Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity.
Viroids are small circular single-stranded infectious RNAs characterized by a relatively high mutation level. Knowledge of their sequence heterogeneity remains largely elusive and previous studies, using Sanger sequencing, were based on a limited number of sequences. In an attempt to address sequence heterogeneity from a population dynamics perspective, a GF305-indicator peach tree was infected with a single variant of the Avsunviroidae family member Peach latent mosaic viroid (PLMVd). Six months post-inoculation, full-length circular conformers of PLMVd were isolated and deep-sequenced. We devised an original approach to the bioinformatics refinement of our sequence libraries involving important phenotypic data, based on the systematic analysis of hammerhead self-cleavage activity. Two distinct libraries yielded a total of 3,939 different PLMVd variants. Sequence variants exhibiting up to ∼17% of mutations relative to the inoculated viroid were retrieved, clearly illustrating the high level of divergence dynamics within a unique population. While we initially assumed that most positions of the viroid sequence would mutate, we were surprised to discover that ∼50% of positions remained perfectly conserved, including several small stretches as well as a small motif reminiscent of a GNRA tetraloop which are the result of various selective pressures. Using a hierarchical clustering algorithm, the different variants harvested were subdivided into 7 clusters. We found that most sequences contained an average of 4.6 to 6.4 mutations compared to the variant used to initially inoculate the plant. Interestingly, it was possible to reconstitute and compare the sequence evolution of each of these clusters. In doing so, we identified several key mutations. This study provides a reliable pipeline for the treatment of viroid deep-sequencing. It also sheds new light on the extent of sequence variation that a viroid population can sustain, and which may give rise to a quasispecies.


Observational research methods. Research design II: cohort, cross sectional, and case-control studies.
Cohort, cross sectional, and case-control studies are collectively referred to as observational studies. Often these studies are the only practicable method of studying various problems, for example, studies of aetiology, instances where a randomised controlled trial might be unethical, or if the condition to be studied is rare. Cohort studies are used to study incidence, causes, and prognosis. Because they measure events in chronological order they can be used to distinguish between cause and effect. Cross sectional studies are used to determine prevalence. They are relatively quick and easy but do not permit distinction between cause and effect. Case controlled studies compare groups retrospectively. They seek to identify possible predictors of outcome and are useful for studying rare diseases or outcomes. They are often used to generate hypotheses that can then be studied via prospective cohort or other studies.


Host effect on the genetic diversification of beet necrotic yellow vein virus single-plant populations.
Theoretical models predict that, under restrictive host conditions, virus populations will exhibit greater genetic variability. This virus response has been experimentally demonstrated in a few cases but its relation with a virus's capability to overcome plant resistance is unknown. To explore the genetic host effects on Beet necrotic yellow vein virus (BNYVV) populations that might be related to resistance durability, a wild-type virus isolate was vector inoculated into partially resistant Rz1, Rz2, and susceptible sugar beet cultivars during a serial planting experiment. Cloning and sequencing a region of the viral RNA-3, involving the pathogenic determinant p25, revealed that virus diversity significantly increased in direct proportion to the strength of host resistance. Thus, whereas virus titers were highest, intermediate, and lowest in susceptible, Rz1, and Rz2 plants, respectively; the average number of nucleotide differences among single-plant populations was 0.8 (±0.1) in susceptible, 1.4 (±0.1) in Rz1, and 2.4 (±0.2) in Rz2 genotypes. A similar relationship between host restriction to BNYVV root accumulation and virus genetic variability was detected in fields of sugar beet where these specific Rz1- and Rz2-mediated resistances have been defeated.


