Transformation and cytotoxicity of iron in siderosis bulbi.
Ocular tissues from two enucleated and one trabeculectomized human eyes with siderosis bulbi were studied by electron microscopy. Ferritin particles were demonstrated in various cell types of the three eyes. Other types of iron were not identifiable. The ferritin particles were scattered throughout the cytoplasm, with a few particles in the nucleus and extracellular space. More ferritin particles were seen in tissues near the iron foreign body. The cells which contained numerous ferritin particles also had siderosomes, most of which were thought to be conglomerates of the ferritin particles in the secondary lysosomes. Cells with numerous ferritin particles, particularly in the siderosomes, showed vacuolar degeneration. The present study indicated that in siderosis bulbi, iron released from the iron foreign body is deposited as ferritin scattered throughout the cytoplasm and is sometimes accumulated as siderosomes, in the affinitive cells. In siderosis bulbi, the cells become damaged by the deposition of ferritin in the cytoplasm, especially in the form of siderosomes.


Assessment of the chest wall thickness of the lawrence livermore torso phantom using a voxel image.
This paper describes the methodology of measuring the chest wall thickness using the voxel image of the Lawrence Livermore National Lab (LLNL) torso phantom. The LLNL phantom is used as a standard to calibrate a lung counter consisting of a 2 × 2 array of germanium detectors. In general, an average thickness estimated from four counting positions is used as the chest wall thickness for a given overlay plate. For a given overlay, the outer chest surface differs from that of inner one, and the chest wall thickness varies from one position to other. The LLNL phantom with chest plate and C4 overlay plate installed was scanned with a CT (computed tomography) scanner. The image data, collected in DICOM (Digital Imaging and Communication) format, were converted to the MCNP input file by using the Scan2Mcnp program. The MCNP file was visualized and analyzed with the Moritz visual editor. An analytic expression was formulated and solved to calculate the chest wall thickness by using the point detector responses (F 5 tally of MCNP). To map the chest thickness, the entire chest wall was meshed into virtual grids of 1 cm width. A source and detector pair was moved along the inner and outer surface of the chest wall from right to left at different heights from neck to abdomen. For each height (z(k)), (x(i), y(j)) coordinates for the detector source pair were calculated from the visual editor and were scaled on-screen. For each (x(i), y(j), z(k)) position, a mesh thickness was measured from on-screen measurement and by solving the detector responses. The chest wall thicknesses at different positions on the outer surface of the chest were compared and verified using two methods.


Leadership in Times of Crisis: The Example of Ebola Virus Disease in Liberia.
The Ebola epidemic of 2014-2015 was one of the most significant public health threats of the 21st century, a crisis that challenged leadership in West Africa and around the world. Using the experience of Liberia's epidemic control efforts, we highlight the critical role that leadership played during four phases of the epidemic response: (1) crisis recognition and early mobilization; (2) the emergency phase; (3) the declining epidemic; and (4) the long tail. We examine how the decisions and actions taken in each phase of the epidemic address key crisis leadership tasks, including sense-making, decision making, meaning-making, crisis termination, and learning, and assess how leadership approaches evolved during the different epidemic phases to accomplish these tasks. A contingency leadership theory lens is used to identify situations where strong leadership, good leader-member relations, and well-structured tasks can facilitate different leadership approaches. The first phase of the epidemic was hampered by insufficient attention to sense-making and weak decision making, in part because of the existing hierarchical leadership approach. This contributed to amplification of the epidemic. The emergency phase of the epidemic brought a change in leadership that focused on sense-making, decision-making, and meaning-making tasks. A distributed leadership approach replaced the old hierarchies. In addition to sharing leadership responsibility and authority, the distributed leadership approach involved strategically engaging stakeholders and communicating intensively. Although much of the hierarchical leadership approaches returned in the latter phases of the epidemic, there remain more empowered leaders at different levels across the country. Systematically tackling crisis leadership tasks, recognizing situations where different leadership approaches can be used, and employing a distributed leadership approach are helpful lessons to prepare for and respond to future crises.


Role of transforming growth factor-alpha (TGF-alpha) in basal and hormone-stimulated growth by estradiol, prolactin and progesterone in human and rat mammary tumor cells: studies using TGF-alpha and EGF receptor antibodies.
The biological role of transforming growth factor-alpha (TGF-alpha) in basal and hormone-stimulated proliferation of primary human and rat mammary tumor cells was studied using antibodies against TGF-alpha and its receptor. A monoclonal antibody, MAb-425 against human EGF receptor was added to in vitro soft agar, clonogenic cultures of human breast carcinoma cells under basal and estradiol(E2)-stimulated conditions. The antibody had an antagonist effect on colony growth in 4 of 10 tumors and an agonist effect in 4 (72 and 153% of control). E2-stimulated colony growth in 5 tumors (167% of control) and the antibody blocked E2-stimulation in 3 of the 5. Inhibition of E2-stimulated growth in 3 and basal growth in 4 other tumors by the EGF receptor antibody suggest that endogenously secreted TGF-alpha has a role as an autocrine/paracrine growth factor in constitutive and E2-stimulated tumor cell proliferation in a majority of human tumors. A polyclonal antibody against TGF-alpha was used to study the role of TGF-alpha in E2-, prolactin(Prl)- and progesterone(Prog)-stimulated proliferation of NMU(nitrosomethylurea)-induced rat mammary tumor cells under similar culture conditions. TGF-alpha, E2, Prl and Prog stimulated colony growth equally to 176, 187, 168 and 181% of control. The antibody produced significant and similar inhibition of TGF-alpha and E2-stimulated growth (95 and 83%). In contrast, inhibition of Prl- and Prog-stimulated growth by the antibody was only 24 and 37%. The TGF-alpha ligand antibody did not have an agonist or antagonist effect when added alone. Thus, TGF-alpha seems to be a major stimulatory growth factor mediating E2-induced tumor cell proliferation in rat mammary tumors. It is less important in Prl- and Prog-induced tumor growth and not essential for basal growth in these tumors. We conclude that TGF-alpha is a biologically important autocrine/paracrine growth factor in primary human breast cancer cell proliferation and in E2-induced rat mammary tumor growth.


Heterogeneous CaMKII-Dependent Synaptic Compensations in CA1 Pyramidal Neurons From Acute Hippocampal Slices.
Prolonged changes in neural activity trigger homeostatic synaptic plasticity (HSP) allowing neuronal networks to operate within functional ranges. Cell-wide or input-specific adaptations can be induced by pharmacological or genetic manipulations of activity, and by sensory deprivation. Reactive functional changes caused by deafferentation may partially share mechanisms with HSP. Acute hippocampal slices are a suitable model to investigate relatively rapid (hours) modifications occurring after denervation and explore the underlying mechanisms. As during slicing many afferents are cut, we conducted whole-cell recordings of miniature excitatory postsynaptic currents (mEPSCs) in CA1 pyramidal neurons to evaluate changes over the following 12 h. As Schaffer collaterals constitute a major glutamatergic input to these neurons, we also dissected CA3. We observed an average increment in mEPSCs amplitude and a decrease in decay time, suggesting synaptic AMPA receptor upregulation and subunit content modifications. Sorting mEPSC by rise time, a correlate of synapse location along dendrites, revealed amplitude raises at two separate domains. A specific frequency increase was observed in the same domains and was accompanied by a global, unspecific raise. Amplitude and frequency increments were lower at sites initially more active, consistent with local compensatory processes. Transient preincubation with a specific Ca2+/calmodulin-dependent kinase II (CaMKII) inhibitor either blocked or occluded amplitude and frequency upregulation in different synapse populations. Results are consistent with the concurrent development of different known CaMKII-dependent HSP processes. Our observations support that deafferentation causes rapid and diverse compensations resembling classical slow forms of adaptation to inactivity. These results may contribute to understand fast-developing homeostatic or pathological events after brain injury.


DNA sequence chromatogram browsing using JAVA and CORBA.
DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.]


Sex influences how attendings evaluate surgical residents in the operating room.
The aim of this study was to evaluate the influence of sex on facultys' perception of resident autonomy and performance. Autonomy/performance/complexity evaluations performed by faculty of categorical general surgery residents (2015-2021) were analyzed. Comparisons of scores by faculty and resident sex were performed. A total of 10967 paper/electronic evaluations were collected. Female attendings rated female residents significantly lower in autonomy when compared to males (2.75 vs 2.91, p = 0.0037). There was no significant difference in autonomy ratings for male versus female residents when evaluated by a male attending (2.93 vs 2.96, p = 0.054) but male attendings did rate female residents significantly lower in autonomy at the highest complexities (2.37 vs 2.50, p = 0.012). The data suggests a unique interaction between attending and resident sex. A periodic evaluation of evaluations within one's program may provide invaluable implicit bias insight and should be considered.


The ethics of scholarly publishing: exploring differences in plagiarism and duplicate publication across nations.
This study explored national differences in plagiarism and duplicate publication in retracted biomedical literature. The national affiliations of authors and reasons for retraction of papers accessible through PubMed that were published from 2008 to 2012 and subsequently retracted were determined in order to identify countries with the largest numbers and highest rates of retraction due to plagiarism and duplicate publication. Authors from more than fifty countries retracted papers. While the United States retracted the most papers, China retracted the most papers for plagiarism and duplicate publication. Rates of plagiarism and duplicate publication were highest in Italy and Finland, respectively. Unethical publishing practices cut across nations.


Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi.
The recent proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete species. We have clustered all predicted protein-encoding gene sequences from these species to provide a means of investigating gene innovations, gene family expansions, protein family diversification, and the conservation of essential gene functions-empirically determined in Saccharomyces cerevisiae-among the fungi. The results are presented with reference to a phylogeny of the 34 fungal species, based on 29 universally conserved protein-encoding gene sequences. We contrast this phylogeny with one based on gene presence and absence and show that, while the two phylogenies are largely in agreement, there are differences in the positioning of some species. We have investigated levels of gene duplication and demonstrate that this varies greatly between fungal species, although there are instances of coduplication in distantly related fungi. We have also investigated the extent of orthology for protein families and demonstrate unexpectedly high levels of diversity among genes involved in lipid metabolism. These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi.


Cellulase adsorption and relationship to features of corn stover solids produced by leading pretreatments.
Although essential to enzymatic hydrolysis of cellulosic biomass to sugars for fermentation to ethanol or other products, enzyme adsorption and its relationship to substrate features has received limited attention, and little data and insight have been developed on cellulase adsorption for promising pretreatment options, with almost no data available to facilitate comparisons. Therefore, adsorption of cellulase on Avicel, and of cellulase and xylanase on corn stover solids resulting from ammonia fiber expansion (AFEX), ammonia recycled percolation (ARP), controlled pH, dilute acid, lime, and sulfur dioxide (SO(2)) pretreatments were measured at 4 degrees C. Langmuir adsorption parameters were then estimated by non-linear regression using Polymath software, and cellulase accessibility to cellulose was estimated based on adsorption data for pretreated solids and lignin left after carbohydrate digestion. To determine the impact of delignification and deacetylation on cellulose accessibility, purified CBHI (Cel7A) adsorption at 4 degrees C and hydrolysis with whole cellulase were followed for untreated (UT) corn stover. In all cases, cellulase attained equilibrium in less than 2 h, and upon dilution, solids pretreated by controlled pH technology showed the greatest desorption followed by solids from dilute acid and SO(2) pretreatments. Surprisingly, the lowest desorption was measured for Avicel glucan followed by solids from AFEX pretreatment. The higher cellulose accessibility for AFEX and lime pretreated solids could account for the good digestion reported in the literature for these approaches. Lime pretreated solids had the greatest xylanase capacity and AFEX solids the least, showing pretreatment pH did not seem to be controlling. The 24 h glucan hydrolysis rate data had a strong relationship to cellulase adsorption capacities, while 24 h xylan hydrolysis rate data showed no relationship to xylanase adsorption capacities. Furthermore, delignification greatly enhanced enzyme effectiveness but had a limited effect on cellulose accessibility. And because delignification enhanced release of xylose more than glucose, it appears that lignin did not directly control cellulose accessibility but restricted xylan accessibility which in turn controlled access to cellulose. Reducing the acetyl content in corn stover solids significantly improved both cellulose accessibility and enzyme effectiveness.


Regulation of the Sko1 transcriptional repressor by the Hog1 MAP kinase in response to osmotic stress.
Exposure of yeast to increases in extracellular osmolarity activates the Hog1 mitogen-activated protein kinase (MAPK), which is essential for the induction of gene expression required for cell survival upon osmotic stress. Several genes are regulated in response to osmotic stress by Sko1, a transcriptional repressor of the ATF/CREB family. We show by in vivo coprecipitation and phosphorylation studies that Sko1 and Hog1 interact and that Sko1 is phosphorylated upon osmotic stress in a Hog1-dependent manner. Hog1 phosphorylates Sko1 in vitro at multiple sites within the N-terminal region. Phosphorylation of Sko1 disrupts the Sko1-Ssn6-Tup1 repressor complex, and consistently, a mutant allele of Sko1, unphosphorylatable by Hog1, exhibits less derepression than the wild type. Interestingly, Sko1 repressor activity is further enhanced in strains with high protein kinase A (PKA) activity. PKA phosphorylates Sko1 near the bZIP domain and mutation of these sites eliminates modulation of Sko1 responses to high PKA activity. Thus, Sko1 transcriptional repression is controlled directly by the Hog1 MAPK in response to stress, and this effect is further modulated by an independent signaling mechanism through the PKA pathway.


Imaging findings of adiposis dolorosa vs. massive localized lymphedema.
Adiposis dolorosa (Dercum's disease) is a condition of benign, painful subcutaneous lipomatous lesions associated with weakness, endocrine and lipid abnormalities, and mental disturbances. There is little information documenting the cross-sectional imaging findings that differentiate it from lipomatous and neoplastic soft tissue masses, or massive localized lymphedema. The purpose of this study was to provide a radiological case series of adiposis dolorosa. A 10-year retrospective review of the picture archiving and communications system was performed. Two musculoskeletal radiologists reviewed images to confirm and document imaging features, location, size, and patient demographics. Medical records were reviewed to characterize patients into three groups: one group met at least three of the four criteria of Dercum's syndrome, the second group met less than three criteria, and the third group had clinical diagnosis of cellulitis of the lower extremity. Seventeen cases (25 masses) of adiposis dolorosa were found, nine cases of which met at least three criteria of Dercum's syndrome. All cases in the first two groups demonstrated skin thickening and lymphedema of subcutaneous fat, which was fluid attenuation on CT and low or intermediate T1-weighted and high STIR/T2-weighted MR signal. Two cases with pathology showed mild fatty infiltration with fibrous septa, and the third case showed massive localized lymphedema. The third group of ten cellulitis patients demonstrated non-mass-like subcutaneous edema with similar CT attenuation and MR signal characteristics to the first two groups, but differed by the presence of post-contrast enhancement and non-mass-like appearance in 90%. Imaging findings of adiposis dolorosa and massive localized lymphedema overlap, as do the symptoms and pathological features. Due to the mass-like engorgement of the soft tissues and pain, patients will often undergo imaging to exclude neoplasm or infection. Knowledge of these conditions and the characteristic imaging findings is important to prevent unnecessary biopsy and misdiagnosis.


[Brain oscillations: pathophysiological and potentially therapeutic role in some neurological and psychiatric diseases].
The terms "oscillations" or "oscillatory activity" are frequently used not only to define the rhythmic fluctuations of the postsynaptic potentials of a neuronal group (local field potentials) or a cortical region (EEG, MEG), but also to indicate the rhythmic discharge pattern of action potentials from a neuron or a small group of neurons. Oscillatory activity makes possible the synchronization of different neuronal groups from nearby or distant cortical regions that participate in the same motor, sensory or cognitive task. The presence of oscillatory activity is usually associated to the existence of synchronization, but both phenomena are not necessarily always equivalent. Abnormalities of oscillatory activities or synchronization within or between different brain structures have been described in several neurological and psychiatric diseases; these abnormalities might play a relevant pathophysiological role in Parkinson's disease (and other movement disorders), schizophrenia or epilepsy. This review discusses all these aspects, with emphasis on their potential role both as a basic mechanism in brain function and as a pathophysiological substrate for some of the symptoms and signs observed in several diseases.


Stabilization of exosome-targeting peptides via engineered glycosylation.
Exosomes are secreted extracellular vesicles that mediate intercellular transfer of cellular contents and are attractive vehicles for therapeutic delivery of bimolecular cargo such as nucleic acids, proteins, and even drugs. Efficient exosome-mediated delivery in vivo requires targeting vesicles for uptake by specific recipient cells. Although exosomes have been successfully targeted to several cellular receptors by displaying peptides on the surface of the exosomes, identifying effective exosome-targeting peptides for other receptors has proven challenging. Furthermore, the biophysical rules governing targeting peptide success remain poorly understood. To evaluate one factor potentially limiting exosome delivery, we investigated whether peptides displayed on the exosome surface are degraded during exosome biogenesis, for example by endosomal proteases. Indeed, peptides fused to the N terminus of exosome-associated transmembrane protein Lamp2b were cleaved in samples derived from both cells and exosomes. To suppress peptide loss, we engineered targeting peptide-Lamp2b fusion proteins to include a glycosylation motif at various positions. Introduction of this glycosylation motif both protected the peptide from degradation and led to an increase in overall Lamp2b fusion protein expression in both cells and exosomes. Moreover, glycosylation-stabilized peptides enhanced targeted delivery of exosomes to neuroblastoma cells, demonstrating that such glycosylation does not ablate peptide-target interactions. Thus, we have identified a strategy for achieving robust display of targeting peptides on the surface of exosomes, which should facilitate the evaluation and development of new exosome-based therapeutics.


Mechanisms used for genomic proliferation by thermophilic group II introns.
Mobile group II introns, which are found in bacterial and organellar genomes, are site-specific retroelements hypothesized to be evolutionary ancestors of spliceosomal introns and retrotransposons in higher organisms. Most bacteria, however, contain no more than one or a few group II introns, making it unclear how introns could have proliferated to higher copy numbers in eukaryotic genomes. An exception is the thermophilic cyanobacterium Thermosynechococcus elongatus, which contains 28 closely related copies of a group II intron, constituting approximately 1.3% of the genome. Here, by using a combination of bioinformatics and mobility assays at different temperatures, we identified mechanisms that contribute to the proliferation of T. elongatus group II introns. These mechanisms include divergence of DNA target specificity to avoid target site saturation; adaptation of some intron-encoded reverse transcriptases to splice and mobilize multiple degenerate introns that do not encode reverse transcriptases, leading to a common splicing apparatus; and preferential insertion within other mobile introns or insertion elements, which provide new unoccupied sites in expanding non-essential DNA regions. Additionally, unlike mesophilic group II introns, the thermophilic T. elongatus introns rely on elevated temperatures to help promote DNA strand separation, enabling access to a larger number of DNA target sites by base pairing of the intron RNA, with minimal constraint from the reverse transcriptase. Our results provide insight into group II intron proliferation mechanisms and show that higher temperatures, which are thought to have prevailed on Earth during the emergence of eukaryotes, favor intron proliferation by increasing the accessibility of DNA target sites. We also identify actively mobile thermophilic introns, which may be useful for structural studies, gene targeting in thermophiles, and as a source of thermostable reverse transcriptases.


