Discovery of a novel transcriptional regulator of sugar catabolism in archaea.

The haloarchaeon Haloferax volcanii degrades D-glucose via the semiphosphorylative Entner-Doudoroff pathway and D-fructose via a modified Embden-Meyerhof pathway. Here, we report the identification of GfcR, a novel type of transcriptional regulator that functions as an activator of both D-glucose and D-fructose catabolism. We find that in the presence of D-glucose, GfcR activates gluconate dehydratase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase and also acts as activator of the phosphotransferase system and of fructose-1,6-bisphosphate aldolase, which are involved in uptake and degradation of D-fructose. In addition, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase are activated by GfcR in the presence of D-fructose and also during growth on D-galactose and glycerol. Electrophoretic mobility shift assays indicate that GfcR binds directly to promoters of regulated genes. Specific intermediates of the degradation pathways of the three hexoses and of glycerol were identified as inducer molecules of GfcR. GfcR is composed of a phosphoribosyltransferase (PRT) domain with an N-terminal helix-turn-helix motif and thus shows homology to PurR of Gram-positive bacteria that is involved in the transcriptional regulation of nucleotide biosynthesis. We propose that GfcR of H. volcanii evolved from a PRT-like enzyme to attain a function as a transcriptional regulator of central sugar catabolic pathways in archaea.

Anastomosis of the caudal thoracic duct and intercostal vein using a microvascular anastomotic coupler device: Experimental study in six dogs.

OBJECTIVE: To describe the technique for anastomosis of the caudal thoracic duct (TD) to the 10th or 11th intercostal vein (ICV) using a microvascular anastomotic coupler (MAC) device in dogs and assess patency of the anastomosis on days 0 and 30. STUDY DESIGN: Experimental study. SAMPLE POPULATION: Six adult Beagle dogs. METHODS: Under general anesthesia, fluoroscopic popliteal lymphangiography was performed and the TD identified. A right ninth or 10th intercostal thoracotomy was performed. Using an operating microscope, the TD and the 10th or 11th ICV were isolated, ligated, and anastomosed using a 1.5 or 2.0 mm MAC. Fluoroscopic popliteal lymphangiography was repeated immediately after surgery and on day 30. RESULTS: The anastomosis was successful and lymphangiography documented flow into the azygos vein in all six dogs immediately after surgery. At day 30, the anastomosis was patent in four of six dogs. In two dogs, flow through the anastomosis was obstructed due to kinking of the ICV just cranial to the MAC. CONCLUSION: Anastomosis of the TD and ICV using a MAC was feasible and was shown to maintain patency up to 30 days. When performing the anastomosis, care should be taken to ensure the ICV is not kinked by the MAC. CLINICAL SIGNIFICANCE: Direct anastomosis of the TD and ICV may have application for treatment of idiopathic chylothorax in dogs by maintaining flow from the abdominal lymphatics to the central venous circulation and thereby preventing the stimulus for collateral circulation and persistent chylous effusion. Further investigation is warranted to assess the efficacy of this technique in dogs affected with idiopathic chylothorax.

Object relations assessment predicts outpatients' attrition, early working alliance and psychotherapy process.

This study investigated the predictive utility of assessing clients' object relations functioning to prognosticate therapy dropout, quality of the early working alliance and psychotherapy process events reported by clients after their first five sessions. Clients accepting a recruitment invitation were administered the thematic apperception test (TAT) shortly after intake, and those still in treatment three to four sessions later rated the working alliance and psychotherapy process events. Participants were 47 clients beginning psychotherapy with advanced doctoral practicum students at a university-based community-serving training clinic. The Social Cognition and Object Relations Scales (SCORS), an object relations scoring system for TAT stories, was used to assess object relations functioning. The California Psychotherapy Alliance Scales-Patient form measured four dimensions of the alliance. The Therapy Orientation Process Scales, created from the Psychotherapy Process Q-set, measured clients' perceptions of therapy process events as involving relatively more psychodynamic or cognitive behavioural techniques. The SCORS significantly predicted remaining in therapy, client ratings of stronger working alliance and typical therapy process as more psychodynamic than cognitive behavioural. SCORS complexity of representations and capacity for emotional investment in relationships scales were the strongest predictors, especially of the patient commitment facet of the alliance. The findings suggest that (1) beginning psychotherapy with object relations assessment can be useful for treatment planning and (2) the relationship between clients' object relations functioning, working alliance and greater sensitivity to psychodynamic than to cognitive behavioural interventions depends on the aspect of object relations that is being assessed.

