Visualization of double-stranded RNA in cells supporting hepatitis C virus RNA replication.
The mechanisms involved in hepatitis C virus (HCV) RNA replication are unknown, and this aspect of the virus life cycle is not understood. It is thought that virus-encoded nonstructural proteins and RNA genomes interact on rearranged endoplasmic reticulum (ER) membranes to form replication complexes, which are believed to be sites of RNA synthesis. We report that, through the use of an antibody specific for double-stranded RNA (dsRNA), dsRNA is readily detectable in Huh-7 cells that contain replicating HCV JFH-1 genomes but is absent in control cells. Therefore, as that of other RNA virus genomes, the replication of the HCV genome may involve the generation of a dsRNA replicative intermediate. In Huh-7 cells supporting HCV RNA replication, dsRNA was observed as discrete foci, associated with virus-encoded NS5A and core proteins and identical in morphology and distribution to structures containing HCV RNA visualized by fluorescence-based hybridization methods. Three-dimensional reconstruction of deconvolved z-stack images of virus-infected cells provided detailed insight into the relationship among dsRNA foci, NS5A, the ER, and lipid droplets (LDs). This analysis revealed that dsRNA foci were located on the surface of the ER and often surrounded, partially or wholly, by a network of ER-bound NS5A protein. Additionally, virus-induced dsRNA foci were juxtaposed to LDs, attached to the ER. Thus, we report the visualization of HCV-induced dsRNA foci, the likely sites of virus RNA replication, and propose that HCV genome synthesis occurs at LD-associated sites attached to the ER in virus-infected cells.


A field study of the effects of elevated CO(2) on plant biomass and community structure in a calcareous grassland.
The effects of elevated CO(2) on plant biomass and community structure have been studied for four seasons in a calcareous grassland in northwest Switzerland. This highly diverse, semi-natural plant community is dominated by the perennial grass Bromus erectus and is mown twice a year to maintain species composition. Plots of 1.3 m(2) were exposed to ambient or elevated CO(2) concentrations (n = 8) using a novel CO(2) exposure technique, screen-aided CO(2) control (SACC) starting in March 1994. In the 1st year of treatment, the annual harvested biomass (sum of aboveground biomass from mowings in June and October) was not significantly affected by elevated CO(2). However, biomass increased significantly at elevated CO(2) in the 2nd (+20%, P = 0.05), 3rd (+21%, P = 0.02) and 4th years (+29%, P = 0.02). There were no detectable differences in root biomass in the top 8 cm of soil between CO(2) treatments on eight out of nine sampling dates. There were significant differences in CO(2) responsiveness between functional groups (legumes, non-leguminous forbs, graminoids) in the 2nd (P = 0.07) and 3rd (P < 0.001) years of the study. The order of CO(2) responsiveness among functional groups changed substantially from the 2nd to the 3rd year; for example, non-leguminous forbs had the smallest relative response in the 2nd year and the largest in the 3rd year. By the 3rd year of CO(2) exposure, large species-specific differences in CO(2) response had developed. For five important species or genera the order of responsiveness was Lotus corniculatus (+271%), Carex flacca (+249%), Bromus erectus (+33%), Sanguisorba minor (no significant CO(2) effect), and six Trifolium species (a negative response that was not significant). The positive CO(2) responses in Bromus and Carex were most closely related to increases in tiller number. Species richness was not affected by CO(2) treatment, but species evenness increased under elevated CO(2) (modified Hill ratio; P = 0.03) in June of the 3rd year, resulting in a marginally significant increase in species diversity (Simpson's index; P = 0.09). This and other experiments with calcareous grassland plants show that elevated atmospheric CO(2) concentrations can substantially alter the structure of calcareous grassland communities and may increase plant community biomass.


Extracts from The Cochrane Library: Tonsillectomy for chronic/recurrent acute tonsillitis.
The "Cochrane Corner" is a quarterly section in the Journal that highlights systematic reviews relevant to otolaryngology-head and neck surgery, with invited commentary to highlight implications for clinical decision making. This installment features a Cochrane Review entitled "Tonsillectomy or adeno-tonsillectomy versus non-surgical treatment for chronic/recurrent acute tonsillitis," which concludes modest efficacy in children for sore throat days and episodes, with greater benefit for those with more severe illness.


A morphometric and molecular study of Anastrepha pickeli Lima (Diptera: Tephritidae).
This study investigated the level of morphometric and genetic variability among populations of Anastrepha pickeli Lima from several localities in Brazil, one locality in Bolivia and one in Paraguay. Traditional and geometric morphometric analyses were used, as well as sequencing of a fragment of the cytochrome oxidase gene (COI). Six variables were measured from the aculeus for traditional morphometric analysis and 14 landmarks from the right wing were used for geometric analysis, using 10 specimes/population. The aculeus tip length, aculeus width at the end of the cloaca opening, and the serrate part length contributed with 62.7% for grouping. According to the results from traditional morphometry, there was no significant difference, but the multivariate tests showed that the canonical variables were statistically significant, indicating a difference in the wing conformation among populations. Molecular phylogenetic analysis indicated that the populations clustered into three clades and revealed a high level of genetic variation within A. pickeli populations from various geographic regions. Anastrepha pickeli populations differed among them according to the methods used in this study, showing incongruence among the methods used.


ortho-Substituted Aryldiazonium Design for the Defect Configuration-Controlled Photoluminescent Functionalization of Chiral Single-Walled Carbon Nanotubes.
Defect functionalization of single-walled carbon nanotubes (SWCNTs) by chemical modification is a promising strategy for near-infrared photoluminescence (NIR PL) generation at >1000 nm, which has advanced telecom and bio/medical applications. The covalent attachment of molecular reagents generates sp3-carbon defects in the sp2-carbon lattice of SWCNTs with bright red-shifted PL generation. Although the positional difference between proximal sp3-carbon defects, labeled as the defect binding configuration, can dominate NIR PL properties, the defect arrangement chemistry remains unexplored. Here, aryldiazonium reagents with π-conjugated ortho-substituents (phenyl and acetylene groups) were developed to introduce molecular interactions with nanotube sidewalls into the defect-formation chemical reaction. The functionalized chiral SWCNTs selectively emitted single defect PL in the wavelength range of ∼1230-1270 nm for (6,5) tubes, indicating the formation of an atypical binding configuration, different from those exhibited by typical aryl- or alkyl-functionalized chiral tubes emitting ∼1150 nm PL. Moreover, the acetylene-based substituent design enabled PL brightening and a subsequent molecular modification of the doped sites using click chemistry.


Therapeutic potential of cannabinoid-based drugs.
Cannabinoid-based drugs modeled on cannabinoids originally isolated from marijuana are now known to significantly impact the functioning of the endocannabinoid system of mammals. This system operates not only in the brain but also in organs and tissues in the periphery including the immune system. Natural and synthetic cannabinoids are tricyclic terpenes, whereas the endogenous physiological ligands are eicosanoids. Several receptors for these compounds have been extensively described, CB1 and CB2, and are G protein-coupled receptors; however, cannabinoid-based drugs are also demonstrated to function independently of these receptors. Cannabinoids regulate many physiological functions and their impact on immunity is generally antiinflammatory as powerful modulators of the cytokine cascade. This anti-inflammatory potency has led to the testing of these drugs in chronic inflammatory laboratory paradigms and even in some human diseases. Psychoactive and nonpsychoactive cannabinoid-based drugs such as Delta9-tetrahydrocannabinol, cannabidiol, HU-211, and ajulemic acid have been tested and found moderately effective in clinical trials of multiple sclerosis, traumatic brain injury, arthritis, and neuropathic pain. Furthermore, although clinical trials are not yet reported, preclinical data with cannabinoid-based drugs suggest efficacy in other inflammatory diseases such as inflammatory bowel disease, Alzheimer's disease, atherosclerosis, and osteoporosis.


Coexistence of Colorectal Adenomas and Coronary Calcification in Asymptomatic Men and Women.
Because of shared risk factors between clinically manifest cardiovascular disease and colorectal cancer, we hypothesized the coexistence of subclinical atherosclerosis measured by coronary artery calcium (CAC) and colorectal adenoma (CRA) and that these 2 processes would also share common risk factors. No study has directly compared the risk factors associated with subclinical coronary atherosclerosis and CRA. This was a cross-sectional study using multinomial logistic regression analysis of 4859 adults who participated in a health screening examination (2010 to 2011; analysis 2014 to 2015). CAC scores were categorized as 0, 1 to 100, or >100. Colonoscopy results were categorized as absent, low-risk, or high-risk CRA. The prevalence of CAC>0, CAC 1 to 100 and >100 was 13.0%, 11.0%, and 2.0%, respectively. The prevalence of any CRA, low-risk CRA, and high-risk CRA was 15.1%, 13.0%, and 2.1%, respectively. The adjusted odds ratios (95% confidence interval) for CAC>0 comparing participants with low-risk and high-risk CRA with those without any CRA were 1.35 (1.06-1.71) and 2.09 (1.29-3.39), respectively. Similarly, the adjusted odds ratios (95% confidence interval) for any CRA comparing participants with CAC 1 to 100 and CAC>100 with those with no CAC were 1.26 (1.00-1.6) and 2.07 (1.31-3.26), respectively. Age, smoking, diabetes, and family history of CRC were significantly associated with both conditions. We observed a graded association between CAC and CRA in apparently healthy individuals. The coexistence of both conditions further emphasizes the need for more evidence of comprehensive approaches to screening and the need to consider the impact of the high risk of coexisting disease in individuals with CAC or CRA, instead of piecemeal approaches restricted to the detection of each disease independently.