Food intolerance mimicking alimentary lymphosarcoma.
A cat with chronic diarrhea was diagnosed as having duodenal lymphosarcoma on two separate sets of endoscopic biopsies. Prednisolone failed to effect any clinical improvement. However, feeding the cat with a hypoallergenic diet resulted in long-term (i.e., six months) resolution of clinical signs. Most clinicians are familiar with the possibility of mistakenly diagnosing inflammatory bowel disease when the patient has lymphosarcoma; however, this case had the opposite problem: lymphosarcoma was diagnosed histologically on two separate occasions when inflammatory bowel disease was the problem.


Bidirectional Mapping-Based Domain Adaptation for Nucleus Detection in Cross-Modality Microscopy Images.
Cell or nucleus detection is a fundamental task in microscopy image analysis and has recently achieved state-of-the-art performance by using deep neural networks. However, training supervised deep models such as convolutional neural networks (CNNs) usually requires sufficient annotated image data, which is prohibitively expensive or unavailable in some applications. Additionally, when applying a CNN to new datasets, it is common to annotate individual cells/nuclei in those target datasets for model re-learning, leading to inefficient and low-throughput image analysis. To tackle these problems, we present a bidirectional, adversarial domain adaptation method for nucleus detection on cross-modality microscopy image data. Specifically, the method learns a deep regression model for individual nucleus detection with both source-to-target and target-to-source image translation. In addition, we explicitly extend this unsupervised domain adaptation method to a semi-supervised learning situation and further boost the nucleus detection performance. We evaluate the proposed method on three cross-modality microscopy image datasets, which cover a wide variety of microscopy imaging protocols or modalities, and obtain a significant improvement in nucleus detection compared to reference baseline approaches. In addition, our semi-supervised method is very competitive with recent fully supervised learning models trained with all real target training labels.


Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.
Crystal structures of L-2-haloacid dehalogenase from Pseudomonas sp. YL complexed with monochloroacetate, L-2-chlorobutyrate, L-2-chloro-3-methylbutyrate, or L-2-chloro-4-methylvalerate were determined at 1.83-, 2.0-, 2.2-, and 2.2-A resolutions, respectively, using the complex crystals prepared with the S175A mutant, which are isomorphous with those of the wild-type enzyme. These structures exhibit unique structural features that correspond to those of the reaction intermediates. In each case, the nucleophile Asp-10 is esterified with the dechlorinated moiety of the substrate. The substrate moieties in all but the monochloroacetate intermediate have a D-configuration at the C2 atom. The overall polypeptide fold of each of the intermediates is similar to that of the wild-type enzyme. However, it is clear that the Asp-10-Ser-20 region moves to the active site in all of the intermediates, and the Tyr-91-Asp-102 and Leu-117-Arg-135 regions make conformational changes in all but the monochloroacetate intermediates. Ser-118 is located near the carboxyl group of the substrate moiety; this residue probably serves as a binding residue for the substrate carboxyl group. The hydrophobic pocket, which is primarily composed of the Tyr-12, Gln-42, Leu-45, Phe-60, Lys-151, Asn-177, and Trp-179 side chains, exists around the alkyl group of the substrate moiety. This pocket may play an important role in stabilizing the alkyl group of the substrate moiety through hydrophobic interactions, and may also play a role in determining the stereospecificity of the enzyme. Moreover, a water molecule, which is absent in the substrate-free enzyme, is present in the vicinities of the carboxyl carbon of Asp-10 and the side chains of Asp-180, Asn-177, and Ala-175 in each intermediate. This water molecule may hydrolyze the ester intermediate and its substrate. These findings crystallographically demonstrate that the enzyme reaction proceeds through the formation of an ester intermediate with the enzyme's nucleophile Asp-10.


A case-control genome wide association study of substance use disorder (SUD) identifies novel variants on chromosome 7p14.1 in patients from the United Arab Emirates (UAE).
Genome wide association studies (GWASs) have provided insights into the molecular basis of the disorder in different population. This study presents the first GWAS of substance use disorder (SUD) in patients from the United Arab Emirates (UAE). The aim was to identify genetic association(s) that may provide insights into the molecular basis of the disorder. The GWAS discovery cohort consisted of 512 (250 cases and 262 controls) male participants from the UAE. Controls with no prior history of SUD were available from the Emirates family registry. The replication cohort consisted of 520 (415 cases and 105 controls) Australian male Caucasian participants. The GWAS discovery samples were genotyped for 4.6 million single nucleotide polymorphism (SNP). The replication cohort was genotyped using TaqMan assay. The GWAS association analysis identified three potential SNPs rs118129027 (p-value = 6.24 × 10-8 ), rs74477937 (p-value = 8.56 × 10-8 ) and rs78707086 (p-value = 8.55 × 10-8 ) on ch7p14.1, that did not meet the GWAS significance threshold but were highly suggestive. In the replication cohort, the association of the three top SNPs did not reach statistical significance. In a meta-analysis of the discovery and the replication cohorts, there were no strengthen evidence for association of the three SNPs. The top identified rs118129027 overlaps with a regulatory factor (enhancer) region that targets three neighboring genes LOC105375237, LOC105375240, and YAE1D1. The YAE1D1, which represents a potential locus that is involved in regulating translation initiation pathway. Novel associations that require further confirmation were identified, suggesting a new insight to the genetic basis of SUD.


IN SILICO STUDY OF NOVEL SULFONAMIDE DERIVATIVES BEARING A 1, 2, 4-TRIAZOLE MOIETY ACT AS CARBONIC ANHYDRASE INHIBITORS WITH PROMISING ANTI-CANCER ACTIVITY.
Aim: To evaluate the theoretical binding affinities of four synthetic compounds that target the carbonic anhydrase IX enzyme in solid tumors. Materials and Methods: To accurately depict the molecular structure, we utilized the Chem Draw Professional 12.0 program. We downloaded the carbonic anhydrase IX enzyme (29.25 KDa) (PDB code: 4YWP) from the Protein Data Bank into the Molecular Operating Environment software. Then, the S-score and rmsd were calculated for the proposed compounds. Results: The theoretically synthesized compounds demonstrated good binding affinities with the receptor active pockets Sa, Sb, and Sd, with S-scores of -7.6491, -8.3789, and -8.3218, respectively. Substitutions improve compound orientation. The substituted triazoles ring increases flexibility and receptor interaction. In addition, the benzyl chloride derivatives play an important role in the interaction, with varying effects dependent on the groups substituted at position 4 of the benzene ring. Conclusions: The synthesized compounds Sb with para Br substitution (S-score = -8.37) and Sd with para Cl substitution (S-score = -8.32) are considered the best ones as they exhibit a high affinity for the receptor.


Reevaluating growing season length controls on net ecosystem production in evergreen conifer forests.
Growing season length (GSL) is a key unifying concept in ecology that can be estimated from eddy covariance-derived estimates of net ecosystem production (NEP). Previous studies disagree on how increasing GSLs may affect NEP in evergreen coniferous forests, potentially due to the variety of methods used to quantify GSL from NEP. We calculated GSL and GSL-NEP regressions at eleven evergreen conifer sites across a broad climatic gradient in western North America using three common approaches: (1) variable length (3-7 days) regressions of day of year versus NEP, (2) a smoothed threshold approach, and (3) the carbon uptake period, followed by a new approach of a method-averaged ensemble. The GSL and the GSL-NEP relationship differed among methods, resulting in linear relationships with variable sign, slope, and statistical significance. For all combinations of sites and methods, the GSL explained between 6% and 82% of NEP with p-values ranging from 0.45 to < 0.01. These results demonstrate the variability among GSL methods and the importance of selecting an appropriate method to accurately project the ecosystem carbon cycling response to longer growing seasons in the future. To encourage this approach in future studies, we outline a series of best practices for GSL method selection depending on research goals and the annual NEP dynamics of the study site(s). These results contribute to understanding growing season dynamics at ecosystem and continental scales and underscore the potential for methodological variability to influence forecasts of the evergreen conifer forest response to climate variability.


Inter-observer reliability of localization of recorded stridor sounds in children.
To determine the inter-observer reliability in localization of recorded stridor sounds in children. The stridor sounds of 28 children programmed for laryngobronchoscopy were recorded with a high quality digital recorder. Nineteen of these recordings with a diagnosis confirmed by endoscopy, were presented to otorhinolaryngology residents, academic specialists and non-academic consultants (n=38) in different situations with and without additional information about the subject. The participants were requested to score the sounds as pharyngeal, supraglottic, glottic, subglottic or tracheal in both situations. The scores were analyzed per group of participants, per location of obstruction and per diagnosis in the different situations. The performance of the total group was just above chance level with an average score of 29.6%. The total results improved slightly with the additional information present, although not significantly. No significant difference was found between the three categories of participants. The supraglottic sounds were significantly better differentiated from the other locations in both assessment types (p<0.001). The tracheal region (p<0.01) and the supraglottic region (p<0.05) received significantly higher scores when the additional information was present. Laryngomalacia was significantly better differentiated (p<0.001) from the other diagnoses. The improvement in assessment with and without additional information present was significant for laryngomalacia (p=0.002) and tracheomalacia (p<0.035). The clinical observation of stridor in children shows poor levels of localization. Even though the two most common diagnoses, laryngomalacia and tracheomalacia are localized more correctly, the general performance is not significantly higher than random. No evidence was found in this study for differences in results by the observer's level of experience. We would recommend that an observational policy is only adequate when clear clinical signs are present that indicate laryngomalacia as first differential diagnosis. In other cases rigid and flexible endoscopy is indicated to locate the site and nature of obstruction.