NTP Toxicology and Carcinogenesis Studies of Nitrofurantoin (CAS No. 67-20-9) in F344/N Rats and B6C3F1 Mice (Feed Studies).
Nitrofurantoin was studied and evaluated because of its widespread use as a drug for treating urinary tract infections in humans, its structural relationship to known carcinogenic 5-nitrofuran compounds, and the lack of adequate studies to assess its carcinogenicity. Toxicology and carcinogenesis studies of nitrofurantoin were conducted by administering nitrofurantoin (greater than 99% pure) in feed to groups of F344/N rats and B6C3F1 mice of each sex for 14 days, 13 weeks, or 2 years. Fourteen-Day and Thirteen-Week Studies: None of the rats (at dietary concentrations up to 20,000 ppm) died before the end of the 14-day studies. Rats that received 5,000, 10,000, or 20,000 ppm lost weight. Four of five male and 4/5 female mice that received 10,000 ppm and 1/5 females that received 5,000 ppm nitrofurantoin died before the end of the studies. Mice that received 5,000 ppm and male mice that received 10,000 ppm lost weight. In the 13-week studies, final mean body weights of rats that received 2,500, 5,000, or 10,000 ppm were 10%, 34%, or 47% lower than that of the controls for males and 15%, 31%, or 41% lower for females. Feed consumption by dosed and control rats was generally similar. Degeneration of the germinal epithelium of the seminiferous tubules of the testis was observed in male rats that received 2,500 to 10,000 ppm nitrofurantoin. Necrosis of the ovarian follicles was observed in 8/10 female rats that received 10,000 ppm, in 3/10 females that received 5,000 ppm, and in 1/10 that received 2,500 ppm. For mice, final mean body weights of the 5,000-ppm groups were 13% lower than that of the controls for males and 15% lower for females. Two of 10 male mice that received 5,000 ppm and 1/10 males that received 300 ppm died before the end of the 13-week studies. Estimated feed consumption was similar for dosed and control groups. Degeneration of the germinal epithelium of the testis was observed in males that received 1,300 to 5,000 ppm; necrosis of the ovarian follicles was observed in females that received 5,000 ppm but not in the lower dose groups. Necrosis of the renal tubular epithelium was observed in 2/9 males that received 5,000 ppm. Based on these results, 2-year studies of nitrofurantoin were conducted by feeding diets containing 0, 1,300, or 2,500 ppm nitrofurantoin to groups of 50 male F344/N rats and to groups of 50 male and female B6C3F1 mice for 103 weeks. Groups of 50 female F344/N rats were fed diets containing 0, 600, or 1,300 ppm nitrofurantoin on the same schedule. Body Weight and Survival in the Two-Year Studies: Mean body weight and average daily feed consumption of dosed male and female rats were similar to those of the controls throughout the studies. The average amount of nitrofurantoin consumed per day was estimated to be 60 and 110 mg/kg for low and high dose male rats and 30 and 60 mg/kg for low and high dose female rats. No significant differences in the number of rats surviving to the end of the studies were observed between any groups of rats of either sex (male: control, 24/50; low dose, 27/50; high dose, 26/50; female: 25/50; 26/50; 31/50). Mean body weights of high dose male and female mice were up to 12% lower than those of the controls throughout most of the studies. The average daily feed consumption by dosed mice ranged from 93% to 100% that by controls. The average amount of nitrofurantoin consumed per day was estimated to be 280-300 mg/kg and 570-580 mg/kg for low and high dose mice. The survival of the control group of female mice was lower than that of the dosed groups (control, 19/50; low dose, 37/50; high dose, 37/50). The decrease in survival was most likely related to the increase in microbial infection in the reproductive tract observed in the controls. Groups of male mice had similar survival (28/50; 29/50; 34/50). Nonneoplastic and Neoplastic Effects in the Two-Year Studies: Organs showing toxicity from nitrofurantoin exposure identified in the short-term studies were the testis in male rats and mice, the ovary in female rats and mice, and the kidney in male mice. Lesions oband mice, the ovary in female rats and mice, and the kidney in male mice. Lesions observed in the 2-year studies were in the testis in male rats and mice, ovary in female mice, and kidney in male rats. Chronic nephropathy was observed in nearly all rats, but the severity of the lesions was judged to be greater in dosed male rats. Hyperplasia of the transitional cell epithelium (control, 0/50; low dose, 5/50; high dose, 2/50) and hydronephrosis of the renal pelvis (0/50; 5/50; 2/50) were also observed in dosed male rats. In the standard single sections of the left and right kidney from each rat, tubular cell adenomas were observed in one low dose and two high dose males; a tubular cell carcinoma was observed in another high dose male. Because the number of renal tubular cell neoplasms identified by standard procedures in the dosed male rats was low, additional step-sections of the kidney were evaluated. The incidences of tubular cell adenomas derived from the step-sections and original sections (combined) were significantly increased in dosed male rats (adenomas: 3/50; 11/50; 19/50); tubular cell carcinomas occurred in two high dose males only. Lesions considered to be associated with the nephropathy and nitrofurantoin exposure were observed in male rats and included hyperplasia of the parathyroid glands (3/49; 18/47; 23/49), fibrous osteodystrophy of the bone (0/50; 5/50; 5/50), and mineralization of the glandular stomach (1/49; 8/50; 14/50). Atypical cells of the epididymis (0/50; 0/50; 12/50) and degeneration of the testis (0/50; 0/50; 36/50) were observed in high dose male rats. Fibrinoid necrosis of arterioles (1/50; 8/50; 15/50) and perivascular infiltration of mononuclear cells (3/50; 9/50; 19/50) were also observed in the testis of male rats. Interstitial cell adenomas of the testis occurred with a negative trend (47/50; 45/50; 21/50), and no adenomas or carcinomas of the preputial gland were seen in high dose male rats (12/48; 11/50; 0/47). The incidence of clitoral gland neoplasms was increased in low dose female rats (5/44; 10/38; 4/42). Osteosarcomas were observed in the bone of one low dose and two high dose male rats. The historical incidence of osteosarcomas in untreated male F344/N rats is 8/1,937 (0.4%). The incidences of subcutaneous tissue neoplasms in dosed male rats were greater than that in the controls (1/50; 7/50; 5/50). No neoplastic lesions in dosed female rats or male mice were considered to be compound related at the doses of nitrofurantoin administered. For female mice, ovarian atrophy was observed in 48/50 low dose and 49/50 high dose mice but not in controls. Tubular cell adenomas of the ovary (0/50; 0/50; 5/50), benign mixed tumors (tubular and stromal) (0/50; 0/50; 4/50), and granulosa cell tumors (0/50; 3/50; 2/50)) were observed in dosed female mice. One granulosa cell tumor in the high dose group was malignant. Ovarian abscesses (18/50) and suppurative inflammation of the uterus (11/50) were observed in control female mice but not in dosed female mice and are believed to be related to indigenous microbial infections and most likely were the cause of early deaths in this group. Adenocarcinomas of the uterus were seen in one low dose and in one high dose mouse. Testicular aspermatogenesis (1/49; 1/49; 16/50), degeneration of the germinal epithelium (0/49; 3/49; 23/50), and atypical cells (0/50; 0/49; 26/50) and depletion (1/50; 1/49; 15/50) of the epididymis were observed at increased incidences in high dose male mice. Spindle cell hyperplasia of the adrenal cortex was observed in dosed female mice (3/50; 41/50; 45/50). A spindle cell adenoma (adrenal capsule adenoma) was seen in one low dose female mouse, and a spindle cell carcinoma (adrenal capsule carcinoma) was seen in one low dose male mouse. Mineralization of the renal medulla (male: 0/50; 0/50; 17/50; female: 0/50; 0/50; 7/50) and dilatation of the renal tubules (male: 0/50; 0/50; 14/50) were observed in high dose mice. Hepatocellular neoplasms (adenomas or carcinomas, combined) were observed at an increased incidence in high dose female mice (2/50; 2/50; 8/50). An Ito cell tumor of the liver was observed in one low dose and one high dose female mouse. Malignant lymphomas occurred in female mice (12/50; 19/50; 24/50). Genetic Toxicology: Nitrofurantoin was mutagenic in Salmonella typhimurium strains TA98 and TA100, with and without metabolic activation, but was not mutagenic for strains TA1535 or TA1537. Nitrofurantoin induced forward mutations at the TK+/- locus of L5178Y mouse lymphoma cells in the absence of metabolic activation (it was not tested with activation). Nitrofurantoin induced increased numbers of sister chromatid exchanges and chromosomal aberrations in cultured Chinese hamster ovary cells with and without metabolic activation. Results of the sex-linked recessive lethal assay in Drosophila were negative after administration of nitrofurantoin by feeding or by injection. Conclusions: Under the conditions of these 2-year feed studies, there was some evidence of carcinogenic activity of nitrofurantoin for male F344/N rats as shown by increased incidences of uncommon kidney tubular cell neoplasms. Uncommon osteosarcomas of the bone and neoplasms of the subcutaneous tissue were observed in dosed male rats. Incidences of interstitial cell adenomas of the testis and neoplasms of the preputial gland were decreased in the 2,500-ppm group of male rats. There was no evidence of carcinogenic activity of nitrofurantoin for female F344/N rats fed diets containing 600 ppm or 1,300 ppm for 2 years. Female rats may have been able to tolerate higher doses. There was no evidence of carcinogenic activity of nitrofurantoin for male B6C3F1 mice fed diets containing 1,300 ppm or 2,500 ppm for 2 years. There was clear evidence of carcinogenic activity of nitrofurantoin for female B6C3F1 mice as shown by increased incidences of tubular adenomas, benign mixed tumors, and granulosa cell tumors of the ovary. Nonneoplastic lesions considered related to nitrofurantoin exposure were chronic nephropathy and associated lesions (hyperplasia of the parathyroid gland, fibrous osteodystrophy of the bone, and mineralization of the glandular stomach) in male rats and testicular degeneration in male rats and mice. Ovarian atrophy and hyperplasia of the adrenal cortex spindle cells were observed in dosed female mice. Synonyms: 1-(((5-nitro-2-furanyl)methylene)amino-2,4-imidazolidinedione); 1-(5-nitro-2-furfurylideneamino)-hydantoin; N-(5-nitro-2-furfurlidene)-1-aminohydantoin; 1-((5-nitrofurfurylidene)amino)hydantoin Trade Names: Benkfuran; Benkfurin; Chemiofuran; Cyantin; Dantafur; Furadantin; Furadantine; Furadantoin; Furadonin; Furadonine; Furantoin; Furatoin; Furobactina; Ituran; Macrodantin; Nifurantin; NSC 2107; N-Toin; Orafuran; Parafuran; Urizept; USAF EA-2; Welfurin; Zoofurin