Sociodemographic and environmental risk factors for American cutaneous leishmaniasis (ACL) in the State of Alagoas, Brazil.
The multiplicity of factors involved in the transmission of the American cutaneous leishmaniasis (ACL) constitutes a challenge to its control. Thus, knowledge of such factors may contribute extremely toward redefining the control strategies. The aim of this study was to identify sociodemographic and environmental factors relating to ACL transmission in the State of Alagoas, Brazil. A case-control study with incident cases was conducted. Diagnostic criteria were the presence of compatible skin lesions, laboratory confirmation, and clinical cure after treatment. Two control groups were matched to cases by sex and age: one comprising neighbors and the other from a community-based draw; controls were individuals with no lesion and a negative Montenegro intradermal reaction. Between July 1, 2004 and February 1, 2007, 98 cases and the same number of controls per group were selected. In the multivariate analysis, for both control groups, ACL was associated with absence of a gas stove and forest less than 200 m away; for neighborhood controls with schooling of 4 years or less, family income greater than one minimum salary, birds inside the home, forest-related leisure activities, and rural work or school activities; and for community controls with non-durable wall material in the house, per capita income greater than US$ 28.31, animals inside the house, and absence of dogs and cats around the house. Specific control measures are recommended for areas with similar characteristics: protection for individuals undertaking forest-related leisure activities; distancing houses from forests by more than 200 m; and elimination of bird or other animal-rearing inside homes. General measures of improved housing and living conditions are also recommended.


Mutation screening of patients with Leber Congenital Amaurosis or the enhanced S-Cone Syndrome reveals a lack of sequence variations in the NRL gene.
To determine if mutations in the retinal transcription factor gene NRL are associated with retinopathies other than autosomal dominant retinitis pigmentosa (adRP). Genomic DNA was isolated from blood samples obtained from 50 patients with Leber Congenital Amaurosis (LCA), 17 patients with the Enhanced S-Cone Syndrome (ESCS), and a patient with an atypical retinal degeneration that causes photoreceptor rosettes with blue cone opsin. The 5' upstream region (putative promoter), untranslated exon 1, coding exons 2 and 3, and exon-intron boundaries of the NRL gene were analyzed by direct sequencing of the PCR-amplified products. Complete sequencing of the NRL gene in DNA samples from this cohort of patients revealed only one nucleotide change. The C->G transversion at nucleotide 711 of NRL exon 3 was detected in one LCA patient; however, this change did not alter the amino acid (L237L). No potential disease causing mutation was identified in the NRL gene in patients with LCA, ESCS, or the atypical retinal degeneration. Together with previous studies, our results demonstrate that mutations in the NRL gene are not a major cause of retinopathy. To date, only missense changes have been reported in adRP patients, and sequence variations are rare. It is possible that the loss of NRL function in humans is associated with a more complex clinical phenotype due to its expression in pineal gland in addition to rod photoreceptors.


Comparison of Neurochemical and BOLD Signal Contrast Response Functions in the Human Visual Cortex.
We investigated the relationship between neurochemical and hemodynamic responses as a function of image contrast in the human primary visual cortex (V1). Simultaneously acquired BOLD-fMRI and single voxel proton MR spectroscopy signals were measured in V1 of 24 healthy human participants of either sex at 7 tesla field strength, in response to presentations (64 s blocks) of different levels of image contrast (3%, 12.5%, 50%, 100%). Our results suggest that complementary measures of neurotransmission and energy metabolism are in partial agreement: BOLD and glutamate signals were linear with image contrast; however, a significant increase in glutamate concentration was evident only at the highest intensity level. In contrast, GABA signals were steady across all intensity levels. These results suggest that neurochemical concentrations are maintained at lower ranges of contrast levels, which match the statistics of natural vision, and that high stimulus intensity may be critical to increase sensitivity to visually modulated glutamate signals in the early visual cortex using MR spectroscopy.SIGNIFICANCE STATEMENT Glutamate and GABA are the major excitatory and inhibitory neurotransmitters of the brain. To better understand the relationship between MRS-visible neurochemicals, the BOLD signal change, and stimulus intensity, we measured combined neurochemical and BOLD signals (combined fMRI-MRS) to different image contrasts in human V1 at 7 tesla. While a linear change to contrast was present for both signals, the increase in glutamate was significant only at the highest stimulus intensity. These results suggest that hemodynamic and neurochemical signals reflect common metabolic markers of neural activity, whereas the mismatch at lower contrast levels may indicate a sensitivity threshold for detecting neurochemical changes during visual processing. Our results highlight the challenge and importance of reconciling cellular and metabolic measures of neural activity in the human brain.


Changes in tobacco smoking following treatment for cocaine dependence.
Incorporation of smoking cessation into cocaine treatment programs remains a challenge. A major concern is that cocaine abusers may tend to substitute one drug for the other. If this is true, successful treatment of cocaine abuse should lead to an increase in tobacco smoking. We compared tobacco smoking at admission, end of treatment and 9-month follow up for 168 crack cocaine dependent patients entering a 12-week outpatient treatment program for substance abuse. Smoking cessation was not a part of treatment. As expected cocaine patients improved with treatment and showed significant reduction in scores on the Addiction Severity Index (ASI). There were no significant changes in number of cigarettes smoked per day or scores on the Fagerstrom Test for Nicotine dependence (FTND) from baseline to end of treatment or follow-up. Also, there were no differences in the proportions of nonsmokers and smokers who changed their smoking habits over the treatment and follow up period. At follow up subjects who were abstinent as well as those using cocaine showed no changes in tobacco smoking. There is no evidence that reduction in crack cocaine smoking following treatment is accompanied by an increase in tobacco smoking. It appears that concerns over tobacco being substituted for cocaine may be unfounded in this population.


Sialic acid linkage in glycosphingolipids is a molecular correlate for trafficking and delivery of extracellular cargo.
Gangliosides, glycosphingolipids containing sialic acid moieties, are well known mediators of transmembrane signaling and endocytosis at the plasma membrane. However, little is known about their precise regulatory role at the cell periphery for intracellular sorting of extracellular cargo. Here we inspected published scientific literature for two types of cargoes, namely bacterial toxins and viruses, regarding their usage of gangliosides. We derived a rather simple yet surprisingly consistent framework to classify 20 viruses from 12 different families and five type AB bacterial toxins into two broad categories. We propose that gangliosides with terminally attached sialic acids classify cargo for uptake and trafficking early in the endocytic pathway while gangliosides with internally attached sialic acids associate with uptake and trafficking of cargo late in the endocytic system. Our study provides a testable hypothesis for future investigations into a wide range of trafficking events. It could be utilized as a framework for other intracellular pathogens where lipids are known to be involved in recognition and trafficking. For instance, predictions can be put forward and evaluated based on ganglioside binding patterns and intracellular trafficking routes. Finally, incorporation of our classifier into large scale systems-biology studies could help reveal related molecular determinants in subcellular sorting.


A study on inhibitory effect of Spica prunellae extract on T lymphoma cell EL-4 tumour.
The objective of the study was to investigate the in-vivo anti-tumour activity of Spica prunellae extract, and to preliminarily explore the possible mechanism of in-vivo anti-tumour effect of Spica prunellae extract. Tumour inhibition rate and tumour apoptosis-related protein status were determined using the mice model of transplanted T lymphoma cell EL-4 tumour, and by immunohistochemical method. The results revealed that Spica prunellae extract showed certain tumour inhibitory effect, and compared with the model group. Tumour weight in Spica prunellae high-dose group was highly significantly different (P<0.01). Tumour weight in Spica prunellae medium-dose group was also significantly different (P<0.05) compared with the model group. Spica prunellae high-dose group enabled the high expression of Bcl-2 protein (47.54%) and low expression of Bax protein (13.14%). The study concluded that Spica prunellae extract has certain in vivo anti-tumour effect, which may be achieved through regulation of apoptosis related proteins.


Healing of diabetic neuropathic foot ulcers receiving standard treatment. A meta-analysis.
The aim of the study was to determine the percentage of individuals with neuropathic diabetic foot ulcers receiving good wound care who heal within a defined period of time. We conducted a systematic review of the control groups of clinical trials that evaluated a treatment for diabetic neuropathic foot ulcers. The meta-analytic techniques used include an estimation of the weighted mean percentage healed by end point, an evaluation of the homogeneity of trials, and an estimate of the 95% CI of the grouped data. Grouped-data univariate and multivariate logistic regression was conducted to assess the impact of mean age, ulcer size, and duration on the percentage of ulcers healed at end point. We found a total of 10 control groups meeting our criteria. Six control groups used 20 weeks as the end point for healing or nonhealing. For the six control arms with a 20-week end point, we found a weighted mean healing rate of 30.9% (95% CI 26.6-35.1). A similar analysis for the four 12-week arms found a mean healing rate of 24.2% (19.5-28.8). We failed to detect any statistically significant heterogeneity for either the 20-week or the 12-week trials. After 20 weeks of good wound care, approximately 31% of diabetic neuropathic ulcers heal. Similarly, after 12 weeks of good care, approximately 24% of neuropathic ulcers attain complete healing. Further patient-level analyses are necessary to definitively determine the associations of age, wound size, and wound duration with likelihood of healing.


Rules for clinical diagnosis in babies with ambiguous genitalia.
Intersex disorders are rare and complex; yet, in each case of genital ambiguity, accurate and expeditious management is required of the clinician. This article reviews the embryology of sexual differentiation, from which some 'rules' of diagnosis are derived. A simplified approach to the interpretation of clinical signs in ambiguous genitalia is presented and discussed.