Interpersonal Decentering and Person-Situation Interaction in the Thematic Apperception Test: Is It all in the Cards? What's the Story?

Assessors using storytelling assessment techniques have debated the relative importance of picture imagery (card pull) versus story content for interpreting clients' stories. This study used generalizability theory to compare sources of variance in scores for Feffer's Interpersonal Decentering as a function of persons, cards, raters, or interactions. Representing situational activation of mature role-taking (mentalizing of interpersonal processes), decentering activity should differ across interpersonal situations according to the social role norms involved, resulting in more variance due to card pull than for previously studied scoring systems. Decentering scores from stories told to heterosexual romantic-pull pictures were compared with those for other pictures and with scores from romantic versus nonromantic stories to identify score variance explained by card pull and story content. Considering cards as analogs for life situations, person-card interaction explained more decentering variance (53.7%) than did other effects. Heterosexual romantic-pull pictures stimulated more mature decentering than others; story content did not explain significant variance. Women told more mature decentering stories to heterosexual romantic-pull pictures than to other pictures, and more so than men did. Finding strong person-card interaction illuminates typically low internal consistency for content-based scoring systems. Recommendations for clinicians include implications for card selection and story content interpretation.

Estimating watershed degradation over the last century and its impact on water-treatment costs for the world's large cities.

Urban water systems are impacted by land use within their source watersheds, as it affects raw water quality and thus the costs of water treatment. However, global estimates of the effect of land cover change on urban water-treatment costs have been hampered by a lack of global information on urban source watersheds. Here, we use a unique map of the urban source watersheds for 309 large cities (population > 750,000), combined with long-term data on anthropogenic land-use change in their source watersheds and data on water-treatment costs. We show that anthropogenic activity is highly correlated with sediment and nutrient pollution levels, which is in turn highly correlated with treatment costs. Over our study period (1900-2005), median population density has increased by a factor of 5.4 in urban source watersheds, whereas ranching and cropland use have increased by a factor of 3.4 and 2.0, respectively. Nearly all (90%) of urban source watersheds have had some level of watershed degradation, with the average pollutant yield of urban source watersheds increasing by 40% for sediment, 47% for phosphorus, and 119% for nitrogen. We estimate the degradation of watersheds over our study period has impacted treatment costs for 29% of cities globally, with operation and maintenance costs for impacted cities increasing on average by 53 ± 5% and replacement capital costs increasing by 44 ± 14%. We discuss why this widespread degradation might be occurring, and strategies cities have used to slow natural land cover loss.

An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism.

Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4 and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene encodes a conserved tail-anchored transmembrane protein; the molecular identity of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4 also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding, maturation, or export from the ER. The physical interaction between human ODR4 and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues required for protease activity can rescue all odr-8 mutant phenotypes tested. Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia, either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and Ufm1-independent functions in GPCR biogenesis.

Auto Therapy: Using Automobiles as Vehicles for Reminiscence With Older Adults.

Reminiscence can be beneficial for older adults and contribute to well-being and ego integrity. In this exploratory pilot study, researchers assessed the feasibility and tolerability of a novel reminiscence intervention using automobiles as the focal point. Nineteen older adults (N = 19) were asked to reminisce using photographs of automobiles from across their lifespan. The RE-AIM framework was used to assess the intervention in terms of reach, effectiveness, adoption, implementation, and maintenance. The intervention was well-received, quickly established rapport, and effectively fostered reminiscence. Social workers may find this intervention useful in helping older adults to explore their lives.

The gut microbiome and sociability.

The human gut microbiome plays an important role in the maturation of the neural, immune, and endocrine systems. Research data from animal models shows that gut microbiota communicate with the host's brain in an elaborate network of signaling pathways, including the vagus nerve. Part of the microbiome's influence extends to the behavioral and social development of its host. As a social species, a human's ability to communicate with others is imperative to their survival and quality of life. Current research explores the gut microbiota's developmental influence as well as how these gut-brain pathways can be leveraged to alleviate the social symptoms associated with various neurodevelopmental and psychiatric diseases. One intriguing vein of research in animal models centers on probiotic treatment, which leads to downstream increased circulation of endogenous oxytocin, a neuropeptide hormone relevant to sociability. Further research may lead to therapeutic applications in humans, particularly in the early stages of their lives.

