Dual gene activation and knockout screen reveals directional dependencies in genetic networks.
Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair. Based on the results from over 100,000 perturbed gene pairs, we reconstruct a directional dependency network for human K562 leukemia cells and demonstrate how our approach allows the determination of directionality in activating genetic interactions. Our interaction network connects previously uncharacterized genes to well-studied pathways and identifies targets relevant for therapeutic intervention.


Timing of muscle response to a sudden leg perturbation: comparison between adolescents and adults with Down syndrome.
Movement disturbances associated with Down syndrome reduce mechanical stability, worsening the execution of important tasks such as walking and upright standing. To compensate these deficits, persons with Down syndrome increase joint stability modulating the level of activation of single muscles or producing an agonist-antagonist co-activation. Such activations are also observed when a relaxed, extended leg is suddenly released and left to oscillate passively under the influence of gravity (Wartenberg test). In this case, the Rectus femoris of adults with Down syndrome displayed peaks of activation after the onset of the first leg flexion. With the aim to verify if these muscular reactions were acquired during the development time and to find evidences useful to give them a functional explanation, we used the Wartenberg test to compare the knee joint kinematics and the surface electromyography of the Rectus femoris and Biceps femoris caput longus between adolescents and adults with Down syndrome. During the first leg flexion, adolescents and adults showed single Rectus femoris activations while, a restricted number of participants exhibited agonist-antagonist co-activations. However, regardless the pattern of activation, adults initiated the muscle activity significantly later than adolescents. Although most of the mechanical parameters and the total movement variability were similar in the two groups, the onset of the Rectus femoris activation was well correlated with the time of the minimum acceleration variability. Thus, in adolescents the maximum mechanical stability occurred short after the onset of the leg fall, while adults reached their best joint stability late during the first flexion. These results suggest that between the adolescence and adulthood, persons with Down syndrome explore a temporal window to select an appropriate timing of muscle activation to overcome their inherent mechanical instability.


Sini decoction as an adjuvant therapy for angina pectoris: a systematic review of randomized controlled trials.
To systematically assess the effects and safety of Sini decoction as an adjuvant therapy for patients with angina pectoris. We searched PubMed, Excerpt Medica Database, the Cochrane library, Wanfang Database, China National Knowledge Infrastructure Database, China Science and Technology Journal Database from the date of its inception until August 1, in 2014. Available literatures were selected according to the inclusion criteria. Two reviewers finished data extraction, checked the data and assessed the methodological quality of studies, independently. The Review Manage Software 5.1.0 was used for data analysis. Six trials involving 453 participants were eligible. None of the trials reported the mortality due to angina pectoris. The secondary outcomes showed that Sini decoction, together with nitroglycerin when necessary, may have some effects on reducing the number of angina attacks and the amount of nitroglycerin. But in terms of reducing the duration of angina and improvement of electrocardiogram, there were no statistical differences between Sini decoction group and isosorbide dinitrate group. Only one reported that no adverse events were found. Based on this systematic review, Sini decoction can reduce the dosage of nitroglycerin, when compared with isosorbide dinitrate group. And there were no enough evidence in the papers to draw any conclusions for the safety of Sini decoction.


Studies on the efficacy of methyl esters of n-alkyl fatty acids as penetration enhancers.
The efficacy of the methyl esters of medium chain n-alkyl fatty acids as penetration enhancers was evaluated in vitro using various animal and human skins with minoxidil as the test drug. Both methyl nonanoate and methyl caprate at a 10% concentration were found to be effective penetration enhancers for a 2% solution of minoxidil in alcohol USP. The percent of the applied radioactive dose of minoxidil penetrated after 17 h was 5-8 times greater for methyl non-anoate and methyl caprate enhanced solutions than for a 2% solution of minoxidil in alcohol USP alone or with the addition of 10% Azone, dimethylsulfoxide (DMSO) or N,N-diethyl-m-toluamide (DEET). The penetration enhancing activity of methyl caprate was effective for human, mouse, and hamster skins. Methyl caprate also enhanced the penetration of vitamin D3, erythromycin, triamcinolone acetonide, testosterone, and hydrocortisone.


Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis.
Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease characterized by airway remodeling, inflammation, alveolar destruction, and fibrosis. We utilized single-cell RNA sequencing (scRNA-seq) to identify epithelial cell types and associated biological processes involved in the pathogenesis of IPF. Transcriptomic analysis of normal human lung epithelial cells defined gene expression patterns associated with highly differentiated alveolar type 2 (AT2) cells, indicated by enrichment of RNAs critical for surfactant homeostasis. In contrast, scRNA-seq of IPF cells identified 3 distinct subsets of epithelial cell types with characteristics of conducting airway basal and goblet cells and an additional atypical transitional cell that contributes to pathological processes in IPF. Individual IPF cells frequently coexpressed alveolar type 1 (AT1), AT2, and conducting airway selective markers, demonstrating "indeterminate" states of differentiation not seen in normal lung development. Pathway analysis predicted aberrant activation of canonical signaling via TGF-β, HIPPO/YAP, P53, WNT, and AKT/PI3K. Immunofluorescence confocal microscopy identified the disruption of alveolar structure and loss of the normal proximal-peripheral differentiation of pulmonary epithelial cells. scRNA-seq analyses identified loss of normal epithelial cell identities and unique contributions of epithelial cells to the pathogenesis of IPF. The present study provides a rich data source to further explore lung health and disease.


Descending necrotizing mediastinitis: a conservative approach.
Descending necrotizing mediastinitis (DNM) is a now-rare complication of dental and pharyngeal infections. Reports in the literature have emphasized the need for early, aggressive surgical intervention. We present a case of DNM with bilateral empyemas that arose secondary to a perforated pharyngeal abscess. The patient was successfully managed conservatively with intravenous antibiotics and intercostal drainage. We conclude that conservative management with antibiotics and image-guided percutaneous pleural drainage may be initially appropriate for the stable patient.


Fluoride resistance and transport by riboswitch-controlled CLC antiporters.
A subclass of bacterial CLC anion-transporting proteins, phylogenetically distant from long-studied CLCs, was recently shown to be specifically up-regulated by F(-). We establish here that a set of randomly selected representatives from this "CLC(F)" clade protect Escherichia coli from F(-) toxicity, and that the purified proteins catalyze transport of F(-) in liposomes. Sequence alignments and membrane transport experiments using (19)F NMR, osmotic response assays, and planar lipid bilayer recordings reveal four mechanistic traits that set CLC(F) proteins apart from all other known CLCs. First, CLC(F)s lack conserved residues that form the anion binding site in canonical CLCs. Second, CLC(F)s exhibit high anion selectivity for F(-) over Cl(-). Third, at a residue thought to distinguish CLC channels and transporters, CLC(F)s bear a channel-like valine rather than a transporter-like glutamate, and yet are F(-)/H(+) antiporters. Finally, F(-)/H(+) exchange occurs with 1:1 stoichiometry, in contrast to the usual value of 2:1.


The deterministic nature of earthquake rupture.
Understanding the earthquake rupture process is central to our understanding of fault systems and earthquake hazards. Multiple hypotheses concerning the nature of fault rupture have been proposed but no unifying theory has emerged. The conceptual hypothesis most commonly cited is the cascade model for fault rupture. In the cascade model, slip initiates on a small fault patch and continues to rupture further across a fault plane as long as the conditions are favourable. Two fundamental implications of this domino-like theory are that small earthquakes begin in the same manner as large earthquakes and that the rupture process is not deterministic--that is, the size of the earthquake cannot be determined until the cessation of rupture. Here we show that the frequency content of radiated seismic energy within the first few seconds of rupture scales with the final magnitude of the event. We infer that the magnitude of an earthquake can therefore be estimated before the rupture is complete. This finding implies that the rupture process is to some degree deterministic and has implications for the physics of the rupture process.


Conjugative mobilization of the rolling-circle plasmid pIP823 from Listeria monocytogenes BM4293 among gram-positive and gram-negative bacteria.
We determined the sequence and genetic organization of plasmid pIP823, which contains the dfrD gene; dfrD confers high-level trimethoprim resistance to Listeria monocytogenes BM4293 by synthesis of dihydrofolate reductase type S2. pIP823 possessed all the features of the pUB110/pC194 plasmid family, whose members replicate by the rolling-circle mechanism. The rep gene encoded a protein identical to RepU, the protein required for initiation of the replication of plasmids pTB913 from a thermophilic Bacillus sp. and pUB110 from Staphylococcus aureus. The mob gene encoded a protein with a high degree of amino acid identity with the Mob proteins involved in conjugative mobilization and interplasmidic recombination of pTB913 and pUB110. The host range of pIP823 was broad and included L. monocytogenes, Enterococcus faecalis, S. aureus, Bacillus subtilis, and Escherichia coli. In all these species, pIP823 replicated by generating single-stranded DNA and was stable. Conjugative mobilization of pIP823 was obtained by self-transferable plasmids between L. monocytogenes and E. faecalis, between L. monocytogenes and E. coli, and between strains of E. coli, and by the streptococcal conjugative transposon Tn1545 from L. monocytogenes to E. faecalis, and from L. monocytogenes and E. faecalis to E. coli. These data indicate that the gene flux observed in nature from gram-positive to gram-negative bacteria can occur by conjugative mobilization. Our results suggest that dissemination of trimethoprim resistance in Listeria spp. and acquisition of other antibiotic resistance determinants in this species can be anticipated.


Tumor stroma derived biomarkers in cancer.
In recent years the importance of the tumor stroma for the development, promotion and invasion of cancer is becoming increasingly clear. Besides a malignantly transformed cancer cell, tumors also contains many other cell types, including endothelial cells, fibroblasts and cells of the immune system. These cells together with the cancer cells produce the sum extracellular matrix (ECM) of the tumor. The ECM and the non-malignant cells of the tumor are defined as the "tumor stroma". Just as the malignant cell itself can be the source of substances that can be used as biomarkers of cancer, the tumor stroma contains factors that potentially can be used as biomarkers when treating patients with cancer. In this review we will discuss the role of the tumor stroma as a source of new cancer biomarkers. This concept highlights a novel view of cancer and treats them as organized organs. Additionally, this further stresses the importance of including factors related to the tumor stroma into the diagnostic and therapeutic equation of cancer.