Bioinformatics Analysis Reveals Genes Involved in the Pathogenesis of Ameloblastoma and Keratocystic Odontogenic Tumor.
Pathogenesis of odontogenic tumors is not well known. It is important to identify genetic deregulations and molecular alterations. This study aimed to investigate, through bioinformatic analysis, the possible genes involved in the pathogenesis of ameloblastoma (AM) and keratocystic odontogenic tumor (KCOT). Genes involved in the pathogenesis of AM and KCOT were identified in GeneCards. Gene list was expanded, and the gene interactions network was mapped using the STRING software. "Weighted number of links" (WNL) was calculated to identify "leader genes" (highest WNL). Genes were ranked by K-means method and Kruskal-Wallis test was used (P<0.001). Total interactions score (TIS) was also calculated using all interaction data generated by the STRING database, in order to achieve global connectivity for each gene. The topological and ontological analyses were performed using Cytoscape software and BinGO plugin. Literature review data was used to corroborate the bioinformatics data. CDK1 was identified as leader gene for AM. In KCOT group, results show PCNA and TP53. Both tumors exhibit a power law behavior. Our topological analysis suggested leader genes possibly important in the pathogenesis of AM and KCOT, by clustering coefficient calculated for both odontogenic tumors (0.028 for AM, zero for KCOT). The results obtained in the scatter diagram suggest an important relationship of these genes with the molecular processes involved in AM and KCOT. Ontological analysis for both AM and KCOT demonstrated different mechanisms. Bioinformatics analyzes were confirmed through literature review. These results may suggest the involvement of promising genes for a better understanding of the pathogenesis of AM and KCOT.


The carboxy terminus of Tub4p is required for gamma-tubulin function in budding yeast.
The role of gamma-tubulin in microtubule nucleation is well established, however, its function in other aspects of microtubule organization is unknown. The carboxy termini of alpha/beta-tubulins influence the assembly and stability of microtubules. We investigated the role of the carboxy terminus of yeast gamma-tubulin (Tub4p) in microtubule organization. This region consists of a conserved domain (DSYLD), and acidic tail. Cells expressing truncations lacking the DSYLD domain, tail or both regions are temperature sensitive for growth. Growth defects of tub4 mutants lacking either or both carboxy-terminal domains are suppressed by the microtubule destabilizing drug benomyl. tub4 carboxy-terminal mutants arrest as large budded cells with short bipolar spindles positioned at the bud neck. Electron microscopic analysis of wild-type and CTR mutant cells reveals that SPBs are tightly associated with the bud neck/cortex by cytoplasmic microtubules in mutants lacking the tail region (tub4-delta 444, tub4-delta 448). Mutants lacking the DSYLD residues (tub4-delta 444, tub4-delta DSYLD) form many cytoplasmic microtubules. We propose that the carboxy terminus of Tub4p is required for re-organization of the microtubules upon completion of nuclear migration, and facilitates spindle elongation into the bud.


Risk Factors for Violent Injuries and Their Severity Among Men in The Gambia.
A matched case-control study was conducted to identify risk factors for injury from physical violence and its severity in Gambian men. Study participants were recruited from eight emergency rooms and outpatient departments in two health administrative regions. Cases were male patients aged ⩾15 years who had been violently injured. A control patient for each case, matched for the hospital or health center, date of injury, gender, and age, was selected from those injured due to nonviolence causes. In total, 447 case-control pairs were recruited. Results of the conditional logistic regression analysis showed that case patients who worked as businessmen (odds ratio [OR], 1.93; 95% confidence interval [CI] [1.16, 3.20]), had monthly household income of ⩾US$311 (OR, 2.12; 95% CI [1.06, 4.24]), had two or more male siblings (OR, 2.20; 95% CI [1.15, 4.21]), had consumed alcohol in the past week (OR, 3.32; 95% CI [1.25, 8.84]), and had been physically abused (OR, 5.10; 95% CI [2.71, 9.62]) or verbally abused (OR, 1.63; 95% CI [1.04, 2.56]) in the past 12 months were significantly associated with the occurrence of injury from physical violence. Severe injuries during the violence were significantly associated with events that took place in public spaces, with certain injury mechanisms (being stabbed/cut/pierced, struck by an object, assaulted by fist punching/leg kicking/head-butting, and scalded/stoned), having injuries to the upper extremities, and smoked cigarettes in the past week. Specific public health programs aimed at preventing physical violence and severe injuries against men should be developed in The Gambia based on modifications of the identified risk factors.


In vivo gene therapy for hyperlipidemia: phenotypic correction in Watanabe rabbits by hepatic delivery of the rabbit LDL receptor gene.
Elevations of plasma total or LDL cholesterol are major risk factors for cardiovascular disease. Efforts directed at preventing and treating cardiovascular disease have often focused on reducing the levels of these substances in the blood. The Watanabe Heritable Hyperlipidemic Rabbit, which has exceedingly high plasma cholesterol levels resulting from an LDL receptor deficiency, provides an excellent animal model for testing new treatments. A recombinant adenoviral vector containing the rabbit LDL receptor cDNA was administered to Watanabe rabbits. Plasma total cholesterol levels in the treated animals were reduced from 825.5 +/- 69.8 (mean +/- SD) to 247.3 +/- 61.5 mg/dl 6 d after infusion. These animals also demonstrated a 300-400% increase in plasma levels of HDL cholesterol and apo AI 10 d after treatment. As a result, the LDL:HDL ratio exhibited a dramatic decrease. Because only the rabbit LDL receptor gene was used for treatment, the results strongly suggest that the elevations of plasma HDL cholesterol and apo AI were secondary to a reduction in plasma total cholesterol in the treated animals. These results suggest an inverse relationship between plasma LDL and HDL cholesterol levels and imply that reduction of LDL cholesterol levels may have a beneficial effect on plasma HDL cholesterol.


Effects of iodine-125 brachytherapy on the proliferative capacity and histopathological features of glioblastoma recurring after initial therapy.
To determine the effect of initial therapy (surgery and external beam radiation) on the proliferative capacity of glioblastoma and whether adjunctive high focused doses of radiation therapy can further reduce the proliferative capacity of the tumor. This would provide a rationale for attempting to further control local tumor growth with the different forms of high-dose focused radiation available. Patients with glioblastoma were initially treated within a randomized, controlled study with or without iodine-125 (125 I) brachytherapy after initial surgical resection and external beam radiation (50 Gy in 25 fractions). Specimens from 24 consecutive patients later reoperated for "recurrence" were used to determine the effects of 125 I brachytherapy on the histological features and proliferating cell nuclear antigen index of the tumor tissue. 125 I brachytherapy reduced histological features prognostic for tumor progression, i.e., cellularity, pleomorphism, vessel hyperplasia, and degree of mitosis (P < 0.05). The degree of mitosis (marker for the mitotic or "M" phase) and proliferating cell nuclear antigen index (market for the late G1 and S phase) provide complementary data on the cell kinetics of the tumor. Proliferating cell nuclear antigen immunostaining was lower in the 125 I brachytherapy group (34.6 +/- 8.2%, mean +/- standard error) compared with the control nonimplant group (68.2 +/- 3.5%). 125 I brachytherapy produced a dramatic reduction in mitotic figures (mean histological score = 0.0 +/- 0.0). Adjunctive treatment of glioblastoma with discrete high doses of radiation therapy delivered by 125 I brachytherapy allows further control of the proliferative capacity of the tumor.


Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models.
Estimating temporal changes in a target population from phylogenetic or count data is an important problem in ecology and epidemiology. Reliable estimates can provide key insights into the climatic and biological drivers influencing the diversity or structure of that population and evidence hypotheses concerning its future growth or decline. In infectious disease applications, the individuals infected across an epidemic form the target population. The renewal model estimates the effective reproduction number, R, of the epidemic from counts of observed incident cases. The skyline model infers the effective population size, N, underlying a phylogeny of sequences sampled from that epidemic. Practically, R measures ongoing epidemic growth while N informs on historical caseload. While both models solve distinct problems, the reliability of their estimates depends on p-dimensional piecewise-constant functions. If p is misspecified, the model might underfit significant changes or overfit noise and promote a spurious understanding of the epidemic, which might misguide intervention policies or misinform forecasts. Surprisingly, no transparent yet principled approach for optimizing p exists. Usually, p is heuristically set, or obscurely controlled via complex algorithms. We present a computable and interpretable p-selection method based on the minimum description length (MDL) formalism of information theory. Unlike many standard model selection techniques, MDL accounts for the additional statistical complexity induced by how parameters interact. As a result, our method optimizes p so that R and N estimates properly and meaningfully adapt to available data. It also outperforms comparable Akaike and Bayesian information criteria on several classification problems, given minimal knowledge of the parameter space, and exposes statistical similarities among renewal, skyline, and other models in biology. Rigorous and interpretable model selection is necessary if trustworthy and justifiable conclusions are to be drawn from piecewise models. [Coalescent processes; epidemiology; information theory; model selection; phylodynamics; renewal models; skyline plots].


Functional chiral asymmetry in descending thoracic aorta.
To determine whether rotational blood flow or chiral asymmetry exists in the human descending thoracic aorta, we established the ability of color Doppler ultrasound to detect rotational flow in a tornado tube model of a vortex descending fluid column. In a model of the human aortic arch with a pulse duplicator, color Doppler was then used to demonstrate that rotational flow occurs first in the transverse arch and then in the proximal descending thoracic aorta. With the use of color Doppler esophageal echocardiography, 53 patients (age range, 25-78 years; mean age, 56.4 years) were prospectively examined for rotational flow in the descending thoracic aorta. At 10 cm superior to retro-left ventricular position, 22 of 38 patients (58%) revealed rotational flow with obvious diastolic counterclockwise rotation but less obvious systolic clockwise rotation. At 5 cm superior to retro-left ventricular position, 29 of 46 patients (63%) revealed rotational flow with a tendency toward systolic clockwise and diastolic counterclockwise rotation. At the retro-left ventricular position, 47 of 53 patients (89%) revealed rotational flow, usually of a clockwise direction, occurring in systole. Our data suggest that aortic flow is not purely pulsatile and axial but has a rotational component. Rotational flow begins in the aortic arch and is carried through to the descending thoracic aorta, where flow is chirally asymmetric with systolic clockwise and diastolic counterclockwise components. These data demonstrate an aortic rotational flow component that may have physiological implications for organ perfusion.