An exploratory survey of diagnostic methods for bone quality assessment used by Brazilian dental implant specialists.
Bone quality (BQ) has been described as an important predictor for the outcome of dental implant treatment. It is, however, unclear how this factor is assessed in the dental practice routine. The aim of this study was to investigate what Brazilian dental implant specialists know and understand about BQ, if they include BQ assessments in their treatment planning and which methods they use to assess BQ. A questionnaire was posted to Brazilian dental implant specialists, containing open and closed questions about their knowledge and understanding of BQ assessment, and 221 answered the questionnaire. Data were gathered and methods for BQ assessment were grouped using hierarchical cluster analysis. Answers about BQ knowledge and understanding were categorized into quantity of cortical and marrow bone (n = 72), density (n = 55), type of bone (n = 35), bone height (n = 30), bone thickness (n = 27), primary stability (n = 24) and other less common categories. BQ assessment was judged relevant to be considered a selection criterion for implant treatment. Overall frequency analysis showed that methods were roughly divided into usual (n > 170) and unusual methods (n < 9). Cluster analysis grouped BQ assessment methods into four clusters: unusual methods (DEXA, resonance frequency, Periotest and occlusal radiography), perioperative methods (peak insertion torque and tactile perception), sectional imaging (computed tomography) and plain films (periapical and panoramic radiographs). No consensus on BQ understanding or the clinical application of methods to assess BQ was found in this survey. The selection of methods shows a clear natural grouping from basic to advanced strategies for BQ assessment by Brazilian specialists in dental implants.


Translational genomics and precision medicine: Moving from the lab to the clinic.
Translational genomics aims to improve human health by building on discoveries made through genetics research and applying them in the clinical setting. This progress has been made possible by technological advances in genomics and analytics and by the digital revolution. Such advances should enable the development of prognostic markers, tailored interventions, and the design of prophylactic preventive approaches. We are at the cusp of predicting disease risk for some disorders by means of polygenic risk scores integrated with classical epidemiological risk factors. This should lead to better risk stratification and clinical decision-making. A deeper understanding of the link between genome-wide sequence and association with well-characterized phenotypes will empower the development of biomarkers to aid diagnosis, inform disease progression trajectories, and allow better targeting of treatments to those patients most likely to respond.


Effect of intermittent three-month treatment with different doses of Ukrain on subregional femoral bone mineral density of sexually mature female rats.
Sexually mature but still growing female Wistar rats received i.p. injections of Ukrain (7, 14 or 28 mg/kg in a volume of 0.5 ml/100g) every other day for 10 days, followed by a 10-day break, and this procedure was performed five times. The control animals received the same volume of injected water. At the end of the experiment the rat right femora were harvested and the bone densitometric parameters of the entire bone, distal metaphyseal and basicervical subregions were assessed using the dual-energy X-ray absorptiometry (DXA) densitometric method. No significant changes were observed in the bone mineral density in experimental groups in comparison with control animals that received the vehicle. A slight decrease in the bone mineral content value was observed in the distal metaphyseal region in animals that were treated with the highest dose of Ukrain.