Improvement of sensitivity in HLA-DRB1 typing by semi-nested PCR-RFLP.
A sensitive method of HLA-DRB1 typing was devised using a semi-nested polymerase chain reaction (PCR) followed by a restriction fragment length polymorphism (RFLP) analysis (semi-nested PCR-RFLP method). The first-round amplification (30 cycles) of the semi-nested PCR was performed using DRB generic primer pairs and the second round of PCRs (20 cycles) were performed using DRB1 group-specific primers. The products of the second round PCRs were digested with restriction endonucleases for the typing of HLA-DRB1 alleles. By this method, HLA-DRB1 typing was possible from 10 pg of genomic DNA extracted from lymphocytes and from 0.5 microliter of 1,000 times diluted blood without DNA extraction. HLA-DRB1 alleles could be typed from a 2-mm long bloodstained cotton thread prepared from 10 times diluted blood and from a 2-mm thread of whole blood bloodstains stored at room temperature for 2 years. From the mixture of blood of two individuals with different genotypes, DRB1 alleles of the minor component were detected down to 1/1,000 of the major component. This semi-nested PCR-RFLP method is useful for HLA-DRB1 typing from extremely small amounts of DNA and from mixed samples.


KIF15 Expression in Tumor-associated Monocytes Is a Prognostic Biomarker in Hepatocellular Carcinoma.
Kinesin family member 15 (KIF15) participates in the transport of macromolecules in essential cellular processes. In this study we evaluated the clinical relevance of KIF15 expression in hepatocellular carcinoma (HCC). Association between KIF15 expression and clinical outcomes in HCC patients was analyzed using three independent cohorts. Localization of KIF15 expression was assessed by immunohistochemical analysis. Co-culture experiments were performed using healthy donor peripheral blood mononuclear cells (PBMC) and HCC cell lines. Immunohistochemical analysis showed that KIF15 was mainly expressed in inflammatory monocytes around cancer cells. Multivariate analysis indicated high KIF15 expression was an independent poor prognostic factor for survival. HCC cells with high expression of minichromosome maintenance protein 2 (MCM2) were located close to KIF15-expressing inflammatory monocytes. The proliferation ability of HCC cells was increased by co-culture with PBMC. High KIF15 expression in inflammatory monocytes in tumor tissues may serve as a prognostic marker for poor outcome in HCC.


Inflammation in Atherosclerosis-No Longer a Theory.
Inflammation links to atherosclerosis and its complications in various experimental investigations. Animal studies have implicated numerous inflammatory mediators in the initiation and complication of atherosclerosis. Numerous studies in humans have shown associations of biomarkers of inflammation with cardiovascular events provoked by atheromata. Inflammatory status, determined by the biomarker C-reactive protein, can guide the allocation of statin therapy to individuals without elevated low-density lipoprotein (LDL) concentrations to prevent first ever adverse cardiovascular events. Until recently, no direct evidence has shown that an intervention that selectively limits inflammation can improve outcomes in patients with atherosclerosis. A recent study, based on decades of preclinical investigation, treated patients who had sustained a myocardial infarction and whose LDL was well-controlled on statin treatment with an antibody that neutralizes interleukin-1 beta. This trial, conducted in over 10 000 individuals, showed a reduction in major adverse cardiac events, establishing for the first time the clinical efficacy of an anti-inflammatory intervention in atherosclerosis. Two large subsequent studies have shown that colchicine treatment can also prevent recurrent events in patients recovering from an acute coronary syndrome or in the stable phase of coronary artery disease. These clinical trials have transformed inflammation in atherosclerosis from theory to practice. Much work remains to optimize further anti-inflammatory interventions, minimize unwanted actions, and refine patient selection. This long road from discovery in the laboratory to successful clinical trials represents a victory for medical science, and opens a new avenue to reducing the risk that remains despite current treatments for atherosclerosis.


Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis.
Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis. Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli, the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli: in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome.


Inguinal lymph node and anorectal mucosal biopsies for human immunodeficiency virus research protocols in an emerging nation: patient outcomes and lessons learned.
Lymph nodes and gut-associated lymphatic tissue are important reservoirs of the human immunodeficiency virus (HIV). Little is known about these reservoirs in different geographic populations. We report the surgical outcomes of excisional lymph node and anorectal mucosal biopsies performed internationally and describe the lessons learned. Patients were recruited through the Joint Clinical Research Center (JCRC) in Kampala, Uganda, where procedures were performed. Studies were approved by the Institutional Review Boards of the JCRC and the University of Minnesota. Instruments and supplies were shipped to Uganda and prepared onsite. Drugs and skin preparations were purchased locally. Lymph nodes were removed through 1-3 cm incisions with ligatures on lymphovascular pedicles. Incisions were closed with subcuticular sutures and epidermal tape. Two to four pieces of anorectal mucosa were obtained through anoscopes using biopsy forceps. One hundred thirty-eight lymph node biopsies and 98 anorectal mucosal biopsies were performed on 71 patients. Forty-one patients were HIV-positive. Many patients had multiple procedures. Two minor complications resulted: One hematoma and one lymphocele. Despite the cost of travel and lodging, cost per biopsy was lower in Uganda compared with the United States. Invasive clinical research can be performed with minimal morbidity in emerging nations with outcomes similar to those found in the United States, but with lower cost.


Methods to estimate the size and shape of the unaccommodated crystalline lens in vivo.
The purpose of this article was to present methods capable of estimating the size and shape of the human eye lens without resorting to phakometry or magnetic resonance imaging (MRI). Previously published biometry and phakometry data of 66 emmetropic eyes of 66 subjects (age range [18, 63] years, spherical equivalent range [-0.75, +0.75] D) were used to define multiple linear regressions for the radii of curvature and thickness of the lens, from which the lens refractive index could be derived. MRI biometry was also available for a subset of 30 subjects, from which regressions could be determined for the vertex radii of curvature, conic constants, equatorial diameter, volume, and surface area. All regressions were compared with the phakometry and MRI data; the radii of curvature regressions were also compared with a method proposed by Bennett and Royston et al. The regressions were in good agreement with the original measurements. This was especially the case for the regressions of lens thickness, volume, and surface area, which each had an R(2) > 0.6. The regression for the posterior radius of curvature had an R(2) < 0.2, making this regression unreliable. For all other regressions we found 0.25 < R(2) < 0.6. The Bennett-Royston method also produced a good estimation of the radii of curvature, provided its parameters were adjusted appropriately. The regressions presented in this article offer a valuable alternative in case no measured lens biometry values are available; however care must be taken for possible outliers.


Epidemiology of tuberculosis in a low-incidence Italian region with high immigration rates: differences between not Italy-born and Italy-born TB cases.
Emilia Romagna, a northern Italian region, has a population of 4.27 million, of which 9.7% are immigrants. The objective of this study was to investigate the epidemiology of tuberculosis (TB) during the period 1996-2006 in not Italy-born compared to Italy-born cases. Data was obtained from the Regional TB surveillance system, from where personal data, clinical features and risk factors of all notified TB cases were extracted. 5377 TB cases were reported. The proportion of immigrants with TB, over the total number of TB cases had progressively increased over the years, from 19.1% to 53.3%. In the not Italy-born population, TB incidence was higher than in Italians (in 2006: 100.7 cases per 100,000 registered not Italy-born subjects and 83.9/100,000 adding 20% of estimated irregular presences to the denominators. TB incidence among Italians was 6.5/100,000 Italians). A progressive rise in the not Italy-born incident cases was observed but associated with a decline in TB incidence. Not Italy-born cases were younger compared to the Italy-born cases, and more frequently classified as "new cases" (OR 2.0 95%CI 1.61-2.49 for age group 20-39); 60.7% had pulmonary TB, 31.6% extra pulmonary and 7.6% disseminated TB. Risk factors for TB in this population group were connected to lower income status (homeless: OR 149.9 95%CI 20.7-1083.3 for age group 40-59). In low-incidence regions, prevention and control of TB among sub-groups at risk such as the foreign-born population is a matter of public health concern. In addition, increasing immigration rates may affect TB epidemiology. TB among immigrants is characterized by particular clinical features and risk factors, which should be analyzed in order to plan effective action.


Simian immunodeficiency virus infection in the brain and lung leads to differential type I IFN signaling during acute infection.
Using an accelerated and consistent SIV pigtailed macaque model of HIV-associated neurologic disorders, we have demonstrated that virus enters the brain during acute infection. However, neurologic symptoms do not manifest until late stages of infection, suggesting that immunological mechanisms exist within the CNS that control viral replication and associated inflammation. We have shown that IFN-β, a type I IFN central to viral innate immunity, is a major cytokine present in the brain during acute infection and is responsible for limiting virus infection and inflammatory cytokine expression. However, the induction and role of IFN-α in the CNS during acute SIV infection has never been examined in this model. In the classical model of IFN signaling, IFN-β signals through the IFN-α/β receptor, leading to expression of IFN-α. Surprisingly, although IFN-β is upregulated during acute SIV infection, we found that IFN-α is downregulated. We demonstrate that this downregulation is coupled with a suppression of signaling molecules downstream of the IFN receptor, namely tyrosine kinase 2, STAT1, and IFN regulatory factor 7, as indicated by either lack of protein phosphorylation, lack of nuclear accumulation, or transcriptional and/or translational repression. In contrast to brain, IFN-α is upregulated in lung and accompanied by activation of tyrosine kinase 2 and STAT1. These data provide a novel observation that during acute SIV infection in the brain, there is differential signaling through the IFN-α/β receptor that fails to activate expression of IFN-α in the brain.