Characterization of rhinovirus C from a 4-year-old boy with acute onset dilated cardiomyopathy in Jakarta, Indonesia.
Myocarditis, inflammation of the heart muscle, can be caused by infections, autoimmune disease or exposure to toxins. The major cause of myocarditis in the paediatric population is viral infection, including coxsackievirus B3, adenovirus, herpesvirus, parvovirus, influenza A and B, and hepatitis. Here, we report the detection of rhinovirus C in a boy with a clinical presentation of myocarditis, suggesting a possible causative role of this virus in this case. A previously well 4.5-year-old boy presented with increasing breathlessness for a week prior to admission. He also had upper respiratory tract infection a few days before the event. An echocardiogram revealed severe left ventricle (LV) systolic dysfunction with dilation of the LV. RNA was extracted from serum and two nasal swabs, and tested with conventional PCR at the family level for viruses including enterovirus, dengue, chikungunya, influenza, herpesvirus, paramyxovirus and coronavirus. Further characterization of the enterovirus group was carried out using PCR with primers targeting the VP4/VP2 gene, followed by sequencing. Molecular tests showed the presence of rhinovirus C genetic material in both serum and swab samples. Phylogenetic analysis of the VP4/VP2 region showed 96-97 % similarity with the closest strain isolated in Ulaanbaatar (Mongolia) and Japan in 2012. We report the possible association of rhinovirus C and myocarditis in a child presenting with acute onset of dilated cardiomyopathy.


Implication of STAT3 signaling in human colonic cancer cells during intestinal trefoil factor 3 (TFF3) -- and vascular endothelial growth factor-mediated cellular invasion and tumor growth.
Signal transducer and activator of transcription (STAT) 3 is overexpressed or activated in most types of human tumors and has been classified as an oncogene. In the present study, we investigated the contribution of the STAT3s to the proinvasive activity of trefoil factors (TFF) and vascular endothelial growth factor (VEGF) in human colorectal cancer cells HCT8/S11 expressing VEGF receptors. Both intestinal trefoil peptide (TFF3) and VEGF, but not pS2 (TFF1), activate STAT3 signaling through Tyr(705) phosphorylation of both STAT3alpha and STAT3beta isoforms. Blockade of STAT3 signaling by STAT3beta, depletion of the STAT3alpha/beta isoforms by RNA interference, and pharmacologic inhibition of STAT3alpha/beta phosphorylation by cucurbitacin or STAT3 inhibitory peptide abrogates TFF- and VEGF-induced cellular invasion and reduces the growth of HCT8/S11 tumor xenografts in athymic mice. Differential gene expression analysis using DNA microarrays revealed that overexpression of STAT3beta down-regulates the VEGF receptors Flt-1, neuropilins 1 and 2, and the inhibitor of DNA binding/differentiation (Id-2) gene product involved in the neoplastic transformation. Taken together, our data suggest that TFF3 and the essential tumor angiogenesis regulator VEGF(165) exert potent proinvasive activity through STAT3 signaling in human colorectal cancer cells. We also validate new therapeutic strategies targeting STAT3 signaling by pharmacologic inhibitors and RNA interference for the treatment of colorectal cancer patients.


Impact of Home-to-Centre Distance on Bone Marrow Transplantation Outcomes.
Haematopoietic stem cell transplantation (HSCT) in Oman started in 1994 at Sultan Qaboos University Hospital (SQUH), Muscat, Oman. Previous studies have suggested that longer driving time to the transplant centre (DTC) independently correlates with worse overall survival (OS). Therefore, this study aimed to examine the impact of DTC on OS and acute graft-versus-host disease (aGvHD). This retrospective study included all patients who underwent HSCT between February 2006 and December 2016 at SQUH. The DTC was determined using Google Maps (Google LLC., Mountain View, California, USA). The probability of OS was estimated using a Kaplan-Meier estimator and the impact of DTC on OS was compared using a Cox model. A total of 170 patients were included in this study of which 52% were male and 28% were from the Al Batinah region. The mean age was 14.2 ± 12.2 years. The mean haemoglobin, platelet and white blood cell counts before the HSCT were 10.3 ± 1.7 g/dL, 207 ± 131 × 109/L and 5.1 ± 5.9 × 109/L, respectively. The median DTC for those with aGvHD was 84 minutes, which is similar to patients without aGvHD (P = 0.918). The hazard ratio for DTC as a predictor of OS was 1.0 (P = 0.901). In this single centre study, DTC did not impact aGvHD or OS in patients post-HSCT. The study was limited by its retrospective design and the small sample size. It is recommended that these results be confirmed in a prospective study.


[Morpho-volumetric assessment of the right ventricle: a comparison between three-dimensional echocardiography and cardiac magnetic resonance].
The morpho-volumetric assessment of the right ventricle (RV) is useful in the diagnosis and prognosis of many congenital and acquired cardiovascular diseases. The complexity of the right ventricular shape does not allow an adequate and satisfactory evaluation of the RV. Two-dimensional (2D) echocardiography is the most used tool for the assessment of RV function, as it is a noninvasive, reproducible and widespread technique, but the geometric assumptions required for measurement of RV volumes reduce its accuracy. At present, cardiac magnetic resonance is the gold standard for the evaluation of RV volumes because it does not need any assumption and is reproducible, though not always available. This imaging tool allows to follow-up patients and to monitor drug therapy. On the other hand, three-dimensional (3D) echocardiography overcomes several limitations of 2D echocardiography, in that it provides an estimation of RV volumes obtained through a real 3D data set, obtaining sections which cannot be technically achieved with 2D echocardiography. It is therefore useful to compare data on RV volumes and function obtained with 3D echocardiography versus cardiac magnetic resonance, mainly considering the lower costs and higher portability and availability of echocardiography.


Genetic Factors, Adherence to Healthy Lifestyle Behavior, and Risk of Invasive Breast Cancer Among Women in the UK Biobank.
Breast cancer is considered to result from a combination of genetic and lifestyle-related factors, but the degree to which an overall healthy lifestyle may attenuate the impact of multiple genetic variants on invasive breast cancer risk remains equivocal. Using Cox proportional hazards regression models, we examined the association of a modified healthy lifestyle index (HLI) with risk of invasive breast cancer by genetic risk group among 146 326 women from the UK Biobank. We generated an HLI score based on a combination of diet, physical activity, smoking, alcohol consumption and anthropometry, and a polygenic risk score (PRS) using 304 breast cancer-associated genetic loci. Among premenopausal and postmenopausal women, a favorable lifestyle (highest tertile) was associated with 22% and 31% reductions in invasive breast cancer risk, respectively (hazard ratio [HR]high vs low = 0.78, 95% confidence interval [CI] = 0.64 to 0.94; HRhigh vs low = 0.69, 95% CI = 0.63 to 0.77, respectively), whereas a high PRS (highest tertile) was associated with more than a doubling in the risk in both groups. For premenopausal women, the greatest risk reduction in association with the HLI was seen among those with a high PRS (HRhigh vs low = 0.73, 95% CI = 0.75 to 0.95). In postmenopausal women, those with a favorable lifestyle had 30%, 29%, and 32% reductions in risk of invasive breast cancer in the low, intermediate, and high PRS groups, respectively (HRhigh vs low = 0.70, 95% CI = 0.56 to 0.88; HRhigh vs low = 0.71, 95% CI = 0.59 to 0.84; and HRhigh vs low = 0.68, 95% CI = 0.59 to 0.78, respectively). There was an additive but not multiplicative interaction between the HLI score and PRS for postmenopausal and, to a lesser extent, premenopausal women. Our findings support the view that an overall healthy lifestyle may attenuate the impact of genetic factors on invasive breast cancer risk among women of European ancestry.


Global tractography with embedded anatomical priors for quantitative connectivity analysis.
Tractography algorithms provide us with the ability to non-invasively reconstruct fiber pathways in the white matter (WM) by exploiting the directional information described with diffusion magnetic resonance. These methods could be divided into two major classes, local and global. Local methods reconstruct each fiber tract iteratively by considering only directional information at the voxel level and its neighborhood. Global methods, on the other hand, reconstruct all the fiber tracts of the whole brain simultaneously by solving a global energy minimization problem. The latter have shown improvements compared to previous techniques but these algorithms still suffer from an important shortcoming that is crucial in the context of brain connectivity analyses. As no anatomical priors are usually considered during the reconstruction process, the recovered fiber tracts are not guaranteed to connect cortical regions and, as a matter of fact, most of them stop prematurely in the WM; this violates important properties of neural connections, which are known to originate in the gray matter (GM) and develop in the WM. Hence, this shortcoming poses serious limitations for the use of these techniques for the assessment of the structural connectivity between brain regions and, de facto, it can potentially bias any subsequent analysis. Moreover, the estimated tracts are not quantitative, every fiber contributes with the same weight toward the predicted diffusion signal. In this work, we propose a novel approach for global tractography that is specifically designed for connectivity analysis applications which: (i) explicitly enforces anatomical priors of the tracts in the optimization and (ii) considers the effective contribution of each of them, i.e., volume, to the acquired diffusion magnetic resonance imaging (MRI) image. We evaluated our approach on both a realistic diffusion MRI phantom and in vivo data, and also compared its performance to existing tractography algorithms.


Measurement and management of human-induced patterns of forest fragmentation: a case study.
In many tropical developing countries, the twin pressures of population and poverty are resulting in substantial fragmentation of forests, increasing the probability of extinction for many species, Forest fragmentation occurs when large contiguous forests are perforated by small holes or broken up into edges and smaller patches to form a nonforested matrix of open spaces. Thus, forest fragmentation refers not only to the area of forest cleared, but also to the pattern of this clearance, the resulting forest's spatial properties. Both characteristics are important for species survivability. Apart from opening up forests to many abiotic and biotic influences, fragmentation can affect species dispersal and migration through its effects on forest connectivity. Landscape ecology conceptualizes connectivity as a gradient of critical thresholds, ranging from the large intact forest to the small unconnected forest patch. This article reports results from a multiple-scale analysis of forest fragmentation in Jamaica's Cockpit Country, an area of once contiguous forest now under threat from human encroachment. Spatial forest data derived from classification of ETM+ satellite imagery are used to measure fragmentation patterns representing various degrees of forest connectivity and density. The results suggest that, overall, 81% of the region is in forest. However, fragmentation patterns also suggest that this forest is riven with extensive perforations indicative of an early stage in the decline of contiguity. The results provided by the spatial fragmentation model are a first step in the design of effective conservation and rehabilitation plans for the area. The article concludes with a discussion of possible multiscale management options for the region.


