insufficient PA (below the guidelines), sufficient PA (concordant with the guidelines), and health-enhancing PA. Inflammation was assessed via high-sensitivity C-reactive protein (hsCRP) level. Study end points were all-cause, cardiovascular-related, and cancer-related mortality. During the 1,976,882 person-years of follow-up (median follow-up duration, 6.17 years), 2062 deaths occurred. Compared with a sedentary lifestyle, the hazard ratios (95% CIs) on the multivariable Cox proportional hazards regression analyses for all-cause mortality by PA level were 0.95 (0.84-1.07), 0.85 (0.72-0.99), and 0.75 (0.60-0.93) (P for trend=.003), and those for cardiovascular- and cancer-related mortality were 0.95, 0.80, and 0.55 (P for trend=.05) and 0.82, 0.83, and 0.78 (P for trend=.01), respectively. Compared with participants with low hsCRP levels and any regular PA, those with high hsCRP levels and no regular PA had a significantly higher risk of mortality (1.59 [1.38-1.84]). Higher PA levels were associated with a dose-dependent reduced risk of cardiovascular-related, cancer-related, and all-cause mortality. Individuals with high hsCRP levels and no regular PA had the highest risk of mortality.


A weighted and directed interareal connectivity matrix for macaque cerebral cortex.
Retrograde tracer injections in 29 of the 91 areas of the macaque cerebral cortex revealed 1,615 interareal pathways, a third of which have not previously been reported. A weight index (extrinsic fraction of labeled neurons [FLNe]) was determined for each area-to-area pathway. Newly found projections were weaker on average compared with the known projections; nevertheless, the 2 sets of pathways had extensively overlapping weight distributions. Repeat injections across individuals revealed modest FLNe variability given the range of FLNe values (standard deviation <1 log unit, range 5 log units). The connectivity profile for each area conformed to a lognormal distribution, where a majority of projections are moderate or weak in strength. In the G29 × 29 interareal subgraph, two-thirds of the connections that can exist do exist. Analysis of the smallest set of areas that collects links from all 91 nodes of the G29 × 91 subgraph (dominating set analysis) confirms the dense (66%) structure of the cortical matrix. The G29 × 29 subgraph suggests an unexpectedly high incidence of unidirectional links. The directed and weighted G29 × 91 connectivity matrix for the macaque will be valuable for comparison with connectivity analyses in other species, including humans. It will also inform future modeling studies that explore the regularities of cortical networks.


The deforestation story: testing for anthropogenic origins of Africa's flammable grassy biomes.
Africa has the most extensive C4 grassy biomes of any continent. They are highly flammable accounting for greater than 70% of the world's burnt area. Much of Africa's savannas and grasslands occur in climates warm enough and wet enough to support closed forests. The combination of open grassy systems and the frequent fires they support have long been interpreted as anthropogenic artefacts caused by humans igniting frequent fires. True grasslands, it was believed, would be restricted to climates too dry or too cold to support closed woody vegetation. The idea that higher-rainfall savannas are anthropogenic and that fires are of human origin has led to initiatives to 'reforest' Africa's open grassy systems paid for by carbon credits under the assumption that the net effect of converting these system to forests would sequester carbon, reduce greenhouse gases and mitigate global warming. This paper reviews evidence for the antiquity of African grassy ecosystems and for the fires that they sustain. Africa's grassy biomes and the fires that maintain them are ancient and there is no support for the idea that humans caused large-scale deforestation. Indicators of old-growth grasslands are described. These can help distinguish secondary grasslands suitable for reforestation from ancient grasslands that should not be afforested.This article is part of the themed issue 'The interaction of fire and mankind'.