A maternal mRNA localized to the animal pole of Xenopus eggs encodes a subunit of mitochondrial ATPase.
We have previously isolated several cDNA clones of mRNAs that have the unusual property of being localized to either the animal pole or the vegetal pole of frog eggs. To gain insight into the function of these maternal mRNAs we have determined their DNA sequence and deduced the sequence of the proteins they encode. Here we report that An2, an mRNA localized to the animal pole of Xenopus oocytes and eggs, codes for the alpha chain of mitochondrial ATPase. Furthermore, we compare the intracellular localization of the An2 mRNA and mitochondria in oocytes and eggs and find that they do not have the same degree of localization. In the light of these results we discuss possible reasons for the maternal localization of the An2 mRNA.


Efficient inhibition of prion replication by PrP-Fc(2) suggests that the prion is a PrP(Sc) oligomer.
Soluble dimeric prion protein (PrP-Fc(2)) binds to the disease-associated prion protein PrP(Sc), and inhibits prion replication when expressed in transgenic mice. Prion inhibition is effective even if PrP-Fc(2) is expressed at low levels, suggesting that its affinity for PrP(Sc) is higher than that of monomeric PrP(C). Here, we model prion accumulation as an exponential replication cycle of prion elongation and breakage. The exponential growth rate corresponding to this cycle is reflected in the incubation period of the disease. We use a mathematical model to calculate the exponential growth rate, and fit the model to in vivo data on prion incubation times corresponding to different levels of PrP(C) and PrP-Fc(2). We find an excellent fit of the model to the data. Surprisingly, targeting of PrP(Sc) can be effective at concentrations of PrP-Fc(2) lower than that of PrP(C), even if PrP-Fc(2) and PrP(C) have the same affinity for PrP(Sc). The best fit of our model to data predicts that the replicative prion consists of PrP(Sc) oligomers with a mean size of four to 15 units.


Review of exemplar programs for adults with early-stage Alzheimer's disease.
In response to the need to develop evidence-based best practices interventions and services for individuals in the early stages of Alzheimer's disease (AD), the authors conducted an interdisciplinary literature review of exemplar programs, defined as those including multimodal or unimodal interventions; shown to be appropriate for individuals in the early stages of AD; demonstrating promise to support, maintain, and improve independent functioning; and shown to have positive effects for a variety of outcomes, including quality of life. This article examines evidence from five kinds of programs: (a) multimodal interventions, (b) programs developed by the Southwest Florida Interdisciplinary Center for Positive Aging, (c) sleep enhancement interventions, (d) managed care programs, and (e) technology-based interventions. Evidence from the review suggests that a number of programs can support functioning and improve quality of life for adults living with the early stages of memory loss. The article concludes with recommendations to advance a national research agenda in this area.


Mueller matrix measurements on absorbing turbid medium.
Polarization parameters of diffuse backscattered light from a turbid sample are sensitive to its structural properties and can, therefore, be used to probe morphological features of tissue and, thus, monitor changes that arise due to a disease. Extraction of morphological information from measured polarization parameters, however, requires a careful understanding of the dependence of these on factors such as size, size distribution, shape, and dielectric constant of the scatterers, which are often quite involved. In particular, the presence of absorption complicates the dependence of polarization parameters on tissue morphological features. We have found that, while for medium comprising small size scatterers (Rayleigh scatterers), the depolarization shows the expected decrease with an increase in the absorption of the scattering medium, a counterintuitive behavior was observed for larger size (>lambda) scatterers. Further analysis of the results suggests that the observed behavior might arise due to the relative contribution of two depolarizing processes, one resulting from a series of out-of-plane scattering and the other due to the angular variation of the state of polarization in a single scattering event.


Pharmacological activation and inhibition of Slack (Slo2.2) channels.
The Slack (Sequence like a calcium-activated K channel) (Slo2.2) gene is abundantly expressed in the mammalian brain and encodes a sodium-activated K+ (KNa) channel. Although the specific roles of Slack channel subunits in neurons remain to be identified, they may play a role in the adaptation of firing rate and in protection against ischemic injury. In the present study, we have generated a stable cell line expressing the Slack channel, and have analyzed the pharmacological properties of these channels in these cells and in Xenopus oocytes. Two known blockers of KNa channels, bepridil and quinidine, inhibited Slack currents in a concentration-dependent manner and decreased channel activity in excised membrane patches. The inhibition by bepridil was potent, with an IC50 of 1.0 microM for inhibition of Slack currents in HEK cells. In contrast, bithionol was found to be a robust activator of Slack currents. When applied to the extracellular face of excised patches, bithionol rapidly induced a reversible increase in channel opening, suggesting that it acts on Slack channels relatively directly. These data establish an important early characterization of agents that modulate Slack channels, a process essential for the experimental manipulation of Slack currents in neurons.


Immature T-cell clustering and efficient differentiation require the polarity protein Scribble.
T-cell polarization is required for cell migration and cell-cell interactions, cellular behaviors crucial for lymphocyte differentiation. Despite expression of the epithelial polarity network in T cells, neither its contribution to thymocyte polarity nor its requirement during development is known. We report here that depletion of the polarity protein Scribble in hematopoietic progenitor cells results in inefficient T-cell development characterized by a partial developmental block during the early double-negative (DN) stage of differentiation. Scribble-depleted hematopoietic progenitor cells exhibit a delayed transition into late CD44(lo/-)CD25(+) DN3 cells, evidenced by the accumulation of early CD44(int)CD25(+) DN3 cells. As a consequence, a limited cellular expansion and a reduced frequency of intracellular T-cell receptor β-positive DN3 cells are observed among Scribble-deficient differentiating T cells. Moreover, whereas purified Scribble-depleted DN2 and DN3 cells do not exhibit compromised spontaneous motility, T-cell clustering and prolonged homotypic interactions among such cells are reduced. This deficiency correlates with a lack of polarization of the integrin LFA-1 during T-cell migration or on the initiation of T-cell-T-cell interactions. Scribble is therefore a critical contributor to the clustering of immature T cells, an event shown here to be necessary for efficient developmental progression.


Estimation of dynamically varying displacement derivatives using fringe projection technique.
This paper presents a pseudo Wigner-Ville-distribution-based method in fringe projection for analyzing temporal behavior of the displacement derivative for a continuously deformed object. In the proposed method, a computer generated fringe pattern is projected on an object undergoing dynamic deformation, and the reflected intensity is recorded in the form of video, i.e., a stack of images are captured sequentially by a CCD camera. Each image represents a recorded fringe pattern at a particular time instant whose phase contains information about the instantaneous out-of-plane displacement or deformation with respect to the undeformed object, and the corresponding spatial phase derivative relates to the displacement derivative. Subsequently, pseudo Wigner-Ville distribution is used for instantaneous phase derivative estimation from the stack of images. Simulation and experimental results are presented to demonstrate the method's potential.


Relationship between inflammatory biomarkers and oxidative stress with uterine health in dairy cows with different dry period lengths.
Earlier studies indicated that the inflammatory status of dairy cows in early lactation could not be fully explained by the negative energy balance (NEB) at that moment. The objective of the present study was to determine relationships between inflammatory biomarkers and oxidative stress with uterine health in dairy cows after different dry period lengths. Holstein-Friesian dairy cows were assigned to one of three dry period lengths (0-, 30-, or 60-d) and one of two early lactation rations (glucogenic or lipogenic ration). Cows were fed either a glucogenic or lipogenic ration from 10-d before the expected calving date. Part of the cows which were planned for a 0-d dry period dried themselves off and were attributed to a new group (0 → 30-d dry period), which resulted in total in four dry period groups. Blood was collected (N = 110 cows) in weeks -3, -2, -1, 1, 2, and 4 relative to calving to determine biomarkers for inflammation, liver function, and oxidative stress. Uterine health status (UHS) was monitored by scoring vaginal discharge (VD) based on a 4-point scoring system (0, 1, 2, or 3) in weeks 2 and 3 after calving. Cows were classified as having a healthy uterine environment (HU, VD score = 0 or 1 in both weeks 2 and 3), nonrecovering uterine environment (NRU, VD score = 2 or 3 in week 3), or a recovering uterine environment (RU, VD score = 2 or 3 in week 2 and VD score= 0 or 1 in week 3). Independent of dry period length, cows with NRU had higher plasma haptoglobin (P = 0.05) and lower paraoxonase levels (P < 0.01) in the first 4 weeks after calving and lower liver functionality index (P < 0.01) compared with cows with HU. Cows with NRU had lower plasma albumin (P = 0.02) and creatinine (P = 0.02) compared with cows with a RU, but not compared with cows with HU. Independent of UHS, cows with a 0 → 30-d dry period had higher bilirubin levels compared with cows with 0-, 30-, or 60-d dry period (P < 0.01). Cows with RU and fed a lipogenic ration had higher levels of albumin in plasma compared with cows with NRU and fed a lipogenic ration (P < 0.01). In conclusion, uterine health was related to biomarkers for inflammation (haptoglobin and albumin) and paraoxonase in dairy cows in early lactation. Cows which were planned for a 0-d dry period, but dried themselves off (0 → 30-d dry period group) had higher bilirubin levels, which was possibly related to a more severe NEB in these cows. Inflammatory biomarkers in dairy cows in early lactation were related to uterine health in this period.