Chloroplast DNA phylogeography of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in Japan.
Betula maximowicziana is an ecologically and economically important tree species in Japan. In order to examine the phylogeographical pattern of the species in detail, maternally inherited chloroplast (cp) DNA variations of 25 natural populations of Betula maximowicziana and a total of 12 populations of three related species were evaluated by PCR-RFLP analysis. Two main haplotypic groups of B. maximowicziana populations (northern and southern) were detected, with the main boundary passing through the Tohoku region in northeastern Japan; in addition there was high genetic differentiation among the 25 populations studied (GST = 0.950, G'ST =0:977). The phylogeographical pattern exhibited by B. maximowicziana was much more similar to that of alpine plants than to that of beech and oak. Comparison of the patterns of genetic structure obtained from the cpDNA with previously and newly acquired data on bi-parentally inherited nuclear DNA indicates that the nuclear genome was transferred via pollen from the northern haplotypic group to the southern group more frequently than it moved in the opposite direction. Although common haplotypes were detected among B. maximowicziana and the two related species examined, these haplotypes were not shared sympatrically, suggesting very rare hybridization among the species currently occurring in their natural populations.


IMRT, RapidArc® and conformal radiotherapy in the treatment of tumours of the anal canal.
To compare dosimetric results of the use of RapidArc® with simultaneous integrated boost, sliding window intensity-modulated radiotherapy (IMRT) with simultaneous integrated boost, and conformal radiotherapy with sequential boost in the management of anal canal cancer. Two patients with squamous cell cancer of the anal canal with compromised inguinal nodes were included. The simulation was performed in the supine position with a customized Vac-Lok™ immobilizer. Treatment volumes and organs at risk were defined in accordance with international recommendations. Dosimetric comparisons were made in the target volume by means of tumour conformity, coverage, and homogeneity indexes; in healthy organs, integral doses were compared. A similar planning target volume coverage was achieved with the three techniques. The two IMRT techniques demonstrated benefits in doses received by healthy organs compared to the conformal radiotherapy. RapidArc® showed reduction in the execution time and monitor units required for treatment compared with sliding window IMRT. The IMRT showed coverage and tumour conformity indexes similar to those of conformal radiotherapy with better dosimetric results in the organs at risk, which should translate into a better toxicity profile. RapidArc® demonstrated benefits over the sliding window IMRT, which makes treatment more comfortable for the patient with less uncertainty about intrafraction motion and a reduced potential for radiation-induced tumours.


Amide proton transfer-weighted magnetic resonance image-guided stereotactic biopsy in patients with newly diagnosed gliomas.
Pathological assessment using World Health Organization (WHO) criteria is the gold standard for diagnosis of gliomas. However, the accuracy of diagnosis is limited by tissue sampling, particularly for infiltrating, heterogeneous tumours. We assessed the accuracy of amide proton transfer-weighted (APTw) magnetic resonance imaging (MRI)-guided tissue sampling to identify regions of high-grade glioma via radiographic-histopathologic correlation in patients with newly suspected glioma. Twenty-four patients with previously undiagnosed gliomas underwent a volumetric APTw MRI prior to their first neurosurgical procedure. A total of 70 specimens were collected via APTw image-directed stereotactic biopsy. Cellularity, necrosis, proliferation and glioma WHO grade were analysed for all specimens and correlated with corresponding APTw signal intensities. Thirty-three specimens displayed grade-II pathology, 14 grade-III, 15 grade-IV, and eight specimens revealed only peritumoural oedema. Multiple glioma grades were found within a single lesion in six patients. APTw signal intensities of the biopsied sites and the maximum APTw values across all biopsied sites in each patient were significantly higher for high-grade versus low-grade specimens. APTw signal intensities were significantly positively correlated with cellularity (R = 0.757) and proliferation (R = 0.538). Multiple linear regression analysis showed that tumour cellularity and proliferation index were the best predictors of APTw signal intensities. APTw imaging identified tumour areas of higher cellularity and proliferation, allowing identification of high-grade regions within heterogeneous gliomas. APTw imaging can be readily translated for more widespread use and can assist diagnostic neurosurgical procedures by increasing the accuracy of tumour sampling in patients with infiltrating gliomas.


Analyzing animal movements using Brownian bridges.
By studying animal movements, researchers can gain insight into many of the ecological characteristics and processes important for understanding population-level dynamics. We developed a Brownian bridge movement model (BBMM) for estimating the expected movement path of an animal, using discrete location data obtained at relatively short time intervals. The BBMM is based on the properties of a conditional random walk between successive pairs of locations, dependent on the time between locations, the distance between locations, and the Brownian motion variance that is related to the animal's mobility. We describe two critical developments that enable widespread use of the BBMM, including a derivation of the model when location data are measured with error and a maximum likelihood approach for estimating the Brownian motion variance. After the BBMM is fitted to location data, an estimate of the animal's probability of occurrence can be generated for an area during the time of observation. To illustrate potential applications, we provide three examples: estimating animal home ranges, estimating animal migration routes, and evaluating the influence of fine-scale resource selection on animal movement patterns.


A comparison of the hourly output between the Ambu® Smart-Infuser™ Pain Pump and the On-Q Pump® with Select-A-Flow™ Variable Rate Controller with standard and overfill volumes.
The Ambu Smart-Infuser Pain Pump and the On-Q Pump with Select-a-Flow Variable Rate Controller are elastomeric devices with a flow regulator that controls the rate of infusion of a local anesthetic agent through a peripheral catheter. As a safety evaluation, we evaluated the infusion characteristics of these two devices when filled with manufacturer recommended standard volumes and when overfilled with a volume 50% in excess of that which is recommended. Nineteen disposable devices from the two manufacturers were used in this study. Nine were filled with 0.9% normal saline according to the respective manufacturers' recommendations (four Ambu pumps were filled with 650 ml and five On-Q pumps were filled with 550 ml) and 10 devices were 150% overfilled (five Ambu pumps were filled with 975 ml and five On-Q pumps were filled with 825 ml). All of the devices were set to infuse at 10 ml · h(-1) at room temperature (21°C) for 12 h. The fluid delivered during each 2-h period was measured using a graduated column. The On-Q pump (in the settings of normal fill and 150% overfill) delivered a significantly higher output per hour than the set rate during the first 8 h, while the Ambu pump delivered a value close to the set rate of 10 ml · h(-1). No significant difference in the hourly delivered output was noted for either device when comparing the normal fill to the 150% overfill groups. This investigation demonstrates that no change in the hourly output occurs with overfilling of these home infusion devices. However, as noted previously, the hourly output from the On-Q device is significantly higher than the set rate during the initial 8 h of infusion which could have potential clinical implications.


Pectin Methylesterases Modulate Plant Homogalacturonan Status in Defenses against the Aphid Myzus persicae.
Because they suck phloem sap and act as vectors for phytopathogenic viruses, aphids pose a threat to crop yields worldwide. Pectic homogalacturonan (HG) has been described as a defensive element for plants during infections with phytopathogens. However, its role during aphid infestation remains unexplored. Using immunofluorescence assays and biochemical approaches, the HG methylesterification status and associated modifying enzymes during the early stage of Arabidopsis (Arabidopsis thaliana) infestation with the green peach aphid (Myzus persicae) were analyzed. Additionally, the influence of pectin methylesterase (PME) activity on aphid settling and feeding behavior was evaluated by free choice assays and the Electrical Penetration Graph technique, respectively. Our results revealed that HG status and HG-modifying enzymes are significantly altered during the early stage of the plant-aphid interaction. Aphid infestation induced a significant increase in total PME activity and methanol emissions, concomitant with a decrease in the degree of HG methylesterification. Conversely, inhibition of PME activity led to a significant decrease in the settling and feeding preference of aphids. Furthermore, we demonstrate that the PME inhibitor AtPMEI13 has a defensive role during aphid infestation, since pmei13 mutants are significantly more susceptible to M. persicae in terms of settling preference, phloem access, and phloem sap drainage.


A preliminary investigation of the effect of selected electromagnetic field devices on healing of cannon bone osteotomies in horses.
The effect of electrical stimulation by means of selected electromagnetic field devices on healing of cannon bone osteotomies in horses was examined. The defects were created as 3 cm x 1 mm longitudinal osteotomies through the dorsal cortices of the mid-metacarpi/metatarsi of adult horses. This type of defect would asses bone healing in a situation similar to an acute, stable fracture of the cortex. Three electromagnetic devices of different design were tested in three different groups of horses. Healing was evaluated radiographically and histologically. Results showed that osteotomies treated with the electromagnetic devices healed similarly to untreated controls. Our conclusion is that the electromagnetic devices studied did not have a local effect on the repair process of an acute, stable, osseous defect.