Automated-detection of risky alcohol use prior to surgery using natural language processing.

BACKGROUND: Preoperative risky alcohol use is one of the most common surgical risk factors. Accurate and early identification of risky alcohol use could enhance surgical safety. Artificial Intelligence-based approaches, such as natural language processing (NLP), provide an innovative method to identify alcohol-related risks from patients' electronic health records (EHR) before surgery. METHODS: Clinical notes (n = 53,629) from pre-operative patients in a tertiary care facility were analyzed for evidence of risky alcohol use and alcohol use disorder. One hundred of these records were reviewed by experts and labeled for comparison. A rule-based NLP model was built, and we assessed the clinical notes for the entire population. Additionally, we assessed each record for the presence or absence of alcohol-related International Classification of Diseases (ICD) diagnosis codes as an additional comparator. RESULTS: NLP correctly identified 87% of the human-labeled patients classified with risky alcohol use. In contrast, diagnosis codes alone correctly identified only 29% of these patients. In terms of specificity, NLP correctly identified 84% of the non-risky cohort, while diagnosis codes correctly identified 90% of this cohort. In the analysis of the full dataset, the NLP-based approach identified three times more patients with risky alcohol use than ICD codes. CONCLUSIONS: NLP, an artificial intelligence-based approach, efficiently and accurately identifies alcohol-related risk in patients' EHRs. This approach could supplement other alcohol screening tools to identify patients in need of intervention, treatment, and/or postoperative withdrawal prophylaxis. Alcohol-related ICD diagnosis had limited utility relative to NLP, which extracts richer information within clinical notes to classify patients.

Oxytocin and the microbiome.

The mammalian host microbiome affects many targets throughout the body, at least in part through an integrated gut-brain-immune axis and neuropeptide hormone oxytocin. It was discovered in animal models that microbial symbionts, such as Lactobacillus reuteri, leverage perinatal niches to promote multigenerational good health and reproductive fitness. While roles for oxytocin were once limited to women, such as giving birth and nurturing offspring, oxytocin is now also proposed to have important roles linking microbial symbionts with overall host fitness and survival throughout the evolutionary journey.

Analysis of C. elegans NR2E nuclear receptors defines three conserved clades and ligand-independent functions.

BACKGROUND: The nuclear receptors (NRs) are an important class of transcription factors that are conserved across animal phyla. Canonical NRs consist of a DNA-binding domain (DBD) and ligand-binding domain (LBD). While most animals have 20-40 NRs, nematodes of the genus Caenorhabditis have experienced a spectacular proliferation and divergence of NR genes. The LBDs of evolutionarily-conserved Caenorhabditis NRs have diverged sharply from their Drosophila and vertebrate orthologs, while the DBDs have been strongly conserved. The NR2E family of NRs play critical roles in development, especially in the nervous system. In this study, we explore the phylogenetics and function of the NR2E family of Caenorhabditis elegans, using an in vivo assay to test LBD function. RESULTS: Phylogenetic analysis reveals that the NR2E family of NRs consists of three broadly-conserved clades of orthologous NRs. In C. elegans, these clades are defined by nhr-67, fax-1 and nhr-239. The vertebrate orthologs of nhr-67 and fax-1 are Tlx and PNR, respectively. While the nhr-239 clade includes orthologs in insects (Hr83), an echinoderm, and a hemichordate, the gene appears to have been lost from vertebrate lineages. The C. elegans and C. briggsae nhr-239 genes have an apparently-truncated and highly-diverged LBD region. An additional C. elegans NR2E gene, nhr-111, appears to be a recently-evolved paralog of fax-1; it is present in C. elegans, but not C. briggsae or other animals with completely-sequenced genomes. Analysis of the relatively unstudied nhr-111 and nhr-239 genes demonstrates that they are both expressed--nhr-111 very broadly and nhr-239 in a small subset of neurons. Analysis of the FAX-1 LBD in an in vivo assay revealed that it is not required for at least some developmental functions. CONCLUSIONS: Our analysis supports three conserved clades of NR2E receptors, only two of which are represented in vertebrates, indicating three ancestral NR2E genes in the urbilateria. The lack of a requirement for a FAX-1 LBD suggests that the relatively high level of sequence divergence for Caenorhabditis LBDs reflects relaxed selection on the primary sequence as opposed to divergent positive selection. This observation is consistent with a model in which divergence of some Caenorhabditis LBDs is allowed, at least in part, by the absence of a ligand requirement.