Assessing radiomic feature robustness to interpolation in 18F-FDG PET imaging.
Radiomic studies link quantitative imaging features to patient outcomes in an effort to personalise treatment in oncology. To be clinically useful, a radiomic feature must be robust to image processing steps, which has made robustness testing a necessity for many technical aspects of feature extraction. We assessed the stability of radiomic features to interpolation processing and categorised features based on stable, systematic, or unstable responses. Here, 18F-fluorodeoxyglucose (18F-FDG) PET images for 441 oesophageal cancer patients (split: testing = 353, validation = 88) were resampled to 6 isotropic voxel sizes (1.5 mm, 1.8 mm, 2.0 mm, 2.2 mm, 2.5 mm, 2.7 mm) and 141 features were extracted from each volume of interest (VOI). Features were categorised into four groups with two statistical tests. Feature reliability was analysed using an intraclass correlation coefficient (ICC) and patient ranking consistency was assessed using a Spearman's rank correlation coefficient (ρ). We categorised 93 features robust and 6 limited robustness (stable responses), 34 potentially correctable (systematic responses), and 8 not robust (unstable responses). We developed a correction technique for features with potential systematic variation that used surface fits to link voxel size and percentage change in feature value. Twenty-nine potentially correctable features were re-categorised to robust for the validation dataset, after applying corrections defined by surface fits generated on the testing dataset. Furthermore, we found the choice of interpolation algorithm alone (spline vs trilinear) resulted in large variation in values for a number of features but the response categorisations remained constant. This study attempted to quantify the diverse response of radiomics features commonly found in 18F-FDG PET clinical modelling to isotropic voxel size interpolation.


PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling.
Activating mutations in the RAS family or BRAF frequently occur in many types of human cancers but are rarely detected in breast tumors. However, activation of the RAS-RAF-MEK-ERK MAPK pathway is commonly observed in human breast cancers, suggesting that other genetic alterations lead to activation of this signaling pathway. To identify breast cancer oncogenes that activate the MAPK pathway, we screened a library of human kinases for their ability to induce anchorage-independent growth in a derivative of immortalized human mammary epithelial cells (HMLE). We identified p21-activated kinase 1 (PAK1) as a kinase that permitted HMLE cells to form anchorage-independent colonies. PAK1 is amplified in several human cancer types, including 30--33% of breast tumor samples and cancer cell lines. The kinase activity of PAK1 is necessary for PAK1-induced transformation. Moreover, we show that PAK1 simultaneously activates MAPK and MET signaling; the latter via inhibition of merlin. Disruption of these activities inhibits PAK1-driven anchorage-independent growth. These observations establish PAK1 amplification as an alternative mechanism for MAPK activation in human breast cancer and credential PAK1 as a breast cancer oncogene that coordinately regulates multiple signaling pathways, the cooperation of which leads to malignant transformation.


Trypanosoma cruzi: do different sylvatic strains trigger distinct immune responses?
Strains of Trypanosoma cruzi are multiclonal populations that can be classified in groups or genotypes, differing in pathogenicity, virulence, and histotropism. In this experiment the distinct behavior of two strains of T. cruzi, MORC-1 and MORC-2, was documented. Blood parasitemia, spleen proliferation, nitric oxide, histopathology of the spleen and heart were used as tools to evaluate parasite persistence. Groups of male mice were separated and divided in three groups: Control (C), Infected (IM-1) and Infected (IM-2). The peak of parasitemia occurred on 10days post infection for both strains. LPS stimulated animals, infected MORC-2 group displayed significant higher concentrations of NO when compared to infected MORC-1 group (P<0.05). For ConA stimulated lymphoproliferation, infected MORC-1 group displayed higher proliferation index as compared to infected MORC-2 group. An opposite behavior for IL-4 and TNF-alpha was observed according to the strain. For MORC-1 enhanced concentrations of IL-4 were present with concomitant reduced levels of TNF-alpha, while for MORC-2 enhanced concentrations of TNF-alpha and reduced levels of IL-4 were found. The histopathology of heart and spleen showed important differences in which MORC-1 displayed statistically enhanced number of amastigote in the heart and spleen as compared to MORC-2. Concluding, each strain triggered a distinct immune response with enhanced cytokine TH-1 profile for MORC-2 and TH-2 for MORC-1.


No association between genetic variants in MAOA, OXTR, and AVPR1a and cooperative strategies.
The effort to understand the genetic basis of human sociality has been encouraged by the diversity and heritability of social traits like cooperation. This task has remained elusive largely because most studies of sociality and genetics use sample sizes that are often unable to detect the small effects that single genes may have on complex social behaviors. The lack of robust findings could also be a consequence of a poor characterization of social phenotypes. Here, we explore the latter possibility by testing whether refining measures of cooperative phenotypes can increase the replication of previously reported associations between genetic variants and cooperation in small samples. Unlike most previous studies of sociality and genetics, we characterize cooperative phenotypes based on strategies rather than actions. Measuring strategies help differentiate between similar actions with different underlaying social motivations while controlling for expectations and learning. In an admixed Latino sample (n = 188), we tested whether cooperative strategies were associated with three genetic variants thought to influence sociality in humans-MAOA-uVNTR, OXTR rs53576, and AVPR1 RS3. We found no association between cooperative strategies and any of the candidate genetic variants. Since we were unable to replicate previous observations our results suggest that refining measurements of cooperative phenotypes as strategies is not enough to overcome the inherent statistical power problem of candidate gene studies.


Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO ) and expected (HE ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.


Biochemical and biophysical characterization of a chimeric TRIM21-TRIM5alpha protein.
The tripartite motif (TRIM) protein, TRIM5alpha, is an endogenous factor in primates that recognizes the capsids of certain retroviruses after virus entry into the host cell. TRIM5alpha promotes premature uncoating of the capsid, thus blocking virus infection. Low levels of expression and tendencies to aggregate have hindered the biochemical, biophysical, and structural characterization of TRIM proteins. Here, a chimeric TRIM5alpha protein (TRIM5(Rh)-21R) with a RING domain derived from TRIM21 was expressed in baculovirus-infected insect cells and purified. Although a fraction of the TRIM5(Rh)-21R protein formed large aggregates, soluble fractions of the protein formed oligomers (mainly dimers), exhibited a protease-resistant core, and contained a high percentage of helical secondary structure. Cross-linking followed by negative staining and electron microscopy suggested a globular structure. The purified TRIM5(Rh)-21R protein displayed E3-ligase activity in vitro and also self-ubiquitylated in the presence of ubiquitin-activating and -conjugating enzymes. The purified TRIM5(Rh)-21R protein specifically associated with human immunodeficiency virus type 1 capsid-like complexes; a deletion within the V1 variable region of the B30.2(SPRY) domain decreased capsid binding. Thus, the TRIM5(Rh)-21R restriction factor can directly recognize retroviral capsid-like complexes in the absence of other mammalian proteins.


Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase.
Movement of the transcription machinery along a template alters DNA topology resulting in the accumulation of supercoils in DNA. The positive supercoils generated ahead of transcribing RNA polymerase (RNAP) and the negative supercoils accumulating behind impose severe topological constraints impeding transcription process. Previous studies have implied the role of topoisomerases in the removal of torsional stress and the maintenance of template topology but the in vivo interaction of functionally distinct topoisomerases with heterogeneous chromosomal territories is not deciphered. Moreover, how the transcription-induced supercoils influence the genome-wide recruitment of DNA topoisomerases remains to be explored in bacteria. Using ChIP-Seq, we show the genome-wide occupancy profile of both topoisomerase I and DNA gyrase in conjunction with RNAP in Mycobacterium tuberculosis taking advantage of minimal topoisomerase representation in the organism. The study unveils the first in vivo genome-wide interaction of both the topoisomerases with the genomic regions and establishes that transcription-induced supercoils govern their recruitment at genomic sites. Distribution profiles revealed co-localization of RNAP and the two topoisomerases on the active transcriptional units (TUs). At a given locus, topoisomerase I and DNA gyrase were localized behind and ahead of RNAP, respectively, correlating with the twin-supercoiled domains generated. The recruitment of topoisomerases was higher at the genomic loci with higher transcriptional activity and/or at regions under high torsional stress compared to silent genomic loci. Importantly, the occupancy of DNA gyrase, sole type II topoisomerase in Mtb, near the Ter domain of the Mtb chromosome validates its function as a decatenase.


Early dynamic imaging in 68Ga- PSMA-11 PET/CT allows discrimination of urinary bladder activity and prostate cancer lesions.
PET/CT with 68Ga-labelled prostate-specific membrane antigen (PSMA)-ligands has been proven to establish a promising imaging modality in the work-up of prostate cancer (PC) patients with biochemical relapse. Despite a high overall detection rate, the visualisation of local recurrence may be hampered by high physiologic tracer accumulation in the urinary bladder on whole body imaging, usually starting 60 min after injection. This study sought to verify whether early dynamic 68Ga-PSMA-11 (HBED-CC)PET/CT can differentiate pathologic PC-related tracer uptake from physiologic tracer accumulation in the urinary bladder. Eighty consecutive PC patients referred to 68Ga -PSMA-11 PET/CT were included in this retrospective analysis (biochemical relapse: n = 64; primary staging: n = 8; evaluation of therapy response/restaging: n = 8). In addition to whole-body PET/CT acquisition 60 min post injection early dynamic imaging of the pelvis in the first 8 min after tracer injection was performed. SUVmax of pathologic lesions was calculated and time-activity curves were generated and compared to those of urinary bladder and areas of physiologic tracer uptake. A total of 55 lesions consistent with malignancy on 60 min whole body imaging exhibited also pathologic 68Ga-PSMA-11 uptake during early dynamic imaging (prostatic bed/prostate gland: n = 27; lymph nodes: n = 12; bone: n = 16). All pathologic lesions showed tracer uptake within the first 3 min, whereas urinary bladder activity was absent within the first 3 min of dynamic imaging in all patients. Suvmax was significantly higher in PC lesions in the first 6 min compared to urinary bladder accumulation (p < 0.001). In the subgroup of PC patients with biochemical relapse the detection rate of local recurrence could be increased from 20.3 to 29.7%. Early dynamic imaging in 68Ga-PSMA-11 PET/CT reliably enables the differentiation of pathologic tracer uptake in PC lesions from physiologic bladder accumulation. Performance of early dynamic imaging in addition to whole body imaging 60 min after tracer injection might improve the detection rate of local recurrence in PC patients with biochemical relapse referred for 68Ga-PSMA-11 PET/CT.