A novel paraplegia model in awake behaving macaques.
Lower limb paralysis from spinal cord injury (SCI) or neurological disease carries a poor prognosis for recovery and remains a large societal burden. Neurophysiological and neuroprosthetic research have the potential to improve quality of life for these patients; however, the lack of an ethical and sustainable nonhuman primate model for paraplegia hinders their advancement. Therefore, our multidisciplinary team developed a way to induce temporary paralysis in awake behaving macaques by creating a fully implantable lumbar epidural catheter-subcutaneous port system that enables easy and reliable targeted drug delivery for sensorimotor blockade. During treadmill walking, aliquots of 1.5% lidocaine with 1:200,000 epinephrine were percutaneously injected into the ports of three rhesus macaques while surface electromyography (EMG) recorded muscle activity from their quadriceps and gastrocnemii. Diminution of EMG amplitude, loss of voluntary leg movement, and inability to bear weight were achieved for 60-90 min in each animal, followed by a complete recovery of function. The monkeys remained alert and cooperative during the paralysis trials and continued to take food rewards, and the ports remained functional after several months. This technique will enable recording from the cortex and/or spinal cord in awake behaving nonhuman primates during the onset, maintenance, and resolution of paraplegia for the first time, thus opening the door to answering basic neurophysiological questions about the acute neurological response to spinal cord injury and recovery. It will also negate the need to permanently injure otherwise high-value research animals for certain experimental paradigms aimed at developing and testing neural interface decoding algorithms for patients with lower extremity dysfunction.NEW & NOTEWORTHY A novel implantable lumbar epidural catheter-subcutaneous port system enables targeted drug delivery and induction of temporary paraplegia in awake, behaving nonhuman primates. Three macaques displayed loss of voluntary leg movement for 60-90 min after injection of lidocaine with epinephrine, followed by a full recovery. This technique for the first time will enable ethical live recording from the proximal central nervous system during the acute onset, maintenance, and resolution of paraplegia.


Hepatitis B core IgM antibody (anti-HBcIgM) among hepatitis B surface antigen (HBsAg) negative blood donors in Nigeria.
Transfusion associated Hepatitis B virus (TAHBV) continues to be a major problem despite mandatory screening for Hepatitis B surface Antigen (HBsAg). Presence of HBsAg is the common method for detecting hepatitis B infection. Unfortunately, this marker is not detected during the window period of the infection. Nigeria being a developing country cannot afford DNA testing of all collected units of blood which serve as the only possibility of achieving zero risk of transfusion associated HBV. Five different serological makers of hepatitis B virus (HBV) infection were therefore assessed to evaluate the reliability of using HBsAg marker alone in diagnosis of HBV infection among blood donors and to detect the serological evidence of the infection at the window period. This will preclude the possibility of transmitting hepatitis B through transfusion of Hepatitis B surface antigen (HBsAg) negative blood in Nigeria. Between July and August 2009, 92 blood donors were enrolled for the study. The prevalence of 5 different markers of Hepatitis B virus infection was detected using Enzyme Linked Immunosorbent Assay (ELISA). Demographic factors were assessed during the study. HBsAg and its antibody (anti-HBs) was detected in 18 (19.6%) and 14(15.2%) of the 92 blood donors respectively. Anti-HBc IgM was found in 12(13.0%) of the 92 blood donors while Hepatitis B envelope antigen (HBeAg) and its antibody (anti-HBe) were detected in 4(8.9%) and 12(26.7%) respectively from 45 donors sampled. HBeAg is a marker of high infectivity and appears after HBsAg. At least one serological marker was detected in 30(32.6%) of the blood donors. Five (5.4%) of the 92 donors had anti-HBc IgM as the only serological evidence of hepatitis B virus infection. The result of this study shows that five donors have anti-HBcIgM as the only serological evidence of HBV infection. Inclusion of anti-HBcIgM in routine screening of blood donors in Nigeria should be encouraged. This is the first study to assess anti-HBcIgM in the country.


Premenstrual dysphoric disorder: burden of illness and treatment update.
Five percent of menstruating women have severe premenstrual symptoms and impairment of functioning defined as premenstrual dysphoric disorder (PMDD). Clinically significant premenstrual symptoms occur in at least an additional 20% of menstruating women. The diagnosis of PMDD should be confirmed by prospective symptom charting over 2 menstrual cycles to confirm the timing of the symptoms and to rule out other diagnoses. The burden of illness of PMDD includes disruption of parenting and partner relationships and decreased productivity in work roles. In addition, women with PMDD have increased use of health care services such as clinician visits and increased use of prescription medications and over-the-counter preparations. The etiology of PMDD is multifactorial. In particular, dysregulation of the serotonin and allopregnanolone systems is implicated. Several effective treatment options exist, including serotonergic antidepressant medications and an oral contraceptive that contains ethinyl estradiol and drosperinone. In addition, other hormones that suppress ovulation, anxiolytics, cognitive therapy, chasteberry and calcium may be helpful.


Estimated liver fibrosis and its impact on all-cause mortality of HCV-monoinfected and HCV/HIV-coinfected drug users.
Progression of liver fibrosis is associated with the risk of cirrhosis and end-stage liver disease. We aimed to evaluate fibrosis of the liver using three non-invasive indexes (FIB-4, Forns, and Pohl score) and its association with mortality of HCV-monoinfected and HCV/HIV-coinfected drug users. longitudinal study in patients admitted to substance abuse treatment between 1994 and 2006. Socio-demographic data, drug use characteristics, blood samples for laboratory tests, and serology for HIV and hepatitis C virus infections were collected at admission. Patients were followed-up until December 2006 and mortality was ascertained through hospital charts and death certificates. Four hundred and ninety-seven patients were included (83.1% men); median age at admission was 31 years (IQR: 27-35). The main drugs of abuse were opiates (89.5%) and cocaine (8.3%). Thirty-two percent of patients reported daily alcohol consumption. The estimated prevalence of advanced liver fibrosis (ALF) was higher among HCV/HIV-coinfected patients (9.2% to 17.3% depending on the index analyzed) than among the HCV-monoinfected patients (3% to 3.5%). Odds ratio (OR) for ALF were 3.3 to 6.0 times higher in coinfected patients as compared to the HCV-monoinfected. After a median follow-up time of 7.7 years (IQR: 4.1-9.9 years), almost 20% of patients had died. The estimated ALF at admission was associated with an increased risk of death (RR 1.85 to 3.89 depending on the index). Among those with ALF, mortality rates were similar in HCV-monoinfected and HCV/HIV-coinfected patients, as determined by the FIB-4 and Forns indexes. Estimation of liver fibrosis using serum markers may help with clinical decisions to facilitate access to treatment of chronic hepatitis C in this population.


Characterization of Blood-Based Molecular Profiling in Pancreatic Adenocarcinoma.
Background: Molecular profiling is being explored in pancreatic adenocarcinoma (PDAC) as a tool to assist with early detection, prognosis, and patient selection in targeted therapy clinical trials. Due to the challenges and risks of traditional tissue biopsies in pancreatic adenocarcinoma, the utility of blood-based molecular profiling is now being explored more broadly. However, given its novelty, what value blood-based molecular profiling may provide to oncologists caring for individuals with PDAC remains unknown. Herein, we characterize the mutational landscape of metastatic PDAC using blood-based circulating tumor DNA (ctDNA) collected in patients with refractory, metastatic PDAC who were referred to an oncology drug development unit in Denver, Colorado, between August 2014 and May 2019. Methods: We retrospectively analyzed results of blood-based molecular profiling that was performed on 77 consecutive patients with metastatic PDAC who underwent Guardant-360 testing for whom results were available. Results: In our data set, 55% of patients (41/77) were men, median (SD) age was 66 (9.3) years (range, 44-83). Of 77 patients, 34 (44%) had 1 or more somatic alterations. Variants reported as being of unknown significance were not included in the analyses. The total number of alterations were 119 (nonunique) and 96 (unique). The median number of alterations per patient was 3 and the median mutant allele frequency was 0.5%. TP53 was the most commonly altered gene (29 unique alterations), followed by KRAS (27 unique alterations). Of the patients with any alteration, 34% had 1 or more actionable alterations that could be potentially targeted in a clinical trial. Conclusions: Detection of genomic alterations in ctDNA from patients with metastatic PDAC is feasible and reveals a wide range of genomic alterations, the actionability of which is being explored in clinical trials. Further investigation is needed to determine the extent to which blood-based molecular profiling can provide clinical utility in helping to select patients into clinical trials and determine its impact on survival.


Conservative treatment of bisphosphonate-related osteonecrosis of the jaw in multiple myeloma patients.
The use of intravenous bisphosphonates (pamidronate or zoledronic acid) is the cornerstone for the management of multiple myeloma-(MM-) related bone disease. However, osteonecrosis of the jaw (ONJ) is a rare, but sometimes difficult to manage, adverse effect of bisphosphonates therapy. A retrospective review of all MM patients who were treated with bisphosphonates in our department, from 2003 to 2013, and developed ONJ was performed. According to inclusion criteria, 38 patients were studied. All these patients were treated as conservatively as possible according to the American Association of Oral and Maxillofacial Surgeons criteria. Patients were managed with observation, oral antibacterial mouth rinse with chlorhexidine, oral antibiotics, pain control with analgesics, nonsurgical sequestrectomy with or without simultaneous administration of antibiotics, or major surgery with or without antibiotics. Healing of the lesions was achieved in 23 (60%) patients who were treated with conservative measures; the median time to healing was 12 months (95% CI: 4-21). The number of bisphosphonates infusions influenced the time to healing: the median time to healing for patients who received <16 infusions was 7 months and for those with >16 infusions was it 14 months (P = 0.017). We conclude that a primarily nonsurgical approach appears to be a successful management strategy for bisphosphonate-related ONJ.


Long-term persistence of cellular hyporesponsiveness to filarial antigens after clearance of microfilaremia.
The persistence of parasite-specific cellular hyporesponsiveness after clearance of blood microfilariae (mf) was studied in 18 individuals who had been treated with a single dose of ivermectin, diethylcarbamazine, or a combination 2-3 years previously and who had initially cleared their parasitemia. At recruitment into the present study, 50% were again mf+ and 50% remained mf-. There were no significant differences between the mf+ and mf- groups in the amount of interferon-gamma (IFN-gamma) produced by peripheral blood mononuclear cells in response to adult or microfilarial antigens, although IFN-gamma production in response to purified protein derivative was greater in the mf+ group (geometric mean [gm] = 3,791 pg/ml; P = 0.02) than in the mf- group (gm = 600 pg/ml). These data suggest that although microfilaremic individuals may temporarily regain the ability to produce IFN-gamma to parasite antigens post-treatment, they subsequently revert to a state of hyporesponsiveness to mf-containing antigens that appears to be independent of the recurrence of microfilaremia and the response to nonparasite antigens.