Maternal Microbiota Modulate a Fragile X-like Syndrome in Offspring Mice.

Maternal microbial dysbiosis has been implicated in adverse postnatal health conditions in offspring, such as obesity, cancer, and neurological disorders. We observed that the progeny of mice fed a Westernized diet (WD) with low fiber and extra fat exhibited higher frequencies of stereotypy, hyperactivity, cranial features and lower FMRP protein expression, similar to what is typically observed in Fragile X Syndrome (FXS) in humans. We hypothesized that gut dysbiosis and inflammation during pregnancy influenced the prenatal uterine environment, leading to abnormal phenotypes in offspring. We found that oral in utero supplementation with a beneficial anti-inflammatory probiotic microbe, Lactobacillus reuteri, was sufficient to inhibit FXS-like phenotypes in offspring mice. Cytokine profiles in the pregnant WD females showed that their circulating levels of pro-inflammatory cytokine interleukin (Il)-17 were increased relative to matched gravid mice and to those given supplementary L. reuteri probiotic. To test our hypothesis of prenatal contributions to this neurodevelopmental phenotype, we performed Caesarian (C-section) births using dissimilar foster mothers to eliminate effects of maternal microbiota transferred during vaginal delivery or nursing after birth. We found that foster-reared offspring still displayed a high frequency of these FXS-like features, indicating significant in utero contributions. In contrast, matched foster-reared progeny of L. reuteri-treated mothers did not exhibit the FXS-like typical features, supporting a key role for microbiota during pregnancy. Our findings suggest that diet-induced dysbiosis in the prenatal uterine environment is strongly associated with the incidence of this neurological phenotype in progeny but can be alleviated by addressing gut dysbiosis through probiotic supplementation.

Characteristics of Patients Discontinuing Care.

Objectives: Due to lower fees, dental school clinics (DSCs) may provide dental care for vulnerable populations. This study evaluates factors associated with patients deciding to discontinue care at a DSC. Methods: This is a retrospective analysis of a patient transfer form that was implemented to smooth transition of a patient when their student provider graduated. Forms provided deidentified information about characteristics and unmet dental needs. Descriptive and bivariate statistics were used to identify associations between patient characteristics and deciding to continue treatment in the student practice. Results: Of 1894 patients, 73.4% continued care. Financial limitations were most commonly reported as the reason for discontinuing care (30.1%). Patients speaking a language other than English or who had reported financial barriers were significantly less likely to continue care. Conclusions: Dental school patients from vulnerable groups are more likely to discontinue care. Dental schools should implement programs that will assist patients in maintaining a dental home.

Comparison of Clarithromycin and Amoxicillin/Clavulanic Acid for Community-Acquired Pneumonia in an Era of Drug-Resistant Streptococcus pneumoniae.