Structural basis for modification of flavonol and naphthol glucoconjugates by Nicotiana tabacum malonyltransferase (NtMaT1).
Plant HXXXD acyltransferase-catalyzed malonylation is an important modification reaction in elaborating the structural diversity of flavonoids and anthocyanins, and a universal adaptive mechanism to detoxify xenobiotics. Nicotiana tabacum malonyltransferase 1 (NtMaT1) is a member of anthocyanin acyltransferase subfamily that uses malonyl-CoA (MLC) as donor catalyzing transacylation in a range of flavonoid and naphthol glucosides. To gain insights into the molecular basis underlying its catalytic mechanism and versatile substrate specificity, we resolved the X-ray crystal structure of NtMaT1 to 3.1 Å resolution. The structure comprises two α/β mixed subdomains, as typically found in the HXXXD acyltransferases. The partial electron density map of malonyl-CoA allowed us to reliably dock the entire molecule into the solvent channel and subsequently define the binding sites for both donor and acceptor substrates. MLC bound to the NtMaT1 occupies one end of the long solvent channel between two subdomains. On superimposing and comparing the structure of NtMaT1 with that of an enzyme from anthocyanin acyltransferase subfamily from red chrysanthemum (Dm3Mat3) revealed large architectural variation in the binding sites, both for the acyl donor and for the acceptor, although their overall protein folds are structurally conserved. Consequently, the shape and the interactions of malonyl-CoA with the binding sites' amino acid residues differ substantially. These major local architectural disparities point to the independent, divergent evolution of plant HXXXD acyltransferases in different species. The structural flexibility of the enzyme and the amendable binding pattern of the substrates provide a basis for the evolution of the distinct, versatile substrate specificity of plant HXXXD acyltransferases.


Does Reactance against Cigarette Warning Labels Matter? Warning Label Responses and Downstream Smoking Cessation amongst Adult Smokers in Australia, Canada, Mexico and the United States.
Some researchers have raised concerns that pictorial health warning labels (HWLs) on cigarette packages may lead to message rejection and reduced effectiveness of HWL messages. This study aimed to determine how state reactance (i.e., negative affect due to perceived manipulation) in response to both pictorial and text-only HWLs is associated with other types of HWL responses and with subsequent cessation attempts. Survey data were collected every 4 months between September 2013 and 2014 from online panels of adult smokers in Australia, Canada, Mexico, and the US were analyzed. Participants with at least one wave of follow-up were included in the analysis (n = 4,072 smokers; 7,459 observations). Surveys assessed psychological and behavioral responses to HWLs (i.e., attention to HWLs, cognitive elaboration of risks due to HWLs, avoiding HWLs, and forgoing cigarettes because of HWLs) and cessation attempts. Participants then viewed specific HWLs from their countries and were queried about affective state reactance. Logistic and linear Generalized Estimating Equation (GEE) models regressed each of the psychological and behavioral HWL responses on reactance, while controlling for socio-demographic and smoking-related variables. Logistic GEE models also regressed having attempted to quit by the subsequent survey on reactance, each of the psychological and behavioral HWL responses (analyzed separately), adjustment variables. Data from all countries were initially pooled, with interactions between country and reactance assessed; when interactions were statistically significant, country-stratified models were estimated. Interactions between country and reactance were found in all models that regressed psychological and behavioral HWL responses on study variables. In the US, stronger reactance was associated with more frequent reading of HWLs and thinking about health risks. Smokers from all four countries with stronger reactance reported greater likelihood of avoiding warnings and forgoing cigarettes due to warnings, although the association appeared stronger in the US. Both stronger HWLs responses and reactance were positively associated with subsequent cessation attempts, with no significant interaction between country and reactance. Reactance towards HWLs does not appear to interfere with quitting, which is consistent with its being an indicator of concern, not a systematic effort to avoid HWL message engagement.


Replacement of miR-155 Elicits Tumor Suppressive Activity and Antagonizes Bortezomib Resistance in Multiple Myeloma.
Aberrant expression of microRNAs (miRNAs) has been associated to the pathogenesis of multiple myeloma (MM). While miR-155 is considered a therapeutic target in several malignancies, its role in MM is still unclear. The analysis of miR-155 expression indicates its down-regulation in MM patient-derived as compared to healthy plasma cells, thus pointing to a tumor suppressor role in this malignancy. On this finding, we investigated miR-155 replacement as a potential anti-tumor strategy in MM. The miR-155 enforced expression triggered anti-proliferative and pro-apoptotic effects in vitro. Given the lower miR-155 levels in bortezomib-resistant as compared to sensitive MM cells, we analyzed the possible involvement of miR-155 in bortezomib resistance. Importantly, miR-155 replacement enhanced bortezomib anti-tumor activity both in vitro and in vivo in a xenograft model of human MM. In primary MM cells, we observed an inverse correlation between miR-155 and the mRNA encoding the proteasome subunit gene PSMβ5, whose dysregulation has been largely implicated in bortezomib resistance, and we validated PSMβ5 3'UTR mRNA targeting, along with reduced proteasome activity, by miR-155. Collectively, our findings demonstrate that miR-155 elicits anti-MM activity, likely via proteasome inhibition, providing the framework for miR-155-based anti-MM therapeutic strategies.


Perinephric and epididymal fat affect hepatic metabolism in rats.
The present study examined whether the perinephric and epididymal visceral fat (PEVF) depot under short-term excess nutrient protected the liver by trapping nutrient-derived nonesterified free fatty acids (NEFAs) or had deleterious effects on hepatic triglycerides (TGs) accumulation and insulin resistance due to adipokine secretion. Young rats pre-emptively underwent surgical PEVF removal or sham operations and were fed with either high-fat diet (HFD) (PEVF-HFD) or regular chow (RC) (PEVF-RC) for 3 days. Insulin sensitivity was measured by hyperinsulinemic-euglycemic clamp. Liver TG, serum NEFA, and fat-derived adipokines were assessed. Insulin and lipogenesis signaling were assessed by western blots. Pre-emptive PEVF removal significantly decreases insulin-induced suppression of hepatic glucose production (HGP) both in RC and in HFD-fed rats. In accordance with the clamp results, hepatic TG accumulation is also significantly reduced by PEVF excision both in RC and HFD-fed rats. These results are further validated by insulin signaling results, which show that pre-emptive PEVF removal increases phosphorylation of hepatic Akt, irrespective of diet. Notably, high levels of serum leptin induced by HFD are significantly reduced by pre-emptive PEVF excision. Additionally, expression of lipogenic enzyme p-acetyl-CoA-carboxylase, denoting reduced lipogenesis, is increased in the PEVF-HFD rats. In conclusion, PEVF has a deleterious effect on the liver as a source of insulin resistance-inducing adipokines irrespective of diet, and does not serve as a buffer for excess nutrients.