Preservation of pulsatile luteinizing hormone release during postpartum lactational amenorrhea.
To evaluate the pulsatile mode of immunoactive LH release during physiological lactational amenorrhea, we withdrew blood samples at 10-min intervals for 24 h from breastfeeding women (n = 9) at both 3 weeks and 3 months postpartum. Nonlactating women (n = 7) were sampled similarly in the early follicular phase of the normal menstrual cycle. Objective LH pulse analysis revealed that the mean frequencies of pulsatile LH release were similar at both times postpartum and in menstruating young women. By 3 months postpartum, mean serum PRL concentrations had declined 50%, and serum LH peak areas doubled. In contrast, LH interpulse interval, peak duration, and maximal, incremental, and fractional LH pulse amplitude did not change significantly. When deconvolution analysis was used to assess pituitary responses to two pulses of exogenous GnRH at 3 months (vs. 3 weeks) postpartum, we found significant increases in maximal LH secretory rates and the total mass of LH secreted. There was no change in the duration or timing of the evoked LH secretory burst and/or the estimated half-life of endogenous LH. In summary, during lactational amenorrhea, pulsatile LH release occurs at a mean frequency no different from that in the normal early follicular phase. As hyperprolactinemia wanes, there is increased pituitary responsiveness to exogenously administered GnRH and a doubling of spontaneous serum LH concentration peak areas. Such amplitude changes are consistent with the hypothesis of increased endogenous GnRH drive (e.g. augmented GnRH secretion per burst and/or increased pituitary responsiveness to available GnRH) during recovery of the postpartum hypothalamopituitary-ovarian axis.


Evaluation of bond strength of soft relining materials to denture base polymers.
To evaluate the initial bonding properties of recently and previously introduced soft relining materials to denture base polymers with different polymerization techniques and different water content. The initial tensile bond strength of 10 soft liners (Mollosil Plus, Dentusil, Ufi gel Soft, GC Reline Soft, Silagum Comfort, Vertex Soft, Astron Soft, Molloplast B, Flexacryl Soft, Triad Resiline) to three denture base polymers (Paladon 65, Palapress Vario, Ivocap Plus) were assessed with a modified method. Paladon 65 specimens immersed in water for 3 months were also used to test the effect of water content of denture base polymer on bond strength results. After testing, a visual examination of the fracture surfaces and a SEM investigation of the interface structure were performed. Tensile strength of each soft liner material was also tested. Data were analyzed statistically by two-way ANOVA (alpha = 0.05). Significant differences were found among tensile bond strength results (P < 0.05). Vinyl poly(organosiloxane) soft liners (Mollosil Plus, Dentusil, Ufi gel Soft, GC Reline Soft, Silagum Comfort) and a plasticized PMMA soft liner (Vertex Soft) gave statistically similar bond strength results for different denture base polymers (P>0.05). For the other materials used (Astron Soft, Molloplast B, Flexacryl Soft, Triad Resiline), different denture base polymers caused significantly different results (P < 0.05). Poly(organosiloxane) based materials gave slightly higher bond strength results with water immersed specimens than with the dry specimens. A wide variety of newly formulated soft liners used in this study gave comparable or better bond strength results compared to Molloplast B.


Incidence of bone metastases and skeletal-related events in breast cancer patients: a population-based cohort study in Denmark.
Breast cancer (BrCa) is the most commonly diagnosed cancer among women in the industrialized world. More than half of women presenting with metastatic BrCa develop bone metastases. Bone metastases increase the risk of skeletal-related events (SREs), defined as pathological fractures, spinal cord compression, bone pain requiring palliative radiotherapy, and orthopaedic surgery. Both bone metastases and SREs are associated with unfavorable prognosis and greatly affect quality of life. Few epidemiological data exist on SREs after primary diagnosis of BrCa and subsequent bone metastasis. We therefore estimated the incidence of bone metastases and SREs in newly-diagnosed BrCa patients in Denmark from 1999 through 2007. We estimated the overall and annual incidence of bone metastases and SREs in newly-diagnosed breast cancer patients in Denmark from January 1, 1999 to December 31, 2007 using the Danish National Patient Registry (DNPR), which covers all Danish hospitals. We estimated the cumulative incidence of bone metastases and SREs and associated 95% confidence intervals (CI) using the Kaplan-Meier method. Of the 35,912 BrCa patients, 178 (0.5%) presented with bone metastases at the time of primary breast cancer diagnosis, and of these, 77 (43.2%) developed an SRE during follow up. A total of 1,272 of 35,690 (3.6%) BrCa patients without bone metastases at diagnosis developed bone metastases during a median follow-up time of 3.4 years. Among these patients, 590 (46.4%) subsequently developed an SRE during a median follow-up time of 0.7 years. Incidence rates of bone metastases were highest the first year after the primary BrCa diagnosis, particularly among patients with advanced BrCa at diagnosis. Similarly, incidence rates of a first SRE was highest the first year after first diagnosis of a bone metastasis. The high incidence of SREs following the first year after first diagnosis of a bone metastasis underscores the need for early BrCa detection and research on effective treatments to delay the onset of SREs.


Intrathoracic gossypiboma.
Gossypiboma refers to retained sponge or swab in any body cavity after surgery. Although it is a rare occurence, it can lead to various complications which include adhesions, abscess formation and subsequent infections. Gossypiboma occurs as a result of not using radio-opaque sponges, poorly performed sponge counts, inadequate wound explorations on suspicion and misread intraoperative radiographs. Therefore, this event can be avoided if strict preventive measures are taken. Moreover, further complications can be avoided following the correct and early diagnosis of gossypiboma. Gossypiboma is an important topic as it carries great medicolegal consequences for the surgeon. We have presented three cases of intrathoracic gossipiboma following previous cardiothoracic surgeries. They presented years after their surgeries, with features varying from patient to patient, ranging from cough and fever to no sypmtoms at all. CT scan only showed a mass lesion in all cases, therefore we proceeded for CT-guided biopsy which was also found to be inconclusive. It was only after entering the thoracic cavity via video-assisted thoracoscopy/thoracotomy that the diagnosis was made and sponges were taken out successfully. All our cases recovered with no further complications.


Climate change and marine life.
A Marine Climate Impacts Workshop was held from 29 April to 3 May 2012 at the US National Center of Ecological Analysis and Synthesis in Santa Barbara. This workshop was the culmination of a series of six meetings over the past three years, which had brought together 25 experts in climate change ecology, analysis of large datasets, palaeontology, marine ecology and physical oceanography. Aims of these workshops were to produce a global synthesis of climate impacts on marine biota, to identify sensitive habitats and taxa, to inform the current Intergovernmental Panel on Climate Change (IPCC) process, and to strengthen research into ecological impacts of climate change.


The effects of continuous positive airway pressure therapy withdrawal on cardiac repolarization: data from a randomized controlled trial.
The preliminary evidence supports an association between obstructive sleep apnoea (OSA), disturbed cardiac repolarization, and consequent cardiac dysrhythmias. The aim of the current trial was to assess the effects of continuous positive airway pressure (CPAP) therapy withdrawal on the measures of cardiac repolarization in patients with OSA. Forty-one OSA patients established on CPAP treatment were randomized to either CPAP withdrawal (subtherapeutic CPAP) or continue therapeutic CPAP for 2 weeks. Polysomnography was performed, and indices of cardiac repolarization (QT(c), TpTe(c) intervals) and dispersion of repolarization (TpTe/QT ratio) were derived from 12-lead electrocardiography (ECG) at baseline and 2 weeks. Continuous positive airway pressure withdrawal led to a recurrence of OSA. Compared with therapeutic CPAP, subtherapeutic CPAP for 2 weeks was associated with a significant increase in the length of the QT(c) and TpTe(c) intervals (mean difference between groups 21.4 ms, 95% CI 11.3-1.6 ms, P < 0.001 and 14.4 ms, 95% CI 7.2-21.5 ms, P < 0.001, respectively) and in the TpTe/QT ratio (mean difference between groups 0.02, 95% CI 0.00-0.03, P = 0.020). There was a statistically significant correlation between the change in apnoea/hypopnoea index (AHI) from baseline, and both the change in the QT(c) interval and the TpTe(c) interval (r = 0.60, 95% CI 0.36-0.77, P < 0.001 and r = 0.45, 95% CI 0.17-0.67, P = 0.003, n = 41, respectively). Continuous positive airway pressure withdrawal is associated with the prolongation of the QT(c) and TpTe(c) intervals and TpTe/QT ratio, which may provide a possible mechanistic link between OSA, cardiac dysrhythmias, and thus sudden cardiac death.


Point of care and oral fluid hepatitis B testing in remote Indigenous communities of northern Australia.
Many Indigenous Australians in northern Australia living with chronic hepatitis B are unaware of their diagnosis due to low screening rates. A venous blood point of care test (POCT) or oral fluid laboratory test could improve testing uptake in this region. The purpose of this study was to assess the field performance of venous blood POCT and laboratory performance of an oral fluid hepatitis B surface antigen (HBsAg) test in Indigenous individuals living in remote northern Australian communities. The study was conducted with four very remote communities in the tropical north of Australia's Northern Territory. Community research workers collected venous blood and oral fluid samples. We performed the venous blood POCT for HBsAg in the field. We assessed the venous blood and oral fluid specimens for the presence of HBsAg using standard laboratory assays. We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the POCT and oral fluid test, using serum laboratory detection of HBsAg as the gold standard. From 215 enrolled participants, 155 POCT and 197 oral fluid tests had corresponding serum HBsAg results. The POCT had a sensitivity of 91.7% and specificity of 100%. Based on a population prevalence of 6%, the PPV was 100% and NPV was 99.5%. The oral fluid test had a sensitivity of 56.8%, specificity of 98.1%, PPV of 97.3% and NPV of 65.9%. The venous blood POCT has excellent test characteristics and could be used to identify individuals with chronic HBV infection in high prevalence communities with limited access to health care. Oral fluid performance was suboptimal.