Determining and interpreting correlations in lipidomic networks found in glioblastoma cells.
Intelligent and multitiered quantitative analysis of biological systems rapidly evolves to a key technique in studying biomolecular cancer aspects. Newly emerging advances in both measurement as well as bio-inspired computational techniques have facilitated the development of lipidomics technologies and offer an excellent opportunity to understand regulation at the molecular level in many diseases. We present computational approaches to study the response of glioblastoma U87 cells to gene- and chemo-therapy. To identify distinct biomarkers and differences in therapeutic outcomes, we develop a novel technique based on graph-clustering. This technique facilitates the exploration and visualization of co-regulations in glioblastoma lipid profiling data. We investigate the changes in the correlation networks for different therapies and study the success of novel gene therapies targeting aggressive glioblastoma. The novel computational paradigm provides unique "fingerprints" by revealing the intricate interactions at the lipidome level in glioblastoma U87 cells with induced apoptosis (programmed cell death) and thus opens a new window to biomedical frontiers.


Glutamate measurement in Parkinson's disease using MRS at 3 T field strength.
Loss of nigral dopamine neurons in Parkinson's disease induces abnormal activation of glutamate systems in the basal ganglia. The purpose of this study was to assess these changes in the lentiform nucleus using MRS with optimized glutamate sensitivity (TE-averaged method). Ten patients with Parkinson's disease and 10 healthy controls were examined. Compared with healthy controls, no significant differences in glutamate were measured in patients, but a trend to lower total creatine was observed.


P0-Deficient Knockout Mice as Tools to Understand Pathomechanisms in Charcot-Marie-Tooth 1B and P0-Related Déjérine-Sottas Syndrome.
P0 (mylin protein zero, MPZ) is one of the four identified culprit genes for hereditary peripheral neuropathies. Homo- or heterozygous null mutants for P0 share pathological features with some patients suffering from P0-related Déjérine-Sottas-Syndrome (DSS) or Charcot-Marie-Tooth (CMT) neuropathy, type 1B, respectively, and can thus be considered as appropiate animal models for the corresponding diseases. This article focuses on distinct histopathological features in these mice. Such features include dysregulation of Schwann cell genes and axonal loss in homozygous mutants and significant infiltration of T-lymphocytes and macrophages in heterozygous mutants. These histological characteristics are instrumental in understanding the pathogenesis of the disease and may help in developing treatments.


Gene targeted agents: new opportunities for rational drug development.
In addition to traditional drug development methods designed to modulate the activity of protein targets, knowledge of disease gene DNA sequences provides an opportunity for the highly rational design of therapeutic agents that act at the DNA level through sequence-specific interactions. Among the ligands capable of binding DNA in a precise, sequence-specific manner are oligonucleotides, peptide nucleic acids and polyamides. Various strategies employing these agents to either transiently or permanently alter gene expression have been investigated over the past decade. During the past two to three years, important steps have been taken to illustrate the therapeutic potential of these ligands. Triple-helix (triplex) forming oligonucleotides have been particularly effective DNA-targeting agents with a wide range of applications, including the positive and negative transcriptional regulation of target genes, as well as the controlled delivery of site-specific mutations. This review will focus upon recent advances involving the use of sequence-specific DNA-binding ligands to modify gene expression and/or structure, with particular emphasis on the use of triplex-forming oligonucleotides in these roles.


Mutagenicity and genotoxicity of acid yellow 17 and its biodegradation products.
Acid yellow 17 (AY17), a very important commercial azo dye used in the textile industry, was degraded by Pseudomonas putida mt-2 at a concentration of up to 200 mg/L. High-performance liquid chromatography analysis of the biodegradation media revealed the presence of 4-aminobenzensulfonic acid (4-ABS) derived from AY17 azoreduction, which attests the expression of an azoreductase by this bacterium. This amine was identified only in the medium of static incubation, which is consistent with its biotransformation under shaken incubation (i.e., aerobic conditions). The mutagenicity of AY17 and its biodegradation products was evaluated by using Salmonella typhimurium TA102 and TA104. No mutagenicity was observed in the presence or absence of a metabolic activation system (S9). In addition, the ability of tested compounds to induce DNA damage in vitro with the DNA strand scission assay was evaluated. Results showed that only static decolorization culture of AY17 showed a significant ability to induce the pKS plasmid DNA opening. The present study showed that P. putida mt-2, cultivated under aerobic conditions, was able to decolorize, and especially to detoxify, AY17.


Nutritional utilization by rats of chickpea (Cicer arietinum) meal and its isolated globulin proteins is poorer than that of defatted soybean or lactalbumin.
The effects on performance, digestibility, N utilization and plasma amino acid concentrations of dietary chickpea (Cicer arietinum, var. Kabuli) seed meal, globulin proteins or buffer-insoluble residue [starch + non-starch polysaccharides (NSP) + lignin] were studied in growing rats. Chickpea meal, defatted soybean meal, chickpea globulins and lactalbumin were each incorporated into diets as the sole source of dietary protein (100 g/kg). In addition, chickpea insoluble residue was included in a control diet in the same proportion found in the chickpea meal. Rats were killed while under halothane anesthesia after 10 d of consuming the diets, and ileal contents were washed out and freeze-dried for digestibility measurements. Weight gains and gain:feed ratios of rats fed chickpea diets for 10 d did not differ from those of rats fed defatted soybean but were significantly lower than those of rats given the control (lactalbumin) diet. However, ileal and fecal N digestibilities and N retention by rats fed the chickpea diet were significantly lower than those obtained with the lactalbumin or soybean diet. The inclusion of both chickpea meal or its globulin proteins in the diet significantly increased the amount of N excreted, primarily as urea, through the urine. However, although ileal N digestibility values for chickpea meal were significantly lower, those for its constituent globulins did not differ from control values. Urea levels in plasma in rats fed diets containing chickpea meal, globulins or soybean meal were significantly higher than in those fed lactalbumin. Furthermore, the concentrations of glycine, phenylalanine, histidine, arginine and ornithine in the plasma of rats fed chickpea meal, its globulins or defatted soybean were significantly higher, whereas those of threonine, leucine, lysine and tryptophan were significantly lower than lactalbumin-fed controls. The chickpea insoluble residue had no adverse effects on performance or N utilization by rats. We conclude that the low nutritional value of chickpea meal is likely to be due mainly to adverse effects of its globulin proteins on growth and N metabolism rather than to the action of any known antinutritional factor present in the diet.


Effect of Adapted Physical Activity in Patients With Advanced Pancreatic Cancer: The APACaP GERCOR Randomized Trial.
The impact of adapted physical activity (APA) on health-related quality of life (HRQoL) in patients with advanced pancreatic ductal adenocarcinoma (aPDAC) is unknown. This study evaluated whether APA in addition to standard care improved HRQoL in patients who have aPDAC who are receiving first-line chemotherapy. Patients with locally advanced/metastatic PDAC and an ECOG performance status of 0 to 2 were randomized (1:1) to receive standard care (standard arm) or standard care plus a home-based 16-week APA program (APA arm). The primary objective was the effect of the APA program on 3 dimensions of the EORTC QLQ-C30: global health status, physical function, and fatigue at week 16 (W16), with a one-sided type I error of 0.017 for each dimension. The primary HRQoL analysis was performed in patients with available baseline and W16 scores for the dimensions (ie, the modified intention-to-treat population 1 [mITT1]), and secondary longitudinal HRQoL analyses using the mixed model for repeated measures (MMRM) and time until definitive deterioration (TUDD) methods were performed in the mITT1 population and in patients with baseline and at least one follow-up questionnaire (mITT2 population). A difference of ≥5 points was considered to be clinically relevant. Of 326 included patients, 313 were randomized to the standard (n=157) or APA (n=156) arms. In the mITT1 population (n=172), the mean differences in global health status, physical function, and fatigue at W16 adjusted from baseline were -0.98 (SD, 23.9; P=.39), -2.08 (SD, 21.3; P=.26), and 4.16 (SD, 29.2; P=.17), respectively, showing a non-statistically significant benefit with APA. In the mITT2 population (n=259), APA was associated with statistically significant and clinically relevant improvement in 5 and 8 dimensions of the HRQoL in the longitudinal MMRM and TUDD analyses, respectively. APA improved several dimensions of HRQoL in patients with aPDAC receiving first-line chemotherapy and standard care.


Bronchial manifestation of acute febrile neutrophilic dermatosis (Sweet's syndrome).
We describe a 62 yr old female with acute febrile neutrophilic dermatosis (AFND) or Sweet's syndrome, involving the bronchial mucosa. The patient presented with classical skin manifestations of AFND accompanied by bilateral pneumonia, pleural effusions and lesions of the oral mucosa. The diagnosis was confirmed by skin and mucosal biopsies. Bronchoscopy revealed raised pustules, similar to the lesions of the skin, suggesting bronchial involvement of AFND. The patient responded to systemic corticosteroids only for a short period and died as a result of multiorgan failure. Postmortem findings confirmed dense, focal neutrophilic infiltrates of the bronchi and bronchioles. No underlying disease was found.


Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection.
The estimation of the accuracy of predictions is a critical problem in QSAR modeling. The "distance to model" can be defined as a metric that defines the similarity between the training set molecules and the test set compound for the given property in the context of a specific model. It could be expressed in many different ways, e.g., using Tanimoto coefficient, leverage, correlation in space of models, etc. In this paper we have used mixtures of Gaussian distributions as well as statistical tests to evaluate six types of distances to models with respect to their ability to discriminate compounds with small and large prediction errors. The analysis was performed for twelve QSAR models of aqueous toxicity against T. pyriformis obtained with different machine-learning methods and various types of descriptors. The distances to model based on standard deviation of predicted toxicity calculated from the ensemble of models afforded the best results. This distance also successfully discriminated molecules with low and large prediction errors for a mechanism-based model developed using log P and the Maximum Acceptor Superdelocalizability descriptors. Thus, the distance to model metric could also be used to augment mechanistic QSAR models by estimating their prediction errors. Moreover, the accuracy of prediction is mainly determined by the training set data distribution in the chemistry and activity spaces but not by QSAR approaches used to develop the models. We have shown that incorrect validation of a model may result in the wrong estimation of its performance and suggested how this problem could be circumvented. The toxicity of 3182 and 48774 molecules from the EPA High Production Volume (HPV) Challenge Program and EINECS (European chemical Substances Information System), respectively, was predicted, and the accuracy of prediction was estimated. The developed models are available online at http://www.qspr.org site.