Use of the Extensible Stylesheet Language (XSL) for medical data transformation.
Recently, the Extensible Markup Language (XML) has received growing attention as a simple but flexible mechanism to represent medical data. As XML-based markups become more common there will be an increasing need to transform data stored in one XML markup into another markup. The Extensible Stylesheet Language (XSL) is a stylesheet language for XML. Development of a new mammography reporting system created a need to convert XML output from the MEDLee natural language processing system into a format suitable for cross-patient reporting. This paper examines the capability of XSL as a rule specification language that supports the medical XML data transformation. A set of nine relevant transformations was identified: Filtering, Substitution, Specification, Aggregation, Merging, Splitting, Transposition, Push-down and Pull-up. XSL-based methods for implementing these transformations are presented. The strengths and limitations of XSL are discussed in the context of XML medical data transformation.


Estrogen receptor expression is high but is of lower intensity in tubular carcinoma than in well-differentiated invasive ductal carcinoma.
Tubular carcinoma (TC) is a rare, luminal A subtype of breast carcinoma with excellent prognosis, for which adjuvant chemotherapy is usually contraindicated. To examine the levels of estrogen receptor (ER) and progesterone receptor expression in cases of TC and well-differentiated invasive ductal carcinoma as compared to normal breast glands and to determine if any significant differences could be detected via molecular testing. We examined ER and progesterone receptor via immunohistochemistry in tubular (N = 27), mixed ductal/tubular (N = 16), and well-differentiated ductal (N = 27) carcinomas with comparison to surrounding normal breast tissue. We additionally performed molecular subtyping of 10 TCs and 10 ductal carcinomas via the PAM50 assay. Although ER expression was high for all groups, TC had statistically significantly lower ER staining percentage (ER%) (P = .003) and difference in ER expression between tumor and accompanying normal tissue (P = .02) than well-differentiated ductal carcinomas, with mixed ductal/tubular carcinomas falling between these 2 groups. Mean ER% was 79%, 87%, and 94%, and mean tumor-normal ER% differences were 13.6%, 25.9%, and 32.6% in tubular, mixed, and ductal carcinomas, respectively. Most tumors that had molecular subtyping were luminal A (9 of 10 tubular and 8 of 10 ductal), and no significant differences in specific gene expression between the 2 groups were identified. Tubular carcinoma exhibited decreased intensity in ER expression, closer to that of normal breast parenchyma, likely as a consequence of a high degree of differentiation. Lower ER% expression by TC may represent a potential pitfall when performing commercially available breast carcinoma prognostic assays that rely heavily on ER-related gene expression.


Crocetin reduces TNBS-induced experimental colitis in mice by downregulation of NFkB.
Ulcerative colitis (UC) is characterized by oxidative and nitrosative stress, leukocyte infiltration and upregulation of proinflammatory cytokines. In this study, we aim to investigate the effects of crocetin and its protective mechanism on 2,4,6- trinitrobenzene sulfonic acid (TNBS)-induced colitis in mice model. Intestinal lesions (judged by macroscopic and histological score) were associated with neutrophil infiltration (measured as increase in myeloperoxidase (MPO) activity in the mucosa), and high levels of malondialdehyde MDA (an indicator of lipid peroxidation). Dose-response studies revealed that treatment of mice with crocetin (50 mg/kg/day) i.g. for 8 days) significantly ameliorated diarrhea and the disruption of colonic architecture. Higher and lower doses (100 and 25 mg/kg/day) did not exhibit comparable effects. In crocetin-treated mice, a significant reduction was noted in the degree of both neutrophil infiltration (measured as decrease in myeloperoxidase activity) and lipid peroxidation (measured as decrease in malondialdehyde activity) in the inflamed colon. Crocetin also reduced the levels of nitric oxide (NO) associated with the favorable expression of TH1 and TH2 cytokines and inducible NO synthase along with the down regulation of nuclear factor-kB (NFkB). These findings suggest that crocetin exerts beneficial effects in experimental colitis, and therefore we propose that this carotenoid may have therapeutic implications for human UC and can be administered along with the conventional therapy of UC.


Disentangling quality and safety indicator data: a longitudinal, comparative study of hand hygiene compliance and accreditation outcomes in 96 Australian hospitals.
The study aims are twofold. First, to investigate the suitability of hand hygiene as an indicator of accreditation outcomes and, second, to test the hypothesis that hospitals with better accreditation outcomes achieve higher hand hygiene compliance rates. A retrospective, longitudinal, multisite comparative survey. Acute public hospitals in New South Wales, Australia. 96 acute hospitals with accreditation survey results from two surveys during 2009-2012 and submitted data for more than four hand hygiene audits between 2010 and 2013. Our primary outcome comprised observational hand hygiene compliance data from eight audits during 2010-2013. The explanatory variables in our multilevel regression model included: accreditation outcomes and scores for the infection control standard; timing of the surveys; and hospital size and activity. Average hand hygiene compliance rates increased from 67.7% to 80.3% during the study period (2010-2013), with 46.7% of hospitals achieving target compliance rates of 70% in audit 1, versus 92.3% in audit 8. Average hand hygiene rates at small hospitals were 7.8 percentage points (pp) higher than those at the largest hospitals (p<0.05). The association between hand hygiene rates, accreditation outcomes and infection control scores is less clear. Our results indicate that accreditation outcomes and hand hygiene audit data are measuring different parts of the quality and safety spectrum. Understanding what is being measured when selecting indicators to assess the impact of accreditation is critical as focusing on accreditation results would discount successful hand hygiene implementation by smaller hospitals. Conversely, relying on hand hygiene results would discount the infection control related research and leadership investment by larger hospitals. Our hypothesis appears to be confounded by an accreditation programme that makes it more difficult for smaller hospitals to achieve high infection control scores.