Central and peripheral autonomic mechanisms involved in the circulatory actions of methyldopa.
Intracisternal (i.c.) and intravenous (i.v.) administration of methyldopa in conscious rabbits produced closely similar changes in hemodynamics, heart rate, and falls in plasma norepinephrine levels. Two weeks after giving i.c. 6-hydroxydopamine (6-OHDA), when there is widespread destruction of central noradrenergic neurons, the effects of i.c. methyldopa virtually were abolished. This suggests that noradrenergic neurons are the major central site of biotransformation into active metabolites. The circulatory and norepinephrine effects of i.v. methyldopa were attenuated but not completely abolished after giving i.c. 6-OHDA. Hence, in the rabbit about 70% of the action of methyldopa was central and about 30% was peripheral in the human therapeutic range of methyldopa concentrations. Preliminary lesion experiments suggest that the A5 nucleus plays an important role in the bradycardia. Two weeks after giving 5,6-dihydroxytryptamine (5,6-DHT) to destroy serotonergic (5HT) neurons the effects of i.c. methyldopa on mean arterial pressure (MAP) and heart rate were attenuated to approximately 50% of control effects. Therefore, some of the central effects of methyldopa apparently are mediated through 5HT pathways. We also compared the effects of i.c. methyldopa with those of i.c. clonidine (an alpha 2-adrenergic receptor agonist) and with the effects of transmitter release from the endings of noradrenergic and 5HT neurons during the first few hours after either 6-OHDA or 5,6-DHT administration. Our findings suggest that after biotransformation of methyldopa its active metabolites increase the activity of the bulbospinal noradrenergic neurons that control MAP and heart rate and reduce the activity of bulbospinal 5HT neurons.


Locally adaptive Nakagami-based ultrasound similarity measures.
The derivation of statistically optimal similarity measures for intensity-based registration is possible by modeling the underlying image noise distribution. The parameters of these distributions are, however, commonly set heuristically across all images. In this article, we show that the estimation of the parameters on the present images largely improves the registration, which is a consequence of the more accurate characterization of the image noise. More precisely, instead of having constant parameters over the entire image domain, we estimate them on patches, leading to a local adaptation of the similarity measure. While this basic idea of creating locally adaptive metrics is interesting for various fields of application, we present the derivation for ultrasound imaging. The domain of ultrasound is particularly appealing for this approach, due to the inherent contamination with speckle noise. Furthermore, there exist detailed analyses of suitable noise distributions in the literature. We present experiments for applying a bivariate Nakagami distribution that facilitates modeling of several scattering scenarios prominent in medical ultrasound. Depending on the number of scatterers per resolution cell and the presence of coherent structures, different Nakagami parameters are required to obtain a valid approximation of the intensity statistics and to account for distributional locality. Our registration results on radio-frequency ultrasound data confirm the theoretical necessity for a spatial adaptation of similarity metrics.


Specific lectin biomarkers for isolation of human pluripotent stem cells identified through array-based glycomic analysis.
Rapid and dependable methods for isolating human pluripotent stem cell (hPSC) populations are urgently needed for quality control in basic research and in cell-based therapy applications. Using lectin arrays, we analyzed glycoproteins extracted from 26 hPSC samples and 22 differentiated cell samples, and identified a small group of lectins with distinctive binding signatures that were sufficient to distinguish hPSCs from a variety of non-pluripotent cell types. These specific biomarkers were shared by all the 12 human embryonic stem cell and the 14 human induced pluripotent stem cell samples examined, regardless of the laboratory of origin, the culture conditions, the somatic cell type reprogrammed, or the reprogramming method used. We demonstrated a practical application of specific lectin binding by detecting hPSCs within a differentiated cell population with lectin-mediated staining followed by fluorescence microscopy and flow cytometry, and by enriching and purging viable hPSCs from mixed cell populations using lectin-mediated cell separation. Global gene expression analysis showed pluripotency-associated differential expression of specific fucosyltransferases and sialyltransferases, which may underlie these differences in protein glycosylation and lectin binding. Taken together, our results show that protein glycosylation differs considerably between pluripotent and non-pluripotent cells, and demonstrate that lectins may be used as biomarkers to monitor pluripotency in stem cell populations and for removal of viable hPSCs from mixed cell populations.


Relative contributions of lipooligosaccharide inner and outer core modifications to nontypeable Haemophilus influenzae pathogenesis.
Nontypeable Haemophilus influenzae (NTHi) is a frequent commensal of the human nasopharynx that causes opportunistic infection in immunocompromised individuals. Existing evidence associates lipooligosaccharide (LOS) with disease, but the specific and relative contributions of NTHi LOS modifications to virulence properties of the bacterium have not been comprehensively addressed. Using NTHi strain 375, an isolate for which the detailed LOS structure has been determined, we compared systematically a set of isogenic mutant strains expressing sequentially truncated LOS. The relative contributions of 2-keto-3-deoxyoctulosonic acid, the triheptose inner core, oligosaccharide extensions on heptoses I and III, phosphorylcholine, digalactose, and sialic acid to NTHi resistance to antimicrobial peptides (AMP), self-aggregation, biofilm formation, cultured human respiratory epithelial infection, and murine pulmonary infection were assessed. We show that opsX, lgtF, lpsA, lic1, and lic2A contribute to bacterial resistance to AMP; lic1 is related to NTHi self-aggregation; lgtF, lic1, and siaB are involved in biofilm growth; opsX and lgtF participate in epithelial infection; and opsX, lgtF, and lpsA contribute to lung infection. Depending on the phenotype, the involvement of these LOS modifications occurs at different extents, independently or having an additive effect in combination. We discuss the relative contribution of LOS epitopes to NTHi virulence and frame a range of pathogenic traits in the context of infection.