Analysis of factors affecting successful discharge in patients undergoing lumbar discectomy for sciatica performed on a day-surgical basis: a prospective study of sequential cohorts.
This is a prospective study of sequential cohorts of patients undergoing elective lumbar discectomy scheduled on a day-surgical basis between April 1995 and October 1998, representing all such cases from the author's practice during the review period. Preliminary review of the first 38 cases was undertaken 18 months after this surgical program was initiated and revealed an 18% rate of failure in achieving same-day discharge. Subsequent review of the balance of 92 additional cases revealed this failure rate was decreased to only 2% through a combination of appropriate perioperative patient education and the institution of a low-dose perioperative narcotic routine.


Catalytic asymmetric propargyl- and allylboration of hydrazonoesters: a metal-free approach to sterically encumbered chiral α-amino acid derivatives.
A new asymmetric catalytic propargyl- and allylboration of hydrazonoesters is reported. The reactions utilize allenyl- and allylboronic acids in the presence of the inexpensive parent BINOL catalyst. The reactions can be performed under mild conditions (0 °C) without any metal catalyst or other additives affording sterically encumbered chiral α-amino acids. This is the first metal-free method for the asymmetric propargyl- and allylboration of hydrazonoesters.


Viruses, neurodevelopmental disorder and childhood psychosis.
Four cases are described of prepubertal boys in whom the convergence of neurodevelopmental disorder, viral infection and psychosis seemed more than coincidental. Review of the literature highlights the possibility that viral infection of the central nervous system may play a contributory role in childhood psychosis. Whilst it is essential to avoid a reductionist stance when investigating these difficult conditions, the emergence of potent anti-viral treatments and sophisticated methods of identifying the presence of viral infection should encourage us to consider more carefully the relevance of viruses in childhood psychosis.


Obligatory role of gamma interferon for host survival in a murine model of infection with Burkholderia pseudomallei.
Burkholderia pseudomallei, the causative agent of melioidosis, is a gram-negative bacterium capable of causing either acute lethal sepsis or chronic but eventually fatal disease in infected individuals. However, despite the clinical importance of this infection in areas where it is endemic, there is essentially no information on the mechanisms of protective immunity to the bacterium. We describe here a murine model of either acute or chronic infection with B. pseudomallei in Taylor Outbred (TO) mice which mimics many features of the human pathology. Intraperitoneal infection of TO mice at doses of >10(6) CFU resulted in acute septic shock and death within 2 days. In contrast, at lower doses mice were able to clear the inoculum from the liver and spleen over a 3- to 4-week period, but persistence of the organism at other sites resulted in a chronic infection of between 2 and 16 months duration which was eventually lethal in all of the animals tested. Resistance to acute infection with B. pseudomallei was absolutely dependent upon the production of gamma interferon (IFN-gamma) in vivo. Administration of neutralizing monoclonal antibody against IFN-gamma lowered the 50% lethal dose from >5 x 10(5) to ca. 2 CFU and was associated with 8,500- and 4,400-fold increases in the bacterial burdens in the liver and spleen, respectively, together with extensive destruction of lymphoid architecture in the latter organ within 48 h. Neutralization of either tumor necrosis factor alpha or interleukin-12 but not granulocyte-macrophage colony-stimulating factor, also increased susceptibility to infection in vivo. Together, these results provide the first evidence of a host protective mechanism against B. pseudomallei. The rapid production of IFN-gamma within the first day of infection determines whether the infection proceeds to an acute lethal outcome or becomes chronic.


Features and machine learning classification of connected speech samples from patients with autopsy proven Alzheimer's disease with and without additional vascular pathology.
Mixed vascular and Alzheimer-type dementia and pure Alzheimer's disease are both associated with changes in spoken language. These changes have, however, seldom been subjected to systematic comparison. In the present study, we analyzed language samples obtained during the course of a longitudinal clinical study from patients in whom one or other pathology was verified at post mortem. The aims of the study were twofold: first, to confirm the presence of differences in language produced by members of the two groups using quantitative methods of evaluation; and secondly to ascertain the most informative sources of variation between the groups. We adopted a computational approach to evaluate digitized transcripts of connected speech along a range of language-related dimensions. We then used machine learning text classification to assign the samples to one of the two pathological groups on the basis of these features. The classifiers' accuracies were tested using simple lexical features, syntactic features, and more complex statistical and information theory characteristics. Maximum accuracy was achieved when word occurrences and frequencies alone were used. Features based on syntactic and lexical complexity yielded lower discrimination scores, but all combinations of features showed significantly better performance than a baseline condition in which every transcript was assigned randomly to one of the two classes. The classification results illustrate the word content specific differences in the spoken language of the two groups. In addition, those with mixed pathology were found to exhibit a marked reduction in lexical variation and complexity compared to their pure AD counterparts.


Evidence of H- and L-chains have co-operative roles in the iron-uptake mechanism of human ferritin.
The ability to incorporate iron in vitro was studied in homopolymers of human ferritin L-chain, human ferritin H-chain and its variants and in homopolymer mixtures. The H-chain variants carried amino acid substitutions in the ferroxidase centre and/or in carboxy residues on the cavity surface. Iron incorporation was examined by gel electrophoresis of the reaction products by staining for iron and protein. It was found that inactivation of the ferroxidase centre combined with the substitution of four carboxy groups on the cavity abolished the ability of H-chain ferritin to incorporate iron. Competition experiments with limited amounts of iron showed that, at neutral pH, L-chain ferritin is more efficient in forming iron cores than the H-chain variants altered at the ferroxidase activity or in the cavity. Competition experiments at pH 5.5 demonstrated that L-chain apoferritin is able to incorporate iron only when in the presence of H-chain variants with ferroxidase activity. The results indicate that L-chain apoferritin has a higher capacity than the H-chain apoferritin to induce iron-core nucleation, whereas H-chain ferritin is superior in promoting Fe(II) oxidation. The finding of cooperative roles of the H- and L-chains in ferritin iron uptake provides a clue to understanding the biological function of isoferritins.


Using pay-for-performance to introduce changes in primary healthcare centres in Spain: first year results.
The article describes evaluation of the first year of implementation of a process-management project and a quality-improvement programme linked to economic incentives carried out at CAPSE (Consortium of Primary Healthcare of Eixample, Barcelona City, Catalonia, Spain). To evaluate the changes and to describe the experience of a variable payment scheme linked to quality objectives in two primary healthcare centres in Spain. Data from a variable payment scheme for professionals, where the variable payment consisted of three parts, were analysed. The three areas included in the variable payment were the results of management by objectives, performance evaluation, and participation in a quality-improvement programme. Parallel to this the actions of continuous quality improvement that had been proposed during 2006 were described and evaluated. Participation among personnel in the quality-improvement programme was high, including 96% of doctors and 100% of nurses. Seventy-two improvement actions were proposed and accepted; 56% of the improvement actions took place within the established period of time, 18% did not finish within the deadline and 26% could not be accomplished for various reasons. The following areas needing improving were detected: process-management training for healthcare professionals, process orientation to the patients, the need to develop a communication plan, the selection of process and outcomes indicators, appropriate use of information systems and the time spent in implementation of the quality-improvement programme. Our preliminary results are encouraging. More studies and comparison of similar experiences are required before widespread use of this system can be recommended.


Discovery and analysis of the first endogenous lentivirus.
The lentiviruses are associated with a wide range of chronic diseases in mammals. These include immunodeficiencies (such as HIV/AIDS in humans), malignancies, and lymphatic and neurological disorders in primates, felids, and a variety of wild and domesticated ungulates. Evolutionary analyses of the genomic sequences of modern-day lentiviruses have suggested a relatively recent date for their emergence, but the failure to identify any endogenous, vertically transmitted examples has meant that their longer term evolutionary history and origin remain unknown. Here we report the discovery and characterization of retroviral sequences belonging to a new lentiviral subgroup from the European rabbit (Oryctolagus cuniculus). These viruses, the first endogenous examples described, are >7 million years old and thus provide the first evidence for an ancient origin of the lentiviruses. Despite being ancient, this subgroup contains many of the features found in present-day lentiviruses, such as the presence of tat and rev genes, thus also indicating an ancient origin for the complex regulation of lentivirus gene expression. Although the virus we describe is defective, reconstruction of an infectious progenitor could provide novel insights into lentivirus biology and host interactions.


Ant-based computing.
A biologically and physically plausible model for ants and pheromones is proposed. It is argued that the mechanisms described in this model are sufficiently powerful to reproduce the necessary components of universal computation. The claim is supported by illustrating the feasibility of designing arbitrary logic circuits, showing that the interactions of ants and pheromones lead to the expected behavior, and presenting computer simulation results to verify the circuits' working. The conclusions of this study can be taken as evidence that coherent deterministic and centralized computation can emerge from the collective behavior of simple distributed Markovian processes such as those followed by biological ants, but also, more generally, by artificial agents with limited computational and communication abilities.


Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri sp. nov., isolated from the biofilm of the methanol-fed denitrification system treating the seawater at the Montreal Biodome.
Two bacterial strains, designated JAM1(T) and JAM7(T), were isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome, Canada. They were affiliated within the genus Methylophaga of the Gammaproteobacteria by analysis of the 16S rRNA gene sequences. Strain JAM1(T) had the capacity to grow under denitrifying conditions by reducing nitrate into nitrite which is unique among the species of the genus Methylophaga. Major fatty acids were C16:1ω7c or ω6c, C16:0 and C18:1ω7c or ω6c. The major ubiquinone was Q8. Both strains required vitamin B12 and Na(+) ions for growth. The genomes of strains JAM1(T) and JAM7(T) have been completely sequenced and showed a DNA G+C content of 44.7 mol% and 47.8 mol%, respectively. Growth occurred at pH 6-11 and at 0.5-8% NaCl. Both genomes contained predicted ORFs encoding the key enzymes of the ribulose monophosphate pathway. Also, operons encoding two nitrate reductases (Nar), two nitric oxide reductases (Nor), one nitrous oxide reductase (Nos) and one truncated nitrite reductase (NirK) were clustered in a 67 kb chromosomal region in strain JAM1(T). No such operons were found in strain JAM7(T). These results supported the affiliation of the two strains as novel species within the genus Methylophaga. The names Methylophaga nitratireducenticrescens sp. nov. for type strain JAM1(T) (=DSM 25689(T)=ATCC BAA-2433(T)) and Methylophaga frappieri sp. nov. for type strain JAM7(T) (=DSM 25690(T)=ATCC BAA-2434(T)) are proposed.