Use of electroporation to construct isogenic mutants of Haemophilus ducreyi.
Little is known about the genetics of Haemophilus ducreyi, the etiologic agent of chancroid. To develop a method for constructing isogenic mutants of this organism that could be utilized in pathogenesis-related studies, electroporation techniques were evaluated as a means of introducing DNA into this organism. Electroporation of the plasmid shuttle vector pLS88 into H. ducreyi yielded approximately 10(6) antibiotic-resistant transformants per microgram of plasmid DNA. Studies of the feasibility of moving mutated genes into H. ducreyi were initiated by using NotI linker insertion and mini-Tn10kan mutagenesis techniques to introduce insertion mutations into cloned H. ducreyi genes encoding cell envelope antigens. In the former case, a gene encoding chloramphenicol acetyltransferase was then inserted into the NotI linker site created in the cloned H. ducreyi gene. The recombinant Escherichia coli strains containing these mutated plasmids no longer expressed the homologous H. ducreyi cell envelope antigens, as evidenced by their lack of reactivity with monoclonal antibody probes for these H. ducreyi proteins. Subsequent electroporation of both circular and linearized forms of plasmids carrying these mutated H. ducreyi genes into the homologous wild-type strain of H. ducreyi yielded antibiotic-resistant transformants which also lacked reactivity with the cell envelope antigen-specific monoclonal antibodies. Southern blot analysis confirmed that homologous recombination had occurred in these monoclonal antibody-unreactive transformants, resulting in the replacement of the wild-type allele with the mutated allele. Allelic exchange was most efficient when linear DNA molecules were used for electroporation. These results indicate that electroporation methods can be utilized to construct isogenic mutants of H. ducreyi.


Age discrimination at its best: should chronological age be a prime factour in medical decision making?
This paper briefly reviews the papers in this special section of HCA and makes the point--a point which should be obvious--that statistics are useful only as guidelines but tell one nothing about the individual patient in front of you. Chronological age merely shows what is true of most but decidedly not of all patients in a particular age group. To ration on the basis of age alone is unfair to the individual denied treatment and damaging to the community because it disturbs the solidarity which comes about because most members of the community feel that the community has obligations beyond those of not directly harming them; indeed, what produces solidarity is the feeling that members of a community will do their best to come to each others help. Rationing on the basis of age alone denies people of equal treatment under the law and--when it comes to the elderly--is a type of age discrimination. It is pointed out that what matters is a patient's disease and not his/her age. A permanently vegetative person 8 years of age is a much sadder occurrence than it would be at age 90--but the critical fact is that both are permanently vegetative. Age cuts both ways--it is irrational to spend hundreds of thousands of dollars, untold amounts of time, energy and devotion to the 520 gm infant with a gr IV diffuse haemorrhage whose chance of leading a sentient life is close to zero and to hesitate before using a diagnostic MRI on a patient who is 90 but fully alert and enjoying life. It is concluded that age as an independent variable in the allocation of resources is ethically highly problematic.


Risk factors for type I diabetes mellitus in children in Austria.
The aim of this study was to investigate environmental risk factors in the development of type 1 diabetes mellitus in a population-based case-control study. Parents of all patients with manifestation of type 1 diabetes between 1989 and 1994 in Vienna were asked to complete a questionnaire (n = 114). Control children (n = 495), matched for age and sex, were randomly recruited from all schools in Vienna. Fathers of diabetic children were significantly older at the time their children were born than fathers of control children (P = 0.015). Children with diabetes were more likely to be second- or third-born children (P<0.05) and fewer went to kindergarten than the control group children (P = 0.007). No significant difference in duration of gestation, percentage of delivery by caesarean section, birth weight or length was found. Neonatal jaundice was more often observed in the patient group (P = 0.038). Breast feeding was reported by 82.7% of mothers of diabetic children and by 81% of mothers of control children, and the duration of breast feeding was longer in patients than in controls (n.s.). In our study, the development of type 1 diabetes mellitus was associated with higher paternal age and neonatal jaundice. No correlation could be found with dietary intake of cow's milk products in early infancy, vaccination and other environmental factors.


Incorporating evolution of transcription factor binding sites into annotated alignments.
Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits)are generated. Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification methods do not explicitly consider this.Additionally, prediction of conserved binding sites is carried out in a multi-step approach that segregates alignment from TFBS annotation. In this paper, we demonstrate how the simultaneous alignment and annotation approach of SimAnn can be further extended to incorporate TFBS evolutionary relationships. We study how alignments and binding site predictions interplay at varying evolutionary distances and for various profile qualities.


Cochlear supporting cell transdifferentiation and integration into hair cell layers by inhibition of ephrin-B2 signalling.
In mammals, cochlear sensory hair cells that are responsible for hearing are postmitotic and are not replaced after loss. One of the most promising strategies to regenerate hair cells is to identify and inhibit the factors preventing the conversion of adjacent non-sensory supporting cells into hair cells. Here we demonstrate that mammalian hair cells can be directly generated from supporting cells by inhibition of ephrin-B2 signalling. Using either ephrin-B2 conditional knockout mice, shRNA-mediated gene silencing or soluble inhibitors, we found that downregulation of ephrin-B2 signalling at embryonic stages results in supporting cell translocation into hair cell layers and subsequent switch in cell identity from supporting cell to hair cell fate. As transdifferentiation is here a result of displacement across boundary, this original finding presents the interest that newly generated hair cells directly integrate either hair cell layer, then would be likely more rapidly able to fit into functional circuitry.