Role of beta2-chimaerin in the behaviour of murine mammary carcinoma cells in response to extracellular matrix components.
Chimaerins are high affinity receptors for phorbol esters and diacylglycerol (DAG), unrelated to the protein kinase C isozymes. These receptors have deep implications in tumour biology since they regulate the activity of Rac1, a small GTP-binding protein of the Ras superfamily. It has been demonstrated that chimaerins have GTPase activating protein (GAP) activity, leading to the acceleration of GTP hydrolysis from Rac1 and therefore facilitating the transition to its inactive state. Rac regulates various cellular events, including gene transcription, cell cycle, adhesion and migration. It has also been described that Rac is implicated in the intracellular response to the binding of specific extracellular matrix proteins to integrin receptors. In this work, we analysed cell morphology, actin cytoskeleton reorganisation and metalloprotease (MMP) secretion in response to matrix proteins in mouse mammary carcinoma cells transfected with the beta2-chimaerin GAP domain. Overexpression of beta2-chimaerin induced important cytoskeletal rearrangements in response to matrix stimuli. Transfectant cells also showed activation of MMP-9 activity after stimulation with collagen IV and epidermal growth factor. The restitution of normal Rac levels by beta2-chimaerin activity induced an increase in the sensitivity of tumour cells to extracellular factors, suggesting a regression of the malignant phenotype.


The factor structure of autistic traits.
Although DSM-IV requires symptoms in three criterion domains for a diagnosis of autistic disorder, the extent to which those domains are phenotypically independent is an unanswered and important question. The identification of 'endophenotypes' of the autistic syndrome may be very useful for genetic and neurobiologic studies of autism, but only if they represent truly independent sub domains of the disorder. In this study we examined the factor structure of autistic traits using data from 226 child psychiatric patients with and without pervasive developmental disorders, employing cluster analysis of data from the Autism Diagnostic Interview-Revised (ADI-r) and principal components factor analysis of data from the Social Responsiveness Scale (SRS, a quantitative genetic measure of autistic traits formerly known as the Social Reciprocity Scale). The results were consistent with the existence of a singular, continuously distributed underlying factor, resulting in disparate phenotypic manifestations across the three criterion domains for autistic disorder (social deficits, language deficits, and repetitive/stereotypic behaviors). The analyses generally failed to support the existence of independent sub domains of dysfunction in autism spectrum conditions. Future studies of the association between genetic/neurobiologic markers and autistic symptomatology may be enhanced by approaches which consider autistic symptoms as quantitative traits, and which are informed by ongoing research on the development and phenomenology of core deficiencies in reciprocal social behavior.


AMPK-α1 or AMPK-α2 Deletion in Smooth Muscles Does Not Affect the Hypoxic Ventilatory Response or Systemic Arterial Blood Pressure Regulation During Hypoxia.
The hypoxic ventilatory response (HVR) is markedly attenuated by AMPK-α1 deletion conditional on the expression of Cre-recombinase in tyrosine hydroxylase (TH) expressing cells, precipitating marked increases in apnea frequency and duration. It was concluded that ventilatory dysfunction caused by AMPK deficiency was driven by neurogenic mechanisms. However, TH is transiently expressed in other cell types during development, and it is evident that central respiratory depression can also be triggered by myogenic mechanisms that impact blood supply to the brain. We therefore assessed the effect on the HVR and systemic arterial blood pressure of AMPK deletion in vascular smooth muscles. There was no difference in minute ventilation during normoxia. However, increases in minute ventilation during severe hypoxia (8% O2) were, if affected at all, augmented by AMPK-α1 and AMPK-α2 deletion in smooth muscles; despite the fact that hypoxia (8% O2) evoked falls in arterial SpO2 comparable with controls. Surprisingly, these mice exhibited no difference in systolic, diastolic or mean arterial blood pressure during normoxia or hypoxia. We conclude that neither AMPK-α1 nor AMPK-α2 are required in smooth muscle for the regulation of systemic arterial blood pressure during hypoxia, and that AMPK-α1 deficiency does not impact the HVR by myogenic mechanisms.


Integrity of the LXXLL motif in Stat6 is required for the inhibition of breast cancer cell growth and enhancement of differentiation in the context of progesterone.
Progesterone is essential for the proliferation and differentiation of mammary gland epithelium. Studies of breast cancer cells have demonstrated a biphasic progesterone response consisting of an initial proliferative burst followed by sustained growth arrest. However, the transcriptional factors acting with the progesterone receptor (PR) to mediate the effects of progesterone on mammary cell growth and differentiation remain to be determined. Recently, it was demonstrated that signal transducer and activator of transcription 6 (Stat6) is a cell growth suppressor. Similar to progesterone-bound PR, Stat6 acts by inducing the expression of the G1 cyclin-dependent kinase inhibitors p21 and p27. The possible interaction between Stat6 and progesterone pathways in mammary cells was therefore investigated in the present study. ChIP and luciferase were assayed to determine whether Stat6 induces p21 and p27 expression by recruitment at the proximal Sp1-binding sites of the gene promoters. Immunoprecipitation and Western blotting were performed to investigate the interaction between Stat6 and PR-B. The cellular DNA content and cell cycle distribution in breast cancer cells were analyzed by FACS. We found that Stat6 interacts with progesterone-activated PR in T47D cells. Stat6 synergizes with progesterone-bound PR to transactivate the p21 and p27 gene promoters at the proximal Sp1-binding sites. Moreover, Stat6 overexpression and knockdown, respectively, increased or prevented the induction of p21 and p27 gene expression by progesterone. Stat6 knockdown also abolished the inhibitory effects of progesterone on pRB phosphorylation, G1/S cell cycle progression, and cell proliferation. In addition, knockdown of Stat6 expression prevented the induction of breast cell differentiation markers, previously identified as progesterone target genes. Finally, Stat6 gene expression levels increased following progesterone treatment, indicating a positive auto-regulatory loop between PR and Stat6. Taken together, these data identify Stat6 as a coactivator of PR mediating the growth-inhibitory and differentiation effects of progesterone on breast cancer cells.


Quantitative analysis of serum IL-6 and its correlation with increased levels of serum IL-2R in HIV-induced diseases.
We have devised a luminescence sandwich ELISA for the quantification of IL-6 in both sera and cell culture supernatants, which had a detection limit of 100 fg/ml of test sample. By using the luminescence sandwich-ELISA, low but measurable levels of IL-6 (9.5 pg/ml on average) were found in the sera from normal individuals. The serum levels of IL-6 were elevated in HIV-seropositive asymptomatic carriers (55.5 pg/ml on average), and the IL-6 levels were correlated with the degree of HIV-induced disease progression (AIDS-related complex 106.8 pg/ml on average and (AIDS 283 pg/ml). IL-6 immunoreactivity in the sera of AIDS patients eluted at a 25,000 m.w. major peak, which was biologically active and heat-stable, and a 500,000 m.w. minor peak in size-exclusion HPLC. Interestingly, a significant correlation was observed between the serum IL-6 levels and soluble IL-2R levels. In vitro, HIV infection of PHA-activated PBMC led to enhanced release of IL-6 into the culture supernatants. Moreover, soluble IL-2R release was markedly increased by adding exogenous IL-6, whereas it was decreased by adding the neutralizing anti-IL-6 mAb to the cultures. These results demonstrate that increased IL-6 levels are significantly associated with sIL-2R levels, and suggest a cause of the increased levels of this receptor in patients with HIV infection. Furthermore, both serum IL-6 and serum IL-2R levels in HIV infection reflect the stage of the HIV-induced disease.


Inhibitory effect of adenosine 3',5'-phosphate on cell division of Escherichia coli K-12 mutant derivatives.
Cell division of Escherichia coli K-12 strain PA3092 was inhibited by the addition of adenosine 3',5'-phosphate (cAMP), and the cellular morphology was changed from rods into filaments. Nucleoids in the filaments were regularly distributed and septum formation was perfectly inhibited. This inhibition of cell division by cAMP was reversed by the addition of guanosine 3',5'-monophosphate. To examine whether the inhibitory effect of cAMP on cell division in E. coli PA3092 was specific, its effect in several parental strains was investigated. Induction of cell filamentation by cAMP was observed in E. coli PA309 and P678, but not in E. coli W505, W1, Y10, or the wild-type strain. This result suggests that filamentation by cAMP in E. coli PA3092, PA309, and P678 was due to the mutagenesis by which E. coli P678 was derived from E. coli W595.


Estimating the impact of cefuroxime versus cefazolin and amoxicillin/clavulanate use on future collateral resistance: a retrospective comparison.
Quantitative estimates of collateral resistance induced by antibiotic use are scarce. To estimate the effects of treatment with amoxicillin/clavulanate or cefazolin, compared with cefuroxime, on future resistance to ceftazidime among hospitalized patients. A retrospective analysis of patients with positive bacterial cultures hospitalized in an Israeli hospital during 2016-19 was conducted. Patients were restricted to those treated with amoxicillin/clavulanate, cefazolin or cefuroxime and re-hospitalized with a positive bacterial culture during the following year. Matching was performed using exact, Mahalanobis and propensity score matching. Each patient in the amoxicillin/clavulanate and cefazolin groups was matched to a single patient from the cefuroxime group, yielding 185:185 and 298:298 matched patients. Logistic regression and the g-formula (standardization) were used to estimate the OR, risk difference (RD) and number needed to harm (NNH). Cefuroxime induced significantly higher resistance to ceftazidime than amoxicillin/clavulanate or cefazolin; the marginal OR was 1.76 (95% CI = 1.16-2.83) compared with amoxicillin/clavulanate and 1.98 (95% CI = 1.41-2.8) compared with cefazolin and the RD was 0.118 (95% CI = 0.031-0.215) compared with amoxicillin/clavulanate and 0.131 (95% CI = 0.058-0.197) compared with cefazolin. We also estimated the NNH; replacing amoxicillin/clavulanate or cefazolin with cefuroxime would yield ceftazidime resistance in 1 more patient for every 8.5 (95% CI = 4.66-32.14) or 7.6 (95% CI = 5.1-17.3) patients re-hospitalized in the following year, respectively. Our results indicate that treatment with amoxicillin/clavulanate or cefazolin is preferable to cefuroxime, in terms of future collateral resistance. The results presented here are a first step towards quantitative estimations of the ecological damage caused by different antibiotics.