Climate-driven deoxygenation elevates fishing vulnerability for the ocean's widest ranging shark.
Climate-driven expansions of ocean hypoxic zones are predicted to concentrate pelagic fish in oxygenated surface layers, but how expanding hypoxia and fisheries will interact to affect threatened pelagic sharks remains unknown. Here, analysis of satellite-tracked blue sharks and environmental modelling in the eastern tropical Atlantic oxygen minimum zone (OMZ) shows shark maximum dive depths decreased due to combined effects of decreasing dissolved oxygen (DO) at depth, high sea surface temperatures, and increased surface-layer net primary production. Multiple factors associated with climate-driven deoxygenation contributed to blue shark vertical habitat compression, potentially increasing their vulnerability to surface fisheries. Greater intensity of longline fishing effort occurred above the OMZ compared to adjacent waters. Higher shark catches were associated with strong DO gradients, suggesting potential aggregation along suitable DO gradients contributed to habitat compression and higher fishing-induced mortality. Fisheries controls to counteract deoxygenation effects on shark catches will be needed as oceans continue warming.


PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects. The relational schemas used to build PlasmoDB [Genomics Unified Schema (GUS) and RNA Abundance Database (RAD)] employ a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically based queries of the database. A version of the database is also available on CD-ROM (Plasmodium GenePlot), facilitating access to the data in situations where Internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community.


The ubiquitin carboxyl hydrolase BAP1 forms a ternary complex with YY1 and HCF-1 and is a critical regulator of gene expression.
The candidate tumor suppressor BAP1 is a deubiquitinating enzyme (DUB) involved in the regulation of cell proliferation, although the molecular mechanisms governing its function remain poorly defined. BAP1 was recently shown to interact with and deubiquitinate the transcriptional regulator host cell factor 1 (HCF-1). Here we show that BAP1 assembles multiprotein complexes containing numerous transcription factors and cofactors, including HCF-1 and the transcription factor Yin Yang 1 (YY1). Through its coiled-coil motif, BAP1 directly interacts with the zinc fingers of YY1. Moreover, HCF-1 interacts with the middle region of YY1 encompassing the glycine-lysine-rich domain and is essential for the formation of a ternary complex with YY1 and BAP1 in vivo. BAP1 activates transcription in an enzymatic-activity-dependent manner and regulates the expression of a variety of genes involved in numerous cellular processes. We further show that BAP1 and HCF-1 are recruited by YY1 to the promoter of the cox7c gene, which encodes a mitochondrial protein used here as a model of BAP1-activated gene expression. Our findings (i) establish a direct link between BAP1 and the transcriptional control of genes regulating cell growth and proliferation and (ii) shed light on a novel mechanism of transcription regulation involving ubiquitin signaling.


Physical activity and sedentary behaviour in daily life: A comparative analysis of the Global Physical Activity Questionnaire (GPAQ) and the SenseWear armband.
Reduction of sedentary time and an increase in physical activity offer potential to improve public health. However, quantifying physical activity behaviour under real world conditions is a major challenge and no standard of good practice is available. Our aim was to compare the results of physical activity and sedentary behaviour obtained with a self-reported instrument (Global Physical Activity Questionnaire (GPAQ)) and a wearable sensor (SenseWear) in a repeated measures study design. Healthy adults (41 in Antwerp, 41 in Barcelona and 40 in London) wore the SenseWear armband for seven consecutive days and completed the GPAQ on the final day. This was repeated three times. We used the Wilcoxon signed rank sum test, Spearman correlation coefficients, mixed effects regression models and Bland-Altman plots to study agreement between both methods. Mixed models were used to assess the effect of personal characteristics on the absolute and relative difference between estimates obtained with the GPAQ and SenseWear. Moderate to vigorous energy expenditure and duration derived from the GPAQ were significantly lower (p<0.05) compared to the SenseWear, yet these variables showed significant correlations ranging from 0.45 to 0.64. Estimates of vigorous-intensity physical activity in particular showed high similarity (r>0.59). Results for sedentary behaviour did not differ, yet were poorly correlated (r<0.25). The differences between all variables were reproducible across repeated measurements. In addition, we observed a relationship between these differences and BMI, body fat and physical activity domain. Due to the lack of a standardized protocol, results from different studies measuring physical activity and sedentary behaviour are difficult to compare. Therefore, we suggested an easy-to-implement approach for future studies adding the GPAQ to the wearable of choice as a basis for comparisons.


Cryopreservation, culture, and transplantation of human fetal mesencephalic tissue into monkeys.
Studies in animals suggest that fetal neural grafts might restore lost neurological function in Parkinson's disease. In monkeys, such grafts survive for many months and reverse signs of parkinsonism, without attendant graft rejection. The successful and reliable application of a similar transplantation procedure to human patients, however, will require neural tissue obtained from human fetal cadavers, with demonstrated cellular identity, viability, and biological safety. In this report, human fetal neural tissue was successfully grafted into the brains of monkeys. Neural tissue was collected from human fetal cadavers after 9 to 12 weeks of gestation and cryopreserved in liquid nitrogen. Viability after up to 2 months of storage was demonstrated by cell culture and by transplantation into monkeys. Cryopreservation and storage of human fetal neural tissue would allow formation of a tissue bank. The stored cells could then be specifically tested to assure their cellular identity, viability, and bacteriological and virological safety before clinical use. The capacity to collect and maintain viable human fetal neural tissue would also facilitate research efforts to understand the development and function of the human brain and provide opportunities to study neurological diseases.


Classification of structural MRI images in Alzheimer's disease from the perspective of ill-posed problems.
Machine learning neuroimaging researchers have often relied on regularization techniques when classifying MRI images. Although these were originally introduced to deal with "ill-posed" problems it is rare to find studies that evaluate the ill-posedness of MRI image classification problems. In addition, to avoid the effects of the "curse of dimensionality" very often dimension reduction is applied to the data. Baseline structural MRI data from cognitively normal and Alzheimer's disease (AD) patients from the AD Neuroimaging Initiative database were used in this study. We evaluated here the ill-posedness of this classification problem across different dimensions and sample sizes and its relationship to the performance of regularized logistic regression (RLR), linear support vector machine (SVM) and linear regression classifier (LRC). In addition, these methods were compared with their principal components space counterparts. In voxel space the prediction performance of all methods increased as sample sizes increased. They were not only relatively robust to the increase of dimension, but they often showed improvements in accuracy. We linked this behavior to improvements in conditioning of the linear kernels matrices. In general the RLR and SVM performed similarly. Surprisingly, the LRC was often very competitive when the linear kernel matrices were best conditioned. Finally, when comparing these methods in voxel and principal component spaces, we did not find large differences in prediction performance. We analyzed the problem of classifying AD MRI images from the perspective of linear ill-posed problems. We demonstrate empirically the impact of the linear kernel matrix conditioning on different classifiers' performance. This dependence is characterized across sample sizes and dimensions. In this context we also show that increased dimensionality does not necessarily degrade performance of machine learning methods. In general, this depends on the nature of the problem and the type of machine learning method.


Clinical roundtable monograph: Emerging treatment options for TKI-resistant chronic myelogenous leukemia.
The development of tyrosine kinase inhibitors (TKIs) that inhibit signaling of the constitutive BCR-ABL protein revolutionized the treatment of chronic myelogenous leukemia (CML). These agents have dramatically changed the treatment landscape for CML, shifting the use of allogeneic stem cell transplantation to selected patients in the salvage setting. Four BCR-ABL TKIs are now commercially available for the treatment of CML: the first-generation TKI imatinib, and the second-generation TKIs dasatinib, nilotinib, and bosutinib. Continuous treatment with these agents induces durable responses in a high proportion of patients with chronic-phase CML. Research is focused on identifying which patients can discontinue therapy without a recurrence of disease. For the group of patients with resistance to TKIs, multiple alternative therapies are being evaluated. The third-generation TKI ponatinib is a BCR-ABL inhibitor that has demonstrated significant activity, including in patients with the TKI resistance mutation T315I. The homoharringtonine derivative omacetaxine mepesuccinate, which inhibits protein synthesis, has also demonstrated clinical activity in CML, including in patients with TKI resistance due to T315I and in patients who have TKI resistance despite no evidence of ABL mutations. It is essential that clinicians implement these new agents with care and change therapies only when appropriate in order to preserve as many options as possible for future use if needed.


Pore architecture of TRIC channels and insights into their gating mechanism.
Intracellular Ca2+ signalling processes are fundamental to muscle contraction, neurotransmitter release, cell growth and apoptosis. Release of Ca2+ from the intracellular stores is supported by a series of ion channels in sarcoplasmic or endoplasmic reticulum (SR/ER). Among them, two isoforms of the trimeric intracellular cation (TRIC) channel family, named TRIC-A and TRIC-B, modulate the release of Ca2+ through the ryanodine receptor or inositol triphosphate receptor, and maintain the homeostasis of ions within SR/ER lumen. Genetic ablations or mutations of TRIC channels are associated with hypertension, heart disease, respiratory defects and brittle bone disease. Despite the pivotal function of TRIC channels in Ca2+ signalling, their pore architectures and gating mechanisms remain unknown. Here we present the structures of TRIC-B1 and TRIC-B2 channels from Caenorhabditis elegans in complex with endogenous phosphatidylinositol-4,5-biphosphate (PtdIns(4,5)P2, also known as PIP2) lipid molecules. The TRIC-B1/B2 proteins and PIP2 assemble into a symmetrical homotrimeric complex. Each monomer contains an hourglass-shaped hydrophilic pore contained within a seven-transmembrane-helix domain. Structural and functional analyses unravel the central role of PIP2 in stabilizing the cytoplasmic gate of the ion permeation pathway and reveal a marked Ca2+-induced conformational change in a cytoplasmic loop above the gate. A mechanistic model has been proposed to account for the complex gating mechanism of TRIC channels.