Effects of exposure to Bovine viral diarrhoea virus 1 on risk of bovine respiratory disease in Australian feedlot cattle.
Viruses play a key role in the complex aetiology of bovine respiratory disease (BRD). Bovine viral diarrhoea virus 1 (BVDV-1) is widespread in Australia and has been shown to contribute to BRD occurrence. As part of a prospective longitudinal study on BRD, effects of exposure to BVDV-1 on risk of BRD in Australian feedlot cattle were investigated. A total of 35,160 animals were enrolled at induction (when animals were identified and characteristics recorded), held in feedlot pens with other cattle (cohorts) and monitored for occurrence of BRD over the first 50days following induction. Biological samples collected from all animals were tested to determine which animals were persistently infected (PI) with BVDV-1. Data obtained from the Australian National Livestock Identification System database were used to determine which groups of animals that were together at the farm of origin and at 28days prior to induction (and were enrolled in the study) contained a PI animal and hence to identify animals that had probably been exposed to a PI animal prior to induction. Multi-level Bayesian logistic regression models were fitted to estimate the effects of exposure to BVDV-1 on the risk of occurrence of BRD. Although only a total of 85 study animals (0.24%) were identified as being PI with BVDV-1, BVDV-1 was detected on quantitative polymerase chain reaction in 59% of cohorts. The PI animals were at moderately increased risk of BRD (OR 1.9; 95% credible interval 1.0-3.2). Exposure to BVDV-1 in the cohort was also associated with a moderately increased risk of BRD (OR 1.7; 95% credible interval 1.1-2.5) regardless of whether or not a PI animal was identified within the cohort. Additional analyses indicated that a single quantitative real-time PCR test is useful for distinguishing PI animals from transiently infected animals. The results of the study suggest that removal of PI animals and/or vaccination, both before feedlot entry, would reduce the impact of BVDV-1 on BRD risk in cattle in Australian feedlots. Economic assessment of these strategies under Australian conditions is required.


Competition and reproduction in mixed infections of pathogenic and non-pathogenic Bacillus spp.
Diamondback moth, Plutella xylostella, larvae were infected with a primary pathogen, Bacillus thuringiensis kurstaki (Btk) in single strain and mixed infections. Mixed infections comprised Btk and a non-pathogenic isolate, either Bacillus thuringiensis tenebrionis (Btt) or Bacillus cereus (Bc). All strains reproduced in larval cadavers, but there was evidence of competition between different isolates within hosts. Non-pathogenic isolates (Btt, Bc) had growth rates that were faster than Btk in vivo, whereas Btk outcompeted Btt in vitro. Passage through insects increased the in vitro competitive ability of Btk against Btt.


Cell growth inhibition and gene expression regulation by (-)-epigallocatechin-3-gallate in human cervical cancer cells.
EGCG [(-)-epigallocatechin-3-gallate] has shown its antitumor ability and perhaps a potential regimen for cancer patients. The goal of this study was to investigate the effect of EGCG on human papilloma virus (HPV) positive cervical cancer cell lines. EGCG inhibited the growth of CaSki (HPV16 positive) and HeLa (HPV18 positive) cells in a time- and concentration-dependent manner. Cell cycle arrest and apoptosis were observed in two cell lines after EGCG exposure. More importantly, we focused on EGCG regulation ability on pivotal genes involved in cervical cancer: viral oncogenes E6/E7, estrogen receptor (ER) and aromatase. Our results suggested that EGCG may be suitable for prevention and treatment of cervical cancer.


Missing and spurious interactions and the reconstruction of complex networks.
Network analysis is currently used in a myriad of contexts, from identifying potential drug targets to predicting the spread of epidemics and designing vaccination strategies and from finding friends to uncovering criminal activity. Despite the promise of the network approach, the reliability of network data is a source of great concern in all fields where complex networks are studied. Here, we present a general mathematical and computational framework to deal with the problem of data reliability in complex networks. In particular, we are able to reliably identify both missing and spurious interactions in noisy network observations. Remarkably, our approach also enables us to obtain, from those noisy observations, network reconstructions that yield estimates of the true network properties that are more accurate than those provided by the observations themselves. Our approach has the potential to guide experiments, to better characterize network data sets, and to drive new discoveries.


Mint2/X11-like colocalizes with the Alzheimer's disease amyloid precursor protein and is associated with neuritic plaques in Alzheimer's disease.
Aberrant metabolism of the amyloid precursor protein (APP) is believed to be at least part of the pathogenic process in Alzheimer's disease. The carboxy-terminus of APP has been shown to interact with the Mint/X11 family of phosphotyrosine binding (PTB) domain-bearing proteins. It is via their PTB domains that the Mints/X11s bind to APP. Here we report the cloning of full-length mouse Mint2 and demonstrate that in primary cortical neurons, Mint2 and APP share highly similar distributions. Mint2 also colocalizes with APP in transfected CHO cells. In Mint2/APP-cotransfected cells, Mint2 reorganizes the subcellular distribution of APP and also increases the steady-state levels of APP. Finally, we demonstrate that Mint2 is associated with the neuritic plaques found in Alzheimer's disease but not with neurofibrillary tangles. These results are consistent with a role for Mint2 in APP metabolism and trafficking, and suggest a possible role for the Mints/X11s in the pathogenesis of Alzheimer's disease.


Whole-genome characterization of a Peruvian alpaca rotavirus isolate expressing a novel VP4 genotype.
The SA44 isolate of Rotavirus A (RVA) was identified from a neonatal Peruvian alpaca presenting with diarrhea, and the full-length genome sequence of the isolate (designated RVA/Alpaca-tc/PER/SA44/2014/G3P[40]) was determined. Phylogenetic analyses showed that the isolate possessed the genotype constellation G3-P[40]-I8-R3-C3-M3-A9-N3-T3-E3-H6, which differs considerably from those of RVA strains isolated from other species of the order Artiodactyla. Overall, the genetic constellation of the SA44 strain was quite similar to those of RVA strains isolated from a bat in Asia (MSLH14 and MYAS33). Nonetheless, phylogenetic analyses of each genome segment identified a distinct combination of genes. Several sequences were closely related to corresponding gene sequences in RVA strains from other species, including human (VP1, VP2, NSP1, and NSP2), simian (VP3 and NSP5), bat (VP6 and NSP4), and equine (NSP3). The VP7 gene sequence was closely related to RVA strains from a Peruvian alpaca (K'ayra/3368-10; 99.0% nucleotide and 99.7% amino acid identity) and from humans (RCH272; 95% nucleotide and 99.0% amino acid identity). The nucleotide sequence of the VP4 gene was distantly related to other VP4 sequences and was designated as the reference strain for the new P[40] genotype. This unique genetic makeup suggests that the SA44 strain emerged from multiple reassortment events between bat-, equine-, and human-like RVA strains.