Is Zolpidem Associated with Increased Risk of Fractures in the Elderly with Sleep Disorders? A Nationwide Case Cross-Over Study in Taiwan.
We conducted a study using a case-crossover design to clarify the risk of acute effects of zolpidem and benzodiazepine on all-sites of fractures in the elderly. Case-crossover design. Elderly enrollees (n = 6010) in Taiwan's National Health Insurance Research Database with zolpidem or benzodiazepine use were analyzed for the risk of developing fractures. After adjusting for medications such as antipsychotics, antidepressants, and diuretics, or comorbidities such as hypertension, osteoarthritis, osteoporosis, rheumatoid arthritis and depression, neither zolpidem nor benzodiazepine was found to be associated with increased risk in all-sites fractures. Subjects without depression were found to have an increased risk of fractures. Diazepam is the only benzodiazepine with increased risk of fractures after adjusting for medications and comorbidities. Hip and spine were particular sites for increased fracture risk, but following adjustment for comorbidities, the associations were found to be insignificant. Neither zolpidem nor benzodiazepine was associated with increased risk of all-site fractures in this case cross-over study after adjusting for medications or comorbidities in elderly individuals with insomnia. Clinicians should balance the benefits and risks for prescribing zolpidem or benzodiazepine in the elderly accordingly.


Novel treatments for melanoma brain metastases.
The development of brain metastases is common in patients with melanoma and is associated with a poor prognosis. Treating patients with melanoma brain metastases (MBMs) is a major therapeutic challenge. Standard approaches with conventional chemotherapy are disappointing, while surgery and radiotherapy have improved outcomes. In this article, we discuss the biology of MBMs, briefly outline current treatment approaches, and emphasize novel and emerging therapies for MBMs. The mechanisms that underlie the metastases of melanoma to the brain are unknown; therefore, it is necessary to identify pathways to target MBMs. Most patients with MBMs have short survival times. Recent use of immune-based and targeted therapies has changed the natural history of metastatic melanoma and may be effective for the treatment of patients with MBMs. Developing a better understanding of the factors responsible for MBMs will lead to improved management of this disease. In addition, determining the optimal treatments for MBMs and how they can be optimized or combined with other therapies, along with appropriate patient selection, are challenges for the management of this disease.


The Xanthomonas campestris type III effector XopJ targets the host cell proteasome to suppress salicylic-acid mediated plant defence.
The phytopathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) requires type III effector proteins (T3Es) for virulence. After translocation into the host cell, T3Es are thought to interact with components of host immunity to suppress defence responses. XopJ is a T3E protein from Xcv that interferes with plant immune responses; however, its host cellular target is unknown. Here we show that XopJ interacts with the proteasomal subunit RPT6 in yeast and in planta to inhibit proteasome activity. A C235A mutation within the catalytic triad of XopJ as well as a G2A exchange within the N-terminal myristoylation motif abolishes the ability of XopJ to inhibit the proteasome. Xcv ΔxopJ mutants are impaired in growth and display accelerated symptom development including tissue necrosis on susceptible pepper leaves. Application of the proteasome inhibitor MG132 restored the ability of the Xcv ΔxopJ to attenuate the development of leaf necrosis. The XopJ dependent delay of tissue degeneration correlates with reduced levels of salicylic acid (SA) and changes in defence- and senescence-associated gene expression. Necrosis upon infection with Xcv ΔxopJ was greatly reduced in pepper plants with reduced expression of NPR1, a central regulator of SA responses, demonstrating the involvement of SA-signalling in the development of XopJ dependent phenotypes. Our results suggest that XopJ-mediated inhibition of the proteasome interferes with SA-dependent defence response to attenuate onset of necrosis and to alter host transcription. A central role of the proteasome in plant defence is discussed.


Mammalian cells contain a DNA-recombining activity that can be dissociated from topoisomerase activity.
The role of the topoisomerase enzyme in DNA recombination was investigated by extracting chromosomal deoxyribonucleoproteins from a variety of cultured mammalian cells and assaying for the formation of recombinant DNA structures. Although each of the crude deoxyribonucleoprotein preparations contained topoisomerase activity, they did not all contain DNA-recombining activity. A distinct, perhaps novel, enzyme may therefore promote DNA recombination in these cell-free systems.


Increased vesicle recycling in response to osmotic cell swelling. Cause and consequence of hypotonicity-provoked ATP release.
Osmotic swelling of Intestine 407 cells leads to an immediate increase in cell surface membrane area as determined using the fluorescent membrane dye FM 1-43. In addition, as measured by tetramethylrhodamine isothiocyanate (TRITC)-dextran uptake, a robust (>100-fold) increase in the rate of endocytosis was observed, starting after a discrete lag time of 2-3 min and lasting for approximately 10-15 min. The hypotonicity-induced increase in membrane surface area, like the cell swelling-induced release of ATP (Van der Wijk, T., De Jonge, H. R., and Tilly, B. C. (1999) Biochem. J. 343, 579-586), was diminished after 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid-acetoxymethyl ester loading or cytochalasin B treatment. Uptake of TRITC-dextrans, however, was not affected. Treatment of the cells with the vesicle-soluble N-ethylmaleimide-sensitive factor attachment protein receptor-specific protease Clostridium botulinum toxin F not only nearly eliminated the hypotonicity-induced increase in membrane surface area but also strongly diminished the release of ATP, indicating the involvement of regulated exocytosis. Both the ATP hydrolase apyrase and the MEK inhibitor PD098059 diminished the osmotic swelling-induced increase in membrane surface area as well as the subsequent uptake of TRITC-dextrans. Taken together, the results indicate that extracellular ATP is required for the hypotonicity-induced vesicle recycling and suggest that a positive feedback loop, involving purinergic activation of the Erk-1/2 pathway, may contribute to the release of ATP from hypo-osmotically stimulated cells.


Subtle Malformation of the Cochlear Apex and Genetic Abnormalities: Beyond the "Thorny" Cochlea.
With the routine use of high-resolution heavily T2-weighted sequences to evaluate patients with hearing deficits, new, subtle phenotypes of cochlear malformations are being discovered and an increasing number of genotype-phenotype correlations are being found through a reverse phenotype approach, which can help guide geneticists. In this brief report, we present subtle malformations of the apical turn of the cochlea related to 3 genetic mutations, emphasizing the importance of a careful assessment of the cochlear apex.


Graviresponsiveness and columella cell structure in primary and secondary roots of Ricinus communis.
In order to determine what structural changes are associated with the onset of graviresponsiveness by plant roots, we have monitored the quantitative ultrastructures of columella (i.e., graviperceptive) cells in primary and secondary roots of Ricinus communis. The relative volumes of cellular components in lateral (i.e., minimally graviresponsive) roots were not significantly different from those of primary roots. The relative volumes of cellular components in secondary roots growing laterally were not significantly different from those of graviresponsive secondary roots. Therefore, the onset of graviresponsiveness by secondary roots of R. communis is not correlated with changes in organellar concentrations in columella cells. These results are discussed relative to a model for the differential graviresponsiveness of plant roots.


Photovoltaic electrical properties of aqueous grown ZnO antireflective nanostructure on Cu(In,Ga)Se₂ thin film solar cells.
A solution-grown subwavelength antireflection coating has been investigated for enhancing the photovoltaic efficiency of thin film solar cells. The 100-nm-height ZnO nanorods coating benefited the photocurrent of Cu(In,Ga)Se2 solar cells from 31.7 to 34.5 mA/cm2 via the decrease of surface light reflectance from 14.5% to 7.0%, contributed by the gradual refractive index profile between air and AZO window layer. The further reduction of surface reflectance to 2.3% in the case of 540-nm-height nanorods, yet, lowered the photocurrent to 29.5 mA/cm2, attributed to the decrease in transmittance. The absorption effect of hydrothermal grown ZnO nanorods was explored to optimize the antireflection function in enhancing photovoltaic performances.


Loss of Extracellular Signal-Regulated Kinase 1/2 in the Retinal Pigment Epithelium Leads to RPE65 Decrease and Retinal Degeneration.
Recent work suggested that the activity of extracellular signal-regulated kinase 1/2 (ERK1/2) is increased in the retinal pigment epithelium (RPE) of age-related macular degeneration (ARMD) patients and therefore could be an attractive therapeutic target. Notably, ERK1/2 pathway inhibitors are used in cancer therapy, with severe and noncharacterized ocular side effects. To decipher the role of ERK1/2 in RPE cells, we conditionally disrupted the Erk1 and Erk2 genes in mouse RPE. The loss of ERK1/2 activity resulted in a significant decrease in the level of RPE65 expression, a decrease in ocular retinoid levels concomitant with low visual function, and a rapid disorganization of RPE cells, ultimately leading to retinal degeneration. Our results identify the ERK1/2 pathway as a direct regulator of the visual cycle and a critical component of the viability of RPE and photoreceptor cells. Moreover, our results caution about the need for a very fine adjustment of kinase inhibition in cancer or ARMD treatment in order to avoid ocular side effects.