The Skull of Epidolops ameghinoi from the Early Eocene Itaboraí Fauna, Southeastern Brazil, and the Affinities of the Extinct Marsupialiform Order Polydolopimorphia.
The skull of the polydolopimorphian marsupialiform Epidolops ameghinoi is described in detail for the first time, based on a single well-preserved cranium and associated left and right dentaries plus additional craniodental fragments, all from the early Eocene (53-50 million year old) Itaboraí fauna in southeastern Brazil. Notable craniodental features of E. ameghinoi include absence of a masseteric process, very small maxillopalatine fenestrae, a prominent pterygoid fossa enclosed laterally by a prominent ectopterygoid crest, an absent or tiny transverse canal foramen, a simple, planar glenoid fossa, and a postglenoid foramen that is immediately posterior to the postglenoid process. Most strikingly, the floor of the hypotympanic sinus was apparently unossified, a feature found in several stem marsupials but absent in all known crown marsupials. "Type II" marsupialiform petrosals previously described from Itaboraí plausibly belong to E. ameghinoi; in published phylogenetic analyses, these petrosals fell outside (crown-clade) Marsupialia. "IMG VII" tarsals previously referred to E. ameghinoi do not share obvious synapomorphies with any crown marsupial clade, nor do they resemble those of the only other putative polydolopimorphians represented by tarsal remains, namely the argyrolagids. Most studies have placed Polydolopimorphia within Marsupialia, related to either Paucituberculata, or to Microbiotheria and Diprotodontia. However, diprotodonty almost certainly evolved independently in polydolopimorphians, paucituberculatans and diprotodontians, and Epidolops does not share obvious synapomorphies with any marsupial order. Epidolops is dentally specialized, but several morphological features appear to be more plesiomorphic than any crown marsupial. It seems likely Epidolops that falls outside Marsupialia, as do morphologically similar forms such as Bonapartherium and polydolopids. Argyrolagids differ markedly in their known morphology from Epidolops but share some potential apomorphies with paucituberculatans. It is proposed that Polydolopimorphia as currently recognised is polyphyletic, and that argyrolagids (and possibly other taxa currently included in Argyrolagoidea, such as groeberiids and patagoniids) are members of Paucituberculata. This hypothesis is supported by Bayesian non-clock phylogenetic analyses of a total evidence matrix comprising DNA sequence data from five nuclear protein-coding genes, indels, retroposon insertions, and morphological characters: Epidolops falls outside Marsupialia, whereas argyrolagids form a clade with the paucituberculatans Caenolestes and Palaeothentes, regardless of whether the Type II petrosals and IMG VII tarsals are used to score characters for Epidolops or not. There is no clear evidence for the presence of crown marsupials at Itaboraí, and it is possible that the origin and early evolution of Marsupialia was restricted to the "Austral Kingdom" (southern South America, Antarctica, and Australia).


Refractory Celiac Disease Successfully Treated With Azathioprine.
Refractory celiac disease (CD) is a clinical diagnosis defined by the persistence of signs/symptoms, laboratory abnormalities or villous atrophy typical of CD despite strict adherence to a gluten-free diet for at least 6 - 12 months. It should be suspected when patients with CD fail to respond primarily or secondarily to a gluten-free diet, especially if there is significant weight loss. Differentiation between types is important both for management and predicting prognosis. Type I can be managed with mild immunosuppression with nutritional support. Type II requires strong immunosuppression like azathioprine. Recently, autologous stem cell transplantation has also been used to treat type II.