OBJECTIVE: To compare the safety and efficacy of clarithromycin and amoxicillin/clavulanic acid in patients with community-acquired pneumonia due to penicillin-resistant and/or macrolide-resistant Streptococcus pneumoniae, by selecting clinical investigators who practice in study populations from geographic areas in which a high incidence of resistant strains is reported by surveillance. DESIGN AND SETTING: Prospective, randomised, investigator-blinded, multicentre study conducted in 45 sites in primary-care and referral centre settings. PATIENTS AND INTERVENTIONS: 327 ambulatory patients diagnosed with radio-graphically confirmed community-acquired pneumonia administered clarithromycin 500mg immediate-release or amoxicillin/clavulanic acid 875mg/125mg twice daily for 7 days. MAIN OUTCOME MEASURES AND RESULTS: Similarly high clinical cure rates were observed among evaluable patients in both treatment groups at the test-of-cure visit (28-35 days post-treatment): 92% (114/124) for clarithromycin and 91% (117/129) for amoxicillin/clavulanic acid. Of 85 S. pneumoniae strains isolated pretreatment, four (5%) were classified as resistant to macrolides (one mefA, two ermB, and one ermB + mefA) and eight (9%) had reduced susceptibility to penicillin. The overall eradication rate for pathogens isolated from bacteriologically and clinically evaluable patients was 91% for clarithromycin and 93% for amoxicillin/clavulanic acid, and 89% and 92%, respectively, for S. pneumoniae strains. The rates of resolution and/or improvement in clinical signs and symptoms and radiological improvement were similar with clarithromycin to those with amoxicillin/clavulanic acid, as was overall incidence of adverse events. CONCLUSION: A 7-day course of clarithromycin immediate-release was similar to amoxicillin/clavulanic acid based on high rates (>90%) of clinical cure, radiological improvement and pathogen eradication among ambulatory-care patients with community-acquired pneumonia. As the resistance rate at baseline was low, no conclusion could be made about clarithromycin's efficacy for infections caused by macrolide-resistant S. pneumoniae. Both treatments were well tolerated.

Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans.

Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication.

Molecular testing for mutations in improving the fine-needle aspiration diagnosis of thyroid nodules.

CONTEXT: Thyroid nodules are common in adults, but only a small fraction of them are malignant. Fine-needle aspiration (FNA) with cytological evaluation is the most reliable tool for cancer diagnosis in thyroid nodules. However, 10-40% of nodules are diagnosed as indeterminate by cytology, making it difficult to optimally manage these patients. OBJECTIVE: The aim of this study was to establish the feasibility and role of testing for tumor-specific mutations in improving the FNA diagnosis of thyroid nodules. DESIGN: The prospective study included 470 FNA samples of thyroid nodules from 328 patients. At the time of aspiration, a small portion of the material was collected and tested for BRAF, RAS, RET/PTC, and PAX8/PPARgamma mutations. The mutational status was correlated with cytology and either surgical pathology diagnosis or follow-up (mean, 34 months). RESULTS: A sufficient amount of nucleic acids were isolated in 98% of samples. Thirty-two mutations were found, including 18 BRAF, eight RAS, five RET/PTC, and one PAX8/PPARgamma. The presence of any mutation was a strong indicator of cancer because 31 (97%) of mutation-positive nodules had a malignant diagnosis after surgery. A combination of cytology and molecular testing showed significant improvement in the diagnostic accuracy and allowed better prediction of malignancy in the nodules with indeterminate cytology. CONCLUSIONS: These results indicate that molecular testing of thyroid nodules for a panel of mutations can be effectively performed in a clinical setting. It enhances the accuracy of FNA cytology and is of particular value for thyroid nodules with indeterminate cytology.

The C. elegans nuclear receptor gene fax-1 and homeobox gene unc-42 coordinate interneuron identity by regulating the expression of glutamate receptor subunits and other neuron-specific genes.

The fax-1 gene of the nematode C. elegans encodes a conserved nuclear receptor that is the ortholog of the human PNR gene and functions in the specification of neuron identities. Mutations in fax-1 result in locomotion defects. FAX-1 protein accumulates in the nuclei of 18 neurons, among them the AVA, AVB, and AVE interneuron pairs that coordinate body movements. The identities of AVA and AVE interneurons are defective in fax-1 mutants; neither neuron expresses the NMDA receptor subunits nmr-1 and nmr-2. Other ionotropic glutamate receptor subunits are expressed normally in the AVA and AVE neurons. The unc-42 homeobox gene also regulates AVA and AVE identity; however, unc-42 mutants display the complementary phenotype: NMDA receptor subunit expression is normal, but some non-NMDA glutamate receptor subunits are not expressed. These observations support a combinatorial role for fax-1 and unc-42 in specifying AVA and AVE identity. However, in four other neuron types, fax-1 is regulated by unc-42, and both transcriptional regulators function in the regulation of the opt-3 gene in the AVE neurons and the flp-1 and ncs-1 genes in the AVK neurons. Therefore, while fax-1 and unc-42 act in complementary parallel pathways in some cells, they function in overlapping or linear pathways in other cellular contexts, suggesting that combinatorial relationships among transcriptional regulators are complex and cannot be generalized from one neuron type to another.