Center of pressure excursion capability in performance of seated lateral-reaching tasks.
Seated center of pressure excursion capability can be used for patient evaluation in a clinical setting and in universal design. A quantification of excursion capability across age and anthropometry has not been previously reported, although some research suggests that the ischial tuberosities are the support structure limiting the excursion. Thirty-eight neurologically healthy adults ranging in age from 21 to 74 years and including 12 obese persons performed a series of 6 lateral-reaching tasks. Participants sat on a platform such that their feet did not touch the ground, leaving their legs free to provide counterbalancing support. Data recorded from a force plate under the platform allowed calculation of the center of pressure throughout the trial and the maximum excursion for each condition was recorded. The average excursion capability for the healthy, experimental population was 148 mm or 37% of seated hip breadth. Taller participants had larger maximum excursions, on average, than shorter participants, and older participants had smaller excursions than younger participants. The greater trochanter of the femur-rather than the ischial tuberosities-appears to be the primary support structure limiting center of pressure excursion in lateral, balance-limited reaches without contralateral support. These measures and concepts can be used for design, accommodation, and clinically for patient assessment.


Inhibition of acrolein-stimulated MUC5AC expression by Platycodon grandiflorum root-derived saponin in A549 cells.
Mucin overproduction is a hallmark of chronic airway diseases such as chronic obstructive pulmonary disease. In this study, we investigated the inhibition of acrolein-induced expression of mucin 5, subtypes A and C (MUC5AC) by Changkil saponin (CKS) in A549 cells. Acrolein, a known toxin in tobacco smoke and an endogenous mediator of oxidative stress, increases the expression of airway MUC5AC, a major component of airway mucus. CKS, a Platycodon grandiflorum root-derived saponin, inhibited acrolein-induced MUC5AC expression and activity, through the suppression of NF-κB activation. CKS also repressed acrolein-induced phosphorylation of ERK1/2, JNK1/2, and p38MAPK, which are upstream signaling molecules that control MUC5AC expression. In addition, the MAPK inhibitors PD98059 (ERK1/2), SP600125 (JNK1/2), and SB203580 (p38 MAPK), and a PKC delta inhibitor (rottlerin; PKCδ) inhibited acrolein-induced MUC5AC expression and activity. CKS repressed acrolein-induced phosphorylation of PKCδ. Moreover, a reactive oxygen species (ROS) inhibitor, N-acetylcysteine, inhibited acrolein-induced MUC5AC expression and activity through the suppression of PKCδ and MAPK activation, and CKS repressed acrolein-induced ROS production. These results suggest that CKS suppresses acrolein-induced MUC5AC expression by inhibiting the activation of NF-κB via ROS-PKCδ-MAPK signaling.


Melanocortin-4 receptor signaling is required for weight loss after gastric bypass surgery.
Roux-en-Y gastric bypass (RYGB) is one of the most effective long-term therapies for the treatment of severe obesity. Recent evidence indicates that RYGB effects weight loss through multiple physiological mechanisms, including changes in energy expenditure, food intake, food preference, and reward pathways. Because central melanocortin signaling plays an important role in the regulation of energy homeostasis, we investigated whether genetic disruption of the melanocortin-4 receptor (MC4R) in rodents and humans affects weight loss after RYGB. Here we report that MC4R(-/-) mice lost substantially less weight after surgery than wild-type animals, indicating that MC4R signaling is necessary for the weight loss effects of RYGB in this model. Mice heterozygous for MC4R remain fully responsive to gastric bypass. To determine whether mutations affect surgically induced weight loss in humans, we sequenced the MC4R gene in 972 patients undergoing RYGB. Patients heterozygous for MC4R mutations exhibited the same magnitude and distribution of postoperative weight loss as patients without such mutations, suggesting that although two normal copies of the MC4R gene are necessary for normal weight regulation, a single normal copy of the MC4R gene is sufficient to mediate the weight loss effects of RYGB. MC4R is the first gene identified that is required for the sustained effects of bariatric surgery. The need for MC4R signaling for the weight loss effects of RYGB in mice underscores the physiological mechanisms of action of this procedure and demonstrates that RYGB both influences and is dependent on the normal pathways that regulate energy balance.


Recommendations for prevention and control of tuberculosis among foreign-born persons. Report of the Working Group on Tuberculosis among Foreign-Born Persons. Centers for Disease Control and Prevention.
During 1986-1997, the number of tuberculosis (TB) cases among foreign-born persons in the United States increased by 56%, from 4,925 cases (22% of the national total) to 7,702 cases (39% of the national total). As the percentage of reported TB cases among foreign-born persons continues to increase, the elimination of TB in the United States will depend increasingly on the elimination of TB among foreign-born persons. On May 16-17, 1997, CDC convened a working group of state and city TB-control program staff, as well as representatives from CDC's Division of TB Elimination and Division of Quarantine, to outline problems and propose solutions for addressing TB among foreign-born persons. The Working Group on Tuberculosis Among Foreign-Born Persons considered a) epidemiologic profiles of TB cases among foreign-born persons, b) case finding, screening, and preventive therapy for the foreign born, c) TB diagnosis and management for the foreign born, d) opportunities for collaborations with community-based organizations (CBOs) to address TB among the foreign born, and e) TB-related training needs. The Working Group's deliberations and the resulting recommendations for action by federal agencies, state and local TB-control programs, CBOs, and private health-care providers form the basis of this report. For each of the five topics of discussion, the group identified key issues, problems, and constraints and suggested solutions in the form of recommendations, which are detailed in this report. The Working Group made the following recommendations: * The epidemiology of TB among foreign-born populations differs considerably from area to area. To tailor TB-control efforts to local needs, TB-control programs should develop epidemiologic profiles to identify groups of foreign-born persons in their jurisdictions who are at high risk for TB. * The priorities of TB control among the foreign born should be the same as those for control of TB among other U.S. populations - completion of treatment by persons infected with active TB, contact tracing, and screening and provision of preventive therapy for groups at high risk. Screening and preventive therapy should be limited to areas where completion of therapy rates and contact-tracing activities are currently adequate. * Based on local epidemiologic profiles, selective screening should be conducted among populations identified as being at high risk for TB. Screening should target groups of persons who are at the highest risk for TB infection and disease, accessible for screening, and likely to complete preventive therapy. The decision to screen for infection, disease, or both should be based on the person's age and time in the United States, prior screening, and locally available resources for the provision of preventive therapy. * TB-control programs should direct efforts towards identifying impediments to TB diagnosis and care among local foreign-born populations, devising strategies to address these barriers, and maximizing activities to ensure completion of treatment. * Providing TB preventive therapy and other TB-related services for foreign-born persons is often impeded by linguistic, cultural, and health-services barriers. TB-control programs can help overcome these barriers by establishing partnerships with CBOs and by strengthening training and education efforts. Collaborations with health-service CBOs should center on developing more complementary roles, more effective coordination of services, and better use of existing resources for serving the foreign born. TB-related training should be linked to overall TB-control strategies for the foreign born. Training and education should be targeted to providers, patients, and community workers.


Disturbed flow-activated p90RSK kinase accelerates atherosclerosis by inhibiting SENP2 function.
Disturbed blood flow (d-flow) causes endothelial cell (EC) dysfunction, leading to atherosclerotic plaque formation. We have previously shown that d-flow increases SUMOylation of p53 and ERK5 through downregulation of sentrin/SUMO-specific protease 2 (SENP2) function; however, it is not known how SENP2 itself is regulated by d-flow. Here, we determined that d-flow activated the serine/threonine kinase p90RSK, which subsequently phosphorylated threonine 368 (T368) of SENP2. T368 phosphorylation promoted nuclear export of SENP2, leading to downregulation of eNOS expression and upregulation of proinflammatory adhesion molecule expression and apoptosis. In an LDLR-deficient murine model of atherosclerosis, EC-specific overexpression of p90RSK increased EC dysfunction and lipid accumulation in the aorta compared with control animals; however, these pathologic changes were not observed in atherosclerotic mice overexpressing dominant negative p90RSK (DN-p90RSK). Moreover, depletion of SENP2 in these mice abolished the protective effect of DN-p90RSK overexpression. We propose that p90RSK-mediated SENP2-T368 phosphorylation is a master switch in d-flow-induced signaling, leading to EC dysfunction and atherosclerosis.


Tailored interventions to implement recommendations for elderly patients with depression in primary care: a study protocol for a pragmatic cluster randomised controlled trial.
The prevalence of depression is high and the elderly have an increased risk of developing chronic course. International data suggest that depression in the elderly is under-recognised, the latency before clinicians provide a treatment plan is longer and elderly patients with depression are not offered psychotherapy to the same degree as younger patients. Although recommendations for the treatment of elderly patients with depression exist, health-care professionals adhere to these recommendations to a limited degree only. We conducted a systematic review to identify recommendations for managing depression in the elderly and prioritised six recommendations. We identified and prioritised the determinants of practice related to the implementation of these recommendations in primary care, and subsequently discussed and prioritised interventions to address the identified determinants. The objective of this study is to evaluate the effectiveness of these tailored interventions for the six recommendations for the management of elderly patients with depression in primary care. We will conduct a pragmatic cluster randomised trial comparing the implementation of the six recommendations using tailored interventions with usual care. We will randomise 80 municipalities into one of two groups: an intervention group, to which we will deliver tailored interventions to implement the six recommendations, and a control group, to which we will not deliver any intervention. We will randomise municipalities rather than patients, individual clinicians or practices, because we will deliver the intervention for the first three recommendations at the municipal level and we want to minimise the risk of contamination across GP practices for the other three recommendations. The primary outcome is the proportion of actions taken by GPs that are consistent with the recommendations. This trial will investigate whether a tailored implementation approach is an effective strategy for improving collaborative care in the municipalities and health-care professionals' practice towards elderly patients with depression in primary care. The effectiveness evaluation described in this protocol will be accompanied with a process evaluation exploring why and how the interventions were effective or ineffective. ClinicalTrials.gov: NCT01913236.


Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability.
Human lysosomal enzymes acid-beta-glucosidase (GCase) and acid-alpha-galactosidase (alpha-Gal A) hydrolyze the sphingolipids glucosyl- and globotriaosylceramide, respectively, and mutations in these enzymes lead to the lipid metabolism disorders Gaucher and Fabry disease, respectively. We have investigated the structure and stability of GCase and alpha-Gal A in a neutral-pH environment reflective of the endoplasmic reticulum and an acidic-pH environment reflective of the lysosome. These details are important for the development of pharmacological chaperone therapy for Gaucher and Fabry disease, in which small molecules bind mutant enzymes in the ER to enable the mutant enzyme to meet quality control requirements for lysosomal trafficking. We report crystal structures of apo GCase at pH 4.5, at pH 5.5, and in complex with the pharmacological chaperone isofagomine (IFG) at pH 7.5. We also present thermostability analysis of GCase at pH 7.4 and 5.2 using differential scanning calorimetry. We compare our results with analogous experiments using alpha-Gal A and the chaperone 1-deoxygalactonijirimycin (DGJ), including the first structure of alpha-Gal A with DGJ. Both GCase and alpha-Gal A are more stable at lysosomal pH with and without their respective iminosugars bound, and notably, the stability of the GCase-IFG complex is pH sensitive. We show that the conformations of the active site loops in GCase are sensitive to ligand binding but not pH, whereas analogous galactose- or DGJ-dependent conformational changes in alpha-Gal A are not seen. Thermodynamic parameters obtained from alpha-Gal A unfolding indicate two-state, van't Hoff unfolding in the absence of the iminosugar at neutral and lysosomal pH, and non-two-state unfolding in the presence of DGJ. Taken together, these results provide insight into how GCase and alpha-Gal A are thermodynamically stabilized by iminosugars and suggest strategies for the development of new pharmacological chaperones for lysosomal storage disorders.


Heat stress and public health: a critical review.
Heat is an environmental and occupational hazard. The prevention of deaths in the community caused by extreme high temperatures (heat waves) is now an issue of public health concern. The risk of heat-related mortality increases with natural aging, but persons with particular social and/or physical vulnerability are also at risk. Important differences in vulnerability exist between populations, depending on climate, culture, infrastructure (housing), and other factors. Public health measures include health promotion and heat wave warning systems, but the effectiveness of acute measures in response to heat waves has not yet been formally evaluated. Climate change will increase the frequency and the intensity of heat waves, and a range of measures, including improvements to housing, management of chronic diseases, and institutional care of the elderly and the vulnerable, will need to be developed to reduce health impacts.


Trading people versus trading time: what is the difference?
Person trade-off (PTO) elicitations yield different values than standard utility measures, such as time trade-off (TTO) elicitations. Some people believe this difference arises because the PTO captures the importance of distributive principles other than maximizing treatment benefits. We conducted a qualitative study to determine whether people mention considerations related to distributive principles other than QALY-maximization more often in PTO elicitations than in TTO elicitations and whether this could account for the empirical differences. 64 members of the general public were randomized to one of three different face-to-face interviews, thinking aloud as they responded to TTO and PTO elicitations. Participants responded to a TTO followed by a PTO elicitation within contexts that compared either: 1) two life-saving treatments; 2) two cure treatments; or 3) a life-saving treatment versus a cure treatment. When people were asked to choose between life-saving treatments, non-maximizing principles were more common with the PTO than the TTO task. Only 5% of participants considered non-maximizing principles as they responded to the TTO elicitation compared to 68% of participants who did so when responding to the PTO elicitation. Non-maximizing principles that emerged included importance of equality of life and a desire to avoid discrimination. However, these principles were less common in the other two contexts. Regardless of context, though, participants were significantly more likely to respond from a societal perspective with the PTO compared to the TTO elicitation. When lives are at stake, within the context of a PTO elicitation, people are more likely to consider non-maximizing principles, including the importance of equal access to a life-saving treatment, avoiding prejudice or discrimination, and in rare cases giving treatment priority based purely on the position of being worse-off.


Multiscale simulations of the hydration shells surrounding spherical Fe3O4 nanoparticles and effect on magnetic properties.
Iron oxide magnetic nanoparticles (NPs) are excellent systems in catalysis and in nanomedicine, where they are mostly immersed in aqueous media. Even though the NP solvation by water is expected to play an active role, the detailed structural insight at the nanostructure oxide/water interface is still missing. Here, based on our previous efforts to obtain accurate models of dehydrated Fe3O4 NPs and of their magnetic properties and through multiscale molecular dynamics simulations combining the density functional tight binding method and force field, we unravel the atomistic details of the short range (chemical) and long range (physical) interfacial effects when magnetite nanoparticles are immersed in water. The influence of the first hydration shell on the structural, electronic and magnetic properties of Fe3O4 NPs is revealed by high-level hybrid density functional calculations. Hydrated Fe3O4 NPs possess larger magnetic moment than dehydrated ones. This work bridges the large gap between experimental studies on solvated Fe3O4 NPs and theoretical investigations on flat Fe3O4 surfaces covered with water and paves the way for further study of Fe3O4 NPs in biological environments.


Ageing and cancer: the telomere and telomerase connection.
Telomeres are repetitive DNA sequences at the ends of linear chromosomes. Telomerase, a cellular reverse transcriptase, helps stabilize telomere length in human stem, reproductive and cancer cells by adding TTAGGG repeats onto the telomeres. Each time a telomerase-negative cell divides some telomeric sequences are lost. When telomeres are short, cells enter an irreversible growth arrest state called replicative senescence. In most instances cells become senescent before they can become cancerous, thus the growth arrest induced by short telomeres may be a potent anti-cancer mechanism. Since most cancers express telomerase, maintenance of telomere stability is likely to be required for the long-term viability of tumours. Inhibition of telomerase results in gradual erosion of telomeres followed by cessation of proliferation or apoptosis, and thus may be a promising target for cancer therapy. Introduction of the telomerase catalytic protein component into telomerase-silent cells is sufficient to restore telomerase activity and extend cellular life span. However, cells with introduced telomerase are not cancer cells since they have not accumulated the other changes needed to become cancerous. This indicates that telomerase-induced telomere length manipulations may have utility for tissue engineering and for dissecting the molecular mechanisms underlying genetic diseases including cancer.


Pregnancy, pregnancy loss and the risk of diabetes in Chinese women: findings from the China Kadoorie Biobank.
Pregnancy and pregnancy loss may be associated with increased risk of diabetes in later life. However, the evidence is inconsistent and sparse, especially among East Asians where reproductive patterns differ importantly from those in the West. We examined the associations of pregnancy and pregnancy loss (miscarriage, induced abortion, and still birth) with the risk of incident diabetes in later life among Chinese women. In 2004-2008, the nationwide China Kadoorie Biobank recruited 302 669 women aged 30-79 years from 10 (5 urban, 5 rural) diverse localities. During 9.2 years of follow-up, 7780 incident cases of diabetes were recorded among 273,383 women without prior diabetes and cardiovascular disease at baseline. Cox regression yielded multiple-adjusted hazard ratios (HRs) for the risk of diabetes associated with pregnancy and pregnancy loss. Overall, 99% of women had been pregnant, of whom 10%, 53%, and 6% reported having a history of miscarriage, induced abortion, and stillbirth, respectively. Among ever pregnant women, each additional pregnancy was associated with an adjusted HR of 1.04 (95% CI 1.03; 1.06) for diabetes. Compared with those without pregnancy loss, women with a history of pregnancy loss had an adjusted HR of 1.07 (1.02; 1.13) and the HRs increased with increasing number of pregnancy losses, irrespective of the number of livebirths; the adjusted HR was 1.03 (1.00; 1.05) for each additional pregnancy loss. The strength of the relationships differed marginally by type of pregnancy loss. Among Chinese women, a higher number of pregnancies and pregnancy losses were associated with a greater risk of diabetes.


Prevalence of Trachoma in Car-Nicobar Island, India after Three Annual Rounds of Mass Drug Administration with Azithromycin.
A high proportion of active trachoma infection in children of Car-Nicobar Island was reported through the Trachoma Rapid Assessment survey conducted in year 2010 by the same researchers. Annual mass drug treatment with azithromycin was administered from years 2010-12 to all individuals residing in this island for reducing the burden of active trachoma infection. A cross-sectional prevalence survey was conducted in the year 2013 to assess the post-treatment burden of trachoma in this population. In the 15 randomly selected compact segments from each village of the island, children aged 1-9 years were examined for evidence of active trachoma infection and participants aged ten years and above were examined for trachomatous trichiasis and corneal opacity. A total of 809 children (1-9 years) and 2735 adults were examined. Coverage with azithromycin for all the three rounds was more than 80%. The prevalence of active trachoma infection in children aged 1-9 years old was 6.8% (95% CI 5.1, 8.5) and Trachomatous Trichiasis (TT) was 3.9% (95% CI 3.2, 4.6). The risk factors associated with active trachoma infection were older age and unclean faces. The risk factors associated with TT were older age and lower literacy level. Trachoma has not been eliminated from Car-Nicobar Island in accordance to 'Global Elimination of Trachoma, 2020' guidelines. Sustained efforts and continuous surveillance admixed with adequate programmatic response is imperative for elimination of trachoma in the island.


Multidisciplinary Management of Breast Cancer Brain Metastases.
This review summarizes the most up-to-date approach to the multidisciplinary management of patients with breast cancer brain metastases. A brief overview of the epidemiology and biology of breast cancer brain metastasis is provided. The perspectives of radiation oncology, neurosurgery, and medical oncology-and landmark studies from each discipline-are all discussed. We also offer practical tips to help guide the treating physician, including data on antiseizure medications. Finally, we introduce the concept of a multidisciplinary clinic that combines input from medical and radiation oncology, neurosurgery, and support services, which we developed at the University of North Carolina as a coordinated and optimal approach to the management of patients with this complex disease.


Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references represent only one version of each locus, ignoring variation in the population. Poor representation of an individual's genome sequence impacts read mapping and introduces bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation across a population, including large-scale structural variation such as inversions and duplications. Previous graph genome software implementations have been limited by scalability or topological constraints. Here we present vg, a toolkit of computational methods for creating, manipulating, and using these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays, with improved accuracy over alignment to a linear reference, and effectively removing reference bias. These capabilities make using variation graphs as references for DNA sequencing practical at a gigabase scale, or at the topological complexity of de novo assemblies.


Target (MexB)- and Efflux-Based Mechanisms Decreasing the Effectiveness of the Efflux Pump Inhibitor D13-9001 in Pseudomonas aeruginosa PAO1: Uncovering a New Role for MexMN-OprM in Efflux of β-Lactams and a Novel Regulatory Circuit (MmnRS) Controlling MexMN Expression.
Efflux pumps contribute to antibiotic resistance in Gram-negative pathogens. Correspondingly, efflux pump inhibitors (EPIs) may reverse this resistance. D13-9001 specifically inhibits MexAB-OprM in Pseudomonas aeruginosa Mutants with decreased susceptibility to MexAB-OprM inhibition by D13-9001 were identified, and these fell into two categories: those with alterations in the target MexB (F628L and ΔV177) and those with an alteration in a putative sensor kinase of unknown function, PA1438 (L172P). The alterations in MexB were consistent with reported structural studies of the D13-9001 interaction with MexB. The PA1438L172P alteration mediated a >150-fold upregulation of MexMN pump gene expression and a >50-fold upregulation of PA1438 and the neighboring response regulator gene, PA1437. We propose that these be renamed mmnR and mmnS for MexMN regulator and MexMN sensor, respectively. MexMN was shown to partner with the outer membrane channel protein OprM and to pump several β-lactams, monobactams, and tazobactam. Upregulated MexMN functionally replaced MexAB-OprM to efflux these compounds but was insusceptible to inhibition by D13-9001. MmnSL172P also mediated a decrease in susceptibility to imipenem and biapenem that was independent of MexMN-OprM. Expression of oprD, encoding the uptake channel for these compounds, was downregulated, suggesting that this channel is also part of the MmnSR regulon. Transcriptome sequencing (RNA-seq) of cells encoding MmnSL172P revealed, among other things, an interrelationship between the regulation of mexMN and genes involved in heavy metal resistance.


The Theta/Beta Ratio as an Index of Cognitive Processing in Adults With the Combined Type of Attention Deficit Hyperactivity Disorder.
An elevated theta/beta ratio in the EEG has long been observed among individuals with Attention Deficit Hyperactivity Disorder (ADHD). The theta/beta ratio was previously hypothesised to be an index of arousal, but a number of studies failed to find any association between the ratio and indices of arousal, instead proposing that the theta/beta ratio may actually be indicative of cognitive processing. This hypothesis was tested by Clarke et al using a sample of healthy adults, with results indicating that the theta/beta ratio correlated with a marker of cognitive processing (P300 latency in an auditory oddball task), while P300 amplitude correlated with an arousal marker (alpha power). The aim of this study was to test whether similar results could be found in a sample of 41 adults with the combined type of ADHD. EEGs were recorded during an eyes-closed resting condition and an auditory oddball task. Results demonstrated that the theta/beta ratio correlated significantly with P300 latency. Absolute alpha power did not correlate significantly with P300 amplitude or P300 latency. These results support the hypotheses that the theta/beta ratio is a marker of cognitive processing capacity in both the general population and in participants with ADHD, and that the alpha/arousal linkage is anomalous in ADHD.


Calorie restriction, aging, and cancer prevention: mechanisms of action and applicability to humans.
Calorie restriction (CR) is the most effective and reproducible intervention for increasing lifespan in a variety of animal species, including mammals. CR is also the most potent, broadly acting cancer-prevention regimen in experimental carcinogenesis models. Translation of the knowledge gained from CR research to human chronic disease prevention and the promotion of healthy aging is critical, especially because obesity, which is an important risk factor for several chronic diseases, including many cancers, is alarmingly increasing in the Western world. This review synthesizes the key biological mechanisms underlying many of the beneficial effects of CR, with a particular focus on the insulin-like growth factor-1 pathway. We also describe some of the opportunities now available for investigations, including gene expression profiling studies, the development of pharmacological mimetics of CR, and the integration of CR regimens with targeted, mechanism-based interventions. These approaches will facilitate the translation of CR research into strategies for effective human chronic disease prevention.


Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.
Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.


More than meets the eye: Expanding and reviewing the clinical and mutational spectrum of brittle cornea syndrome.
Brittle cornea syndrome (BCS) is a rare autosomal recessive disorder characterized by corneal thinning and fragility, leading to corneal rupture, the main hallmark of this disorder. Non-ocular symptoms include not only hearing loss but also signs of connective tissue fragility, placing it in the Ehlers-Danlos syndrome (EDS) spectrum. It is caused by biallelic pathogenic variants in ZNF469 or PRDM5, which presumably encode transcription factors for extracellular matrix components. We report the clinical and molecular features of nine novel BCS families, four of which harbor variants in ZNF469 and five in PRDM5. We also performed a genotype- and phenotype-oriented literature overview of all (n = 85) reported patients with ZNF469 (n = 53) and PRDM5 (n = 32) variants. Musculoskeletal findings may be the main reason for referral and often raise suspicion of another heritable connective tissue disorder, such as kyphoscoliotic EDS, osteogenesis imperfecta, or Marfan syndrome, especially when a corneal rupture has not yet occurred. Our findings highlight the multisystemic nature of BCS and validate its inclusion in the EDS classification. Importantly, gene panels for heritable connective tissue disorders should include ZNF469 and PRDM5 to allow for timely diagnosis and appropriate preventive measures for this rare condition.


Adalimumab regulates intracellular TNFα production in patients with rheumatoid arthritis.
Adalimumab is a fully human anti-tumor necrosis factor α (anti-TNFα) monoclonal antibody that specifically blocks the interaction of TNFα with its receptors. It binds both soluble and transmembrane TNFα. We hypothesized that blocking these TNFα signals regulates the altered TNFα production in rheumatoid arthritis (RA) patients. We compared, by flow cytometry, Toll-like receptor induction levels of membrane and intracellular TNFα in monocytes (iTNFα + CD14+ cells) from 12 patients before and after adalimumab treatment with those from 5 healthy donors. Before starting the treatment, the percentage of iTNFα+ CD14+ cells in the RA patients was significantly lower than that in healthy donors (mean ± SEM = 33.16 ± 4.82% vs 66.51 ± 2.4%, P < 0.001). When we added in vitro TNFα to healthy donor culture cells, levels of iTNFα+ CD14+ cells decreased, suggesting that the TNFα signal was responsible for the iTNFα+ CD14+ cell downregulation observed in the RA patients. After 2, 6 and 12 adalimumab injections, we observed significant blocking of membrane and soluble TNFα and a progressive increase in iTNFα+ CD14+ cells in ten patients with a good to moderate response as defined by the European League Against Rheumatism (EULAR) criteria. Levels of iTNFα+ CD14+ cells after 12 injections in these 10 patients were comparable to levels in healthy donors. In two patients, iTNFα+ CD14+ cell upregulation was not observed, and their EULAR-defined responses had not improved. The first patient developed antiadalimumab antibodies, explaining why adalimumab was not able to block membrane and soluble TNFα. In the second patient, adalimumab was discontinued because of adverse effects, which led to a decrease in iTNFα+ CD14+ cells to levels measured before treatment. Our findings suggest that adalimumab treatment in RA patients can return iTNFα levels to those of healthy donors. This effect was not observed in the presence of neutralizing antiadalimumab antibodies.


DNA polymerase theta (POLQ) can extend from mismatches and from bases opposite a (6-4) photoproduct.
DNA polymerase theta (pol theta) is a nuclear A-family DNA polymerase encoded by the POLQ gene in vertebrate cells. The biochemical properties of pol theta and of Polq-defective mice have suggested that pol theta participates in DNA damage tolerance. For example, pol theta was previously found to be proficient not only in incorporation of a nucleotide opposite a thymine glycol or an abasic site, but also extends a polynucleotide chain efficiently from the base opposite the lesion. We carried out experiments to determine whether this ability to extend from non-standard termini is a more general property of the enzyme. Pol theta extended relatively efficiently from matched termini as well as termini with A:G, A:T and A:C mismatches, with less descrimination than a well-studied A-family DNA polymerase, exonuclease-free pol I from E. coli. Although pol theta was unable to, by itself, bypass a cyclobutane pyrimidine dimer or a (6-4) photoproduct, it could perform some extension from primers with bases placed across from these lesions. When pol theta was combined with DNA polymerase iota, an enzyme that can insert a base opposite a UV-induced (6-4) photoproduct, complete bypass of a (6-4) photoproduct was possible. These data show that in addition to its ability to insert nucleotides opposite some DNA lesions, pol theta is proficient at extension of unpaired termini. These results show the potential of pol theta to act as an extender after incorporation of nucleotides by other DNA polymerases, and aid in understanding the role of pol theta in somatic mutagenesis and genome instability.


Evidence for NO(x) control over nighttime SOA formation.
Laboratory studies have established a number of chemical pathways by which nitrogen oxides (NO(x)) affect atmospheric organic aerosol (OA) production. However, these effects have not been directly observed in ambient OA. We report measurements of particulate organic nitrates in Bakersfield, California, the nighttime formation of which increases with NO(x) and is suppressed by high concentrations of organic molecules that rapidly react with nitrate radical (NO(3))--evidence that multigenerational chemistry is responsible for organic nitrate aerosol production. This class of molecules represents about a third of the nighttime increase in OA, suggesting that most nighttime secondary OA is due to the NO(3) product of anthropogenic NO(x) emissions. Consequently, reductions in NO(x) emissions should reduce the concentration of organic aerosol in Bakersfield and the surrounding region.