Black and gold howler monkeys (Alouatta caraya) as sentinels of ecosystem health: patterns of zoonotic protozoa infection relative to degree of human-primate contact.
Exponential expansion of human populations and human activities within primate habitats has resulted in high potential for pathogen exchange creating challenges for biodiversity conservation and global health. Under such conditions, resilient habitat generalists such as black and gold howler monkeys (Alouatta caraya) may act as effective sentinels to overall ecosystem health and alert us to impending epidemics in the human population. To better understand this potential, we examined noninvasively collected fecal samples from black and gold howler monkeys from remote, rural, and village populations in Northern Argentina. We examined all samples (n=90) for the zoonotic protozoa Cryptosporidium sp. and Giardia sp. via immunofluorescent antibody (IFA) detection. All samples were negative for Cryptosporidium sp. The prevalence of Giardia sp. was significantly higher at the rural site (67%) compared with the remote forest (57%) and village (40%) sites. A lack of Cryptosporidium sp. in all samples examined suggests that this pathogen is not a natural component of the howler parasite communities at these sites and that current land-use patterns and livestock contact are not exposing Argentine howler monkeys to this pathogen. High prevalence of Giardia sp. at all sites suggests that howler monkeys may serve as a viable reservoir for Giardia. Significantly higher prevalence of Giardia sp. at the rural site, where primate-livestock contact is highest, suggests the presence of multiple Giardia clades or increased exposure to Giardia through repeated zoonotic transmission among nonhuman primates, livestock, and/or people. These results highlight the need for future research into the epidemiology, cross-species transmission ecology, and clinical consequences of Giardia and other infectious agents not only in humans and livestock, but also in the wild animals that share their environments.


Using household survey data to identify large-scale food security patterns across Uganda.
To target food security interventions for smallholder households, decision makers need large-scale information, such as maps on poverty, food security and key livelihood activities. Such information is often based on expert knowledge or aggregated data, despite the fact that food security and poverty are driven largely by processes at the household level. At present, it is unclear if and how household level information can contribute to the spatial prediction of such welfare indicators or to what extent local variability is ignored by current mapping efforts. A combination of geo-referenced household level information with spatially continuous information is an underused approach to quantify local and large-scale variation, while it can provide a direct estimate of the variability of welfare indicators at the most relevant scale. We applied a stepwise regression kriging procedure to translate point information to spatially explicit patterns and create country-wide predictions with associated uncertainty estimates for indicators on food availability and related livelihood activities using household survey data from Uganda. With few exceptions, predictions of the indicators were weak, highlighting the difficulty in capturing variability at larger scale. Household explanatory variables identified little additional variation compared to environmental explanatory variables alone. Spatial predictability was strongest for indicators whose distribution was determined by environmental gradients. In contrast, indicators of crops that were more ubiquitously present across agroecological zones showed large local variation, which often overruled large-scale patterns. Our procedure adds to existing approaches that often only show large-scale patterns by revealing that local variation in welfare is large. Interventions that aim to target the poor must recognise that diversity in livelihood activities for income generation within any given area often overrides the variability of livelihood activities between distant regions in the country.


Identifying Dyscalculia Symptoms Related to Magnocellular Reasoning Using Smartphones.
This paper presents a study that has developed a mobile software application for assisting diagnosis of learning disabilities in mathematics, called dyscalculia, and measuring correlations between dyscalculia symptoms and magnocellular reasoning. Usually, software aids for dyscalculic individuals are focused on both assisting diagnosis and teaching the material. The software developed in this study however maintains a specific focus on the former, and in the process attempts to capture alleged correlations between dyscalculia symptoms and possible underlying causes of the condition. Classification of symptoms is performed by k-Nearest Neighbor algorithm classifying five parameters evaluating user's skills, returning calculated performance in each category as well as correlation strength between detected symptoms and magnocellular reasoning abilities. Expert evaluations has found the application to be appropriate and productive for its intended purpose, proving that mobile software is a suitable and valuable tool for assisting dyscalculia diagnosis and identifying root causes of developing the condition.


The optimal number of heifer calves to be reared as dairy replacements.
Dairy farmers often keep almost all their newborn heifer calves despite the high cost of rearing. By rearing all heifer calves, farmers have more security and retain flexibility to cope with the uncertainty in the availability of replacement heifers in time. This uncertainty is due to mortality or infertility during the rearing period and the variation in culling rate of lactating cows. The objective of this study is to provide insight in the economically optimal number of heifer calves to be reared as replacements. A herd-level stochastic simulation model was developed specific for this purpose with a herd of 100 dairy cows; the biological part of the model consisted of a dairy herd unit and rearing unit for replacement heifers. The dairy herd unit included variation in the number of culled dairy cows. The rearing unit incorporated variation in the number of heifers present in the herd by including uncertainty in mortality and variation in fertility. The dairy herd unit and rearing unit were linked by the number of replacement heifers and culled dairy cows. When not enough replacement heifers were available to replace culled dairy cows, the herd size was temporarily reduced, resulting in an additional cost for the empty slots. When the herd size reached 100 dairy cows, the available replacement heifers that were not needed were sold. It was assumed that no purchase of cows and calves occurred. The optimal percentage of 2-wk-old heifer calves to be retained was defined as the percentage of heifer calves that minimized the average net costs of rearing replacement heifers. In the default scenario, the optimal retention was 73% and the total net cost of rearing was estimated at €40,939 per herd per year. This total net cost was 6.5% lower than when all heifer calves were kept. An earlier first-calving age resulted in an optimal retention of 75%, and the net costs of rearing were €581 per herd per year lower than in the default scenario. For herds with a lower or higher culling rate of dairy cows (10 or 40% instead of 25% in the default scenario), it was optimal to retain 35 or 100% of the heifer calves per year. Herds that had a lower or higher cost of empty slots (€50 or €120 per month instead of €82 in the default scenario) had an optimal retention of 49 or 83% per year; the optimal retention percentage was dependent on farm and herd characteristics. For Dutch dairy farming conditions, it was not optimal to keep all heifer calves.


CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells.
Metabolic reprogramming by oncogenic signals promotes cancer initiation and progression. The oncogene KRAS and tumour suppressor STK11, which encodes the kinase LKB1, regulate metabolism and are frequently mutated in non-small-cell lung cancer (NSCLC). Concurrent occurrence of oncogenic KRAS and loss of LKB1 (KL) in cells specifies aggressive oncological behaviour. Here we show that human KL cells and tumours share metabolomic signatures of perturbed nitrogen handling. KL cells express the urea cycle enzyme carbamoyl phosphate synthetase-1 (CPS1), which produces carbamoyl phosphate in the mitochondria from ammonia and bicarbonate, initiating nitrogen disposal. Transcription of CPS1 is suppressed by LKB1 through AMPK, and CPS1 expression correlates inversely with LKB1 in human NSCLC. Silencing CPS1 in KL cells induces cell death and reduces tumour growth. Notably, cell death results from pyrimidine depletion rather than ammonia toxicity, as CPS1 enables an unconventional pathway of nitrogen flow from ammonia into pyrimidines. CPS1 loss reduces the pyrimidine to purine ratio, compromises S-phase progression and induces DNA-polymerase stalling and DNA damage. Exogenous pyrimidines reverse DNA damage and rescue growth. The data indicate that the KL oncological genotype imposes a metabolic vulnerability related to a dependence on a cross-compartmental pathway of pyrimidine metabolism in an aggressive subset of NSCLC.


Detecting activations in event-related fMRI using analysis of variance.
The most common design of a functional MRI (fMRI) experiment is a block design. The use of rapid imaging, however, and carefully designed paradigms makes the separation of cognitive events possible. Such experiments make use of event-related paradigms, in which a task involving several cognitive processes is repeated. In analyzing data from such experiments, existing methods often prove inadequate, because the prediction of the exact shape or timing of the time course is difficult. Here we present an analysis of variance (ANOVA) method for analyzing fMRI data that does not require any assumptions about the shape of the activation time course. Consequently, this method can simultaneously detect brain areas showing a variety of stimulus-locked time courses in the same experiment. The utility of this technique is demonstrated by the analysis of data from two event-related paradigms in which regions of activation are detected that correspond to a variety of distinct neural processes, yielding significantly different temporal signal changes. Magn Reson Med 42:1117-1122, 1999.


Impact of a pharmaceutical care programme for patients with chronic disease initiated at the emergency department on drug-related negative outcomes: a randomised controlled trial.
The resolution of potential drug-related problems is a priority of pharmaceutical care programmes. To assess the clinical impact on drug-related negative outcomes of a pharmaceutical care programme focusing on the resolution of potential drug-related problems, initiated in the emergency department for patients with heart failure (HF) and/or chronic obstructive pulmonary disease (COPD). Controlled trials, in which older adults (≥65 years) receiving four or more medications admitted to the emergency department for ≥12 hours for worsening of HF and/or COPD were randomised (1:1) to either a pharmaceutical care programme focusing on resolving potential drug-related problems initiated at the emergency department (intervention group (IG)) or standard care (control group). Comparisons between the groups were made for the proportion of patients with drug-related negative outcomes, number of drug-related negative outcomes per patient, mean stay, patients readmitted within 180 days and 180-day mortality. 118 patients were included, 59 in each group. Fewer patients in the IG had drug-related negative outcomes (37 (62.7%) vs 47 (79.7%) in the control group (p=0.042)). Fewer drug-related negative outcomes per patient occurred in the IG (56 (0.95 per patient) vs 85 (1.44 per patient) in the control group (p=0.01)). The mean stay was similar between groups (194.7 hours in the IG vs 242.5 hours in the control group (p=0.186)). No difference in revisits within 180 days was found (32 (54.24%) in the IG vs 22 (37.3%) in the control group (p=0.065)). 180-Day mortality was detected in 11 (18.6%) patients in the IG compared with 13 (22%) in the control group (p=0.647). A pharmaceutical care programme focusing on resolving potential drug-related problems initiated at the emergency department has a favourable clinical impact, as it reduces the number and prevalence of drug-related negative outcomes. No difference was found in other outcome variables.Trial registration number NCT02368548.