Exploring the Mechanism Responsible for Cellulase Thermostability by Structure-Guided Recombination.
Cellulases from Bacillus and Geobacillus bacteria are potentially useful in the biofuel and animal feed industries. One of the unique characteristics of these enzymes is that they are usually quite thermostable. We previously identified a cellulase, GsCelA, from thermophilic Geobacillus sp. 70PC53, which is much more thermostable than its Bacillus homolog, BsCel5A. Thus, these two cellulases provide a pair of structures ideal for investigating the mechanism regarding how these cellulases can retain activity at high temperature. In the present study, we applied the SCHEMA non-contiguous recombination algorithm as a novel tool, which assigns protein sequences into blocks for domain swapping in a way that lessens structural disruption, to generate a set of chimeric proteins derived from the recombination of GsCelA and BsCel5A. Analyzing the activity and thermostability of this designed library set, which requires only a limited number of chimeras by SCHEMA calculations, revealed that one of the blocks may contribute to the higher thermostability of GsCelA. When tested against swollen Avicel, the highly thermostable chimeric cellulase C10 containing this block showed significantly higher activity (22%-43%) and higher thermostability compared to the parental enzymes. With further structural determinations and mutagenesis analyses, a 310 helix was identified as being responsible for the improved thermostability of this block. Furthermore, in the presence of ionic calcium and crown ether (CR), the chimeric C10 was found to retain 40% residual activity even after heat treatment at 90°C. Combining crystal structure determinations and structure-guided SCHEMA recombination, we have determined the mechanism responsible for the high thermostability of GsCelA, and generated a novel recombinant enzyme with significantly higher activity.


Newly diagnosed epilepsy in children: presentation at diagnosis.
The current understanding of epilepsy has changed significantly in the past 2 decades. This report presents a description of newly diagnosed childhood-onset epilepsy, with a special emphasis on epilepsy syndromes, in a large, prospectively ascertained community-based cohort evaluated and diagnosed in the mid-1990s. Children, aged 0 through 15 years at the time of the first seizure, were prospectively identified at the time of diagnosis of epilepsy through the practices of 16 of the 17 child neurologists in Connecticut as well as five adult neurologists and seven pediatricians from January 1993 through December 1997. Parents were interviewed, and all relevant medical records were reviewed. Classification of seizures and of epilepsy syndromes was done for each child by each of three pediatric neurologists. Discrepancies were resolved in conference. A total of 613 children was recruited into the study. The median age at time of the first seizure was 5.3 years. Half the cohort was boys. Eighteen percent had a remote symptomatic etiology. Epilepsy syndromes were classifiable in all but four children, although some syndromes are, by definition, relatively nonspecific. In this childhood-onset cohort, 58.6% of the syndromes were localization related, 29.0% generalized, and 12.4% undetermined as to whether focal or generalized. Benign rolandic epilepsy occurred in 10% of the cohort. Primarily generalized syndromes accounted for 20.6%, with childhood absence being the single most common syndrome in this subgroup (12.1% of the cohort). Secondarily generalized syndromes accounted for 8.5% of the total, with infantile spasms being the most common in this grouping (3.9% of the cohort). This study presents a description of childhood- and adolescent-onset epilepsy as it is diagnosed and evaluated in the 1990s in one state in the United State and based on current classification guidelines. The results should be generalizable to the rest of the country. The prognostic value of early identification of epilepsy syndromes will be determined through subsequent follow-up of this cohort.


Clinical review 97: Potential health benefits of dietary phytoestrogens: a review of the clinical, epidemiological, and mechanistic evidence.
Phytoestrogens represent a family of plant compounds that have been shown to have both estrogenic and antiestrogenic properties. A variety of these plant compounds and their mammalian metabolic products have been identified in various human body fluids and fall under two main categories: isoflavones and lignans. A wide range of commonly consumed foods contain appreciable amounts of these different phytoestrogens. For example, soy and flax products are particularly good sources of isoflavones and lignans, respectively. Accumulating evidence from molecular and cellular biology experiments, animal studies, and, to a limited extent, human clinical trials suggests that phytoestrogens may potentially confer health benefits related to cardiovascular diseases, cancer, osteoporosis, and menopausal symptoms. These potential health benefits are consistent with the epidemiological evidence that rates of heart disease, various cancers, osteoporotic fractures, and menopausal symptoms are more favorable among populations that consume plant-based diets, particularly among cultures with diets that are traditionally high in soy products. The evidence reviewed here will facilitate the identification of what is known in this area, the gaps that exist, and the future research that holds the most potential and promise.