Measurement of the W boson polarisation in [Formula: see text] events from pp collisions at [Formula: see text] = 8 TeV in the lepton + jets channel with ATLAS.
This paper presents a measurement of the polarisation of W bosons from [Formula: see text] decays, reconstructed in events with one high-[Formula: see text] lepton and at least four jets. Data from pp collisions at the LHC were collected at [Formula: see text] = 8 TeV and correspond to an integrated luminosity of 20.2 fb[Formula: see text]. The angle [Formula: see text] between the b-quark from the top quark decay and a direct W boson decay product in the W boson rest frame is sensitive to the W boson polarisation. Two different W decay products are used as polarisation analysers: the charged lepton and the down-type quark for the leptonically and hadronically decaying W boson, respectively. The most precise measurement of the W boson polarisation via the distribution of [Formula: see text] is obtained using the leptonic analyser and events in which at least two of the jets are tagged as b-quark jets. The fitted fractions of longitudinal, left- and right-handed polarisation states are [Formula: see text], [Formula: see text] and [Formula: see text], and are the most precisely measured W boson polarisation fractions to date. Limits on anomalous couplings of the Wtb vertex are set.


Technical report: treatment of the child with simple febrile seizures.
Simple febrile seizures that occur in children ages 6 months to 5 years are common events with few adverse outcomes. Those who advocate therapy for this disorder have been concerned that such seizures lead to additional febrile seizures, to epilepsy, and perhaps even to brain injury. Moreover, they note the potential for such seizures to cause parental anxiety. We examined the literature to determine whether there was demonstrable benefit to the treatment of simple febrile seizures and whether such benefits exceeded the potential side effects and risks of therapy. The therapeutic approaches considered included continuous anticonvulsant therapies, intermittent therapy, or no anticonvulsant therapy. This analysis focused on the neurologically healthy child between 6 months and 5 years of age whose seizure is brief (<15 minutes), generalized, and occurs only once during a 24-hour period during a fever. Children whose seizures are attributable to a central nervous system infection and those who have had a previous afebrile seizure or central nervous system abnormality were excluded. A review of the current literature was conducted using articles obtained through searches in MEDLINE and additional databases. Articles were obtained following defined criteria and data abstracted using a standardized literature review form. Abstracted data were summarized into evidence tables (Tables 1 through 7). Epidemiologic studies demonstrate a high risk of recurrent febrile seizures but a low, though increased, risk of epilepsy. Other adverse outcomes either don't occur or occur so infrequently that their presence is not convincingly demonstrated by the available studies. Although daily anticonvulsant therapy with phenobarbital or valproic acid is effective in decreasing recurrent febrile seizures, the risks and potential side effects of these medications outweigh this benefit. No medication has been shown to prevent the future onset of recurrent afebrile seizures (epilepsy). The use of intermittent diazepam with fever after an initial febrile seizure is likely to decrease the risk of another febrile seizure, but the rate of side effects is high although most families find the perceived benefits to be low. Although antipyretic therapy has other benefits, it does not prevent additional simple febrile seizures. The Febrile Seizures Subcommittee of the American Academy of Pediatrics' Committee on Quality Improvement used the results of this analysis to derive evidence-based recommendations for the treatment of simple febrile seizures. The outcomes anticipated as a result of the analysis and development of the practice guideline include: 1) to optimize practitioner understanding of the scientific basis for using or avoiding various proposed treatments for children with simple febrile seizures; 2) to improve the health of children with simple febrile seizures by avoiding therapies with high potential for side effects and no demonstrated ability to improve children's eventual outcomes; 3) to reduce costs by avoiding therapies that will not demonstrably improve children's long-term outcomes; and 4) to help the practitioner educate caregivers about the low risks associated with simple febrile seizures.


Retrospective Assessment of Desmopressin Effectiveness and Safety in Patients With Antiplatelet-Associated Intracranial Hemorrhage.
Current international guidelines offer a conditional recommendation to consider a single dose of IV desmopressin (DDAVP) for antiplatelet-associated intracranial hemorrhage based on low-quality evidence. We provide the first comparative assessment analyzing DDAVP effectiveness and safety in antiplatelet-associated intracranial hemorrhage. Retrospective chart review. Single tertiary care academic medical center. Adult patients taking at least one antiplatelet agent based on presenting history and documented evidence of intracranial hemorrhage on cerebral CT scan were included. Patients were excluded for the following reasons: repeat cerebral CT scan not performed within the first 24 hours, noncomparative repeat cerebral CT scan, chronic anticoagulation, administration of fibrinolytic medications, concurrent ischemic stroke, and neurosurgical intervention. In total, 124 patients were included, 55 received DDAVP and 69 did not. DDAVP treatment at recognition of antiplatelet-associated intracranial hemorrhage versus nontreatment. Primary effectiveness outcome was intracranial hemorrhage expansion greater than or equal to 3 mL during the first 24 hospital hours. Primary safety outcomes were the largest absolute decrease from baseline serum sodium during the first 3 treatment days and new-onset thrombotic events during the first 7 days. DDAVP was associated with 88% decreased likelihood of intracranial hemorrhage expansion during the first 24 hours ([+] DDAVP, 10.9% vs [-] DDAVP, 36.2%; p = 0.002; odds ratio [95% CI], 0.22 [0.08-0.57]). Largest median absolute decrease from baseline serum sodium ([+] DDAVP, 0 mEq/L [0-5 mEq/L] vs [-] DDAVP, 0 mEq/L [0-2 mEq/L]; p = 0.089) and thrombotic events ([+] DDAVP, 7.3% vs [-] DDAVP, 1.4%; p = 0.170; odds ratio [95% CI], 5.33 [0.58-49.16]) were similar between groups. DDAVP was associated with a decreased likelihood of intracranial hemorrhage expansion during the first 24 hours. DDAVP administration did not significantly affect serum sodium and thrombotic events during the study period.


A rapid and eco-friendly isothermal amplification microdevice for multiplex detection of foodborne pathogens.
In this study, a plastic microdevice based on loop-mediated isothermal amplification (LAMP) was fabricated for the amplification and on-chip fluorescence detection of multiple pathogens. Papers infused with LAMP reagents and specific primers were embedded inside the multiple reaction chambers of the microdevice. A solution