CO₂ adsorption on amine-functionalized periodic mesoporous benzenesilicas.
CO2 adsorption was investigated on amine-functionalized mesoporous silica (SBA-15) and periodic mesoporous organosilica (PMO) samples. Hexagonally (p6mm) ordered mesoporous SBA-15 and benzene-PMO (BPMO) samples were prepared in the presence of Pluronic P123 block copolymer template under acidic conditions. Three kinds of amine-containing organosilanes and polyethylenimine were used to functionalize SBA-15 and BPMO. Small-angle X-ray scattering and nitrogen adsorption isotherms showed that these samples featured ordered mesostructure, high surface area, and narrow pore size distributions. Solid-state (13)C- and (29)Si cross-polarization magic-angle spinning NMR spectra showed chemical linkage between amine-containing modifiers and the surface of mesoporous materials. The chemically linked amine-containing modifiers were found to be on both the inner and outer surfaces. N-[3-(trimethoxysilyl)propyl]ethylenediamine-modified BPMO (A2-BPMO) sample exhibited the highest CO2 uptake (i.e., ∼3.03 mmol/g measured on a volumetric adsorption analyzer) and the fastest adsorption rate (i.e., ∼13 min to attain 90% of the maximum amount) among all the samples studied. Selectivity and reproducibility measurements for the A2-BPMO sample showed quite good performance in flowing N2 gas at 40 mL/min and CO2 gas of 60 mL/min at 25 °C.


[Cytological analysis of the intact and regenerating liver of different strains of rats].
Comparative cytological studies were conducted on control and regenerating liver of two strains (August and Cotton) of rats, 2/3 of the liver was resected; 5 or 6 animals were sacrificed at each of the following postoperative periods: in 30 hours, 3, 8, 42 and 120 days. The number of binuclear cells, the size of mononuclear hepatocytes and their nuclei, the mitotic activity, and ploidity of hepatocytes were determined. The intact and regenerating liver of the August rats differed from the intact and regenerating liver of the Cotton rats by a number of cytological indices, excluding the mitotic activity. A conclusion was drawn that the observed interstrain differences in the cytological indices providing regeneration of the liver after resection in the August and Cotton rats depended on the genotype of the given strain.


Human cooperation based on punishment reputation.
The threat of punishment usually promotes cooperation. However, punishing itself is costly, rare in nonhuman animals, and humans who punish often finish with low payoffs in economic experiments. The evolution of punishment has therefore been unclear. Recent theoretical developments suggest that punishment has evolved in the context of reputation games. We tested this idea in a simple helping game with observers and with punishment and punishment reputation (experimentally controlling for other possible reputational effects). We show that punishers fully compensate their costs as they receive help more often. The more likely defection is punished within a group, the higher the level of within-group cooperation. These beneficial effects perish if the punishment reputation is removed. We conclude that reputation is key to the evolution of punishment.


Plasma Metabolites Alert Patients With Chest Pain to Occurrence of Myocardial Infarction.
Myocardial infarction (MI) is one of the leading causes of death worldwide, and knowing the early warning signs of MI is lifesaving. To expand our knowledge of MI, we analyzed plasma metabolites in MI and non-MI chest pain cases to identify markers for alerting about MI occurrence based on metabolomics. A total of 230 volunteers were recruited, consisting of 146 chest pain patients admitted with suspected MI (85 MIs and 61 non-MI chest pain cases) and 84 control individuals. Non-MI cardiac chest pain cases include unstable angina (UA), myocarditis, valvular heart diseases, etc. The blood samples of all suspected MI cases were collected not longer than 6 h since the onset of chest pain. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry were applied to identify and quantify the plasma metabolites. Multivariate statistical analysis was utilized to analyze the data, and principal component analysis showed MI could be clearly distinguished from non-MI chest pain cases (including UA and other cases) in the scores plot of metabolomic data, better than that based on the data constructed with medical history and clinical biochemical parameters. Pathway analysis highlighted an upregulated methionine metabolism and downregulated arginine biosynthesis in MI cases. Receiver operating characteristic curve (ROC) and adjusted odds ratio (OR) were calculated to evaluate potential markers for the diagnosis and prediction ability of MI (MI vs. non-MI cases). Finally, gene expression profiles from the Gene Expression Omnibus (GEO) database were briefly discussed to study differential metabolites' connection with plasma transcriptomics. Deoxyuridine (dU), homoserine, and methionine scored highly in ROC analysis (AUC > 0.91), sensitivity (>80%), and specificity (>94%), and they were correlated to LDH and AST (p < 0.05). OR values suggested, after adjusting for gender, age, lipid levels, smoking, type II diabetes, and hypertension history, that high levels of dU of positive logOR = 3.01, methionine of logOR = 3.48, and homoserine of logOR = 1.61 and low levels of isopentenyl diphosphate (IDP) of negative logOR = -5.15, uracil of logOR = -2.38, and arginine of logOR = -0.82 were independent risk factors of MI. Our study highlighted that metabolites belonging to pyrimidine, methionine, and arginine metabolism are deeply influenced in MI plasma samples. dU, homoserine, and methionine are potential markers to recognize MI cases from other cardiac chest pain cases after the onset of chest pains. Individuals with high plasma abundance of dU, homoserine, or methionine have increased risk of MI, too.


CRIM1 complexes with ß-catenin and cadherins, stabilizes cell-cell junctions and is critical for neural morphogenesis.
In multicellular organisms, morphogenesis is a highly coordinated process that requires dynamically regulated adhesion between cells. An excellent example of cellular morphogenesis is the formation of the neural tube from the flattened epithelium of the neural plate. Cysteine-rich motor neuron protein 1 (CRIM1) is a single-pass (type 1) transmembrane protein that is expressed in neural structures beginning at the neural plate stage. In the frog Xenopus laevis, loss of function studies using CRIM1 antisense morpholino oligonucleotides resulted in a failure of neural development. The CRIM1 knockdown phenotype was, in some cases, mild and resulted in perturbed neural fold morphogenesis. In severely affected embryos there was a dramatic failure of cell adhesion in the neural plate and complete absence of neural structures subsequently. Investigation of the mechanism of CRIM1 function revealed that it can form complexes with ß-catenin and cadherins, albeit indirectly, via the cytosolic domain. Consistent with this, CRIM1 knockdown resulted in diminished levels of cadherins and ß-catenin in junctional complexes in the neural plate. We conclude that CRIM1 is critical for cell-cell adhesion during neural development because it is required for the function of cadherin-dependent junctions.


Data harmonization and federated analysis of population-based studies: the BioSHaRE project.
Individual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses. Eight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study's questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis. Retrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method. New Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co-analyse internationally harmonized research databases while allowing each study to retain full control over individual-level data. We encourage additional collaborative research networks in epidemiology, public health, and the social sciences to make use of the open source tools presented herein.


Human bone marrow mesenchymal stem cells in vivo.
Great confusion still exists amongst cell biologists, musculoskeletal and other specialists interested in regenerative medicine regarding the in vivo identity of human bone marrow (BM) mesenchymal stem cells (MSCs). Contrary to views held in some quarters, methods for the robust identification and purification of BM MSCs are now well established. Human BM MSCs represent a phenotypically homogeneous cell population that share an identical phenotype with marrow adventitial reticular cells (ARCs), which are stromal cells similar in nature to pericytes. When an extensive panel of markers is used to characterize BM MSCs, it appears that the diverse MSC markers described in different laboratories are expressed on the same cell population. Rare cell phenotypical analysis and in vitro colony forming unit-fibroblast (CFU-F) assays produce no compelling evidence that BM MSCs circulate in healthy man. Furthermore, although investigators speak of a number of specific MSC markers, a true marker of MSC 'stemness' and multipotentiality has not yet been defined since culture-expanded MSCs may lose some of these markers, but remain multipotential. This knowledge provides a platform for understanding MSCs in vivo leading to novel approaches for therapy development, including in situ tissue engineering.


The calmodulin content of normal and leukaemic lymphocytes.
Normal human peripheral blood mononuclear cells (PBMC) and leukaemic cell lines (three of human and one of gibbon origin) were found to contain similar levels of calmodulin (CaM) when expressed relative to the total cell protein. Two of the cell lines examined further were found to contain much higher amounts of CaM per cell (up to 5-fold) than PBMC but this was readily explained by their much greater cell size. Variations in CaM levels were noted during culture of both PBMC and leukaemic cells which were apparently independent of the percentage of cells undergoing active division in these cultures. These results do not support the contention that transformed cells contain a higher proportion of CaM than normal cells.


Control of oligodendroglial cell number by the miR-17-92 cluster.
The generation of myelinating cells in the central nervous system requires the initiation of specific gene expression programs in oligodendrocytes. We reasoned that microRNAs (miRNAs) could play an important role in this process by regulating crucial developmental genes. Microarray profiling of cultured oligodendrocytes identified the miR-17-92 miRNA cluster as highly enriched in oligodendrocytes. We specifically deleted the miR-17-92 cluster in oligodendrocytes using 2',3'-cyclic nucleotide 3' phosphodiesterase (Cnp)-Cre mice. Absence of miR-17-92 leads to a reduction in oligodendrocyte number in vivo and we find that the expression of these miRNAs in primary cultures of oligodendrocyte precursor cells promotes cell proliferation by influencing Akt signaling. Together, these results suggest that the miRNA pathway is essential in determining oligodendroglial cell number and that the miR-17-92 cluster is crucial in this process.


Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts.
The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL-F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum-likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9-93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2-52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio-Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long-distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large-scale distribution of humid tropical angiosperm forests in the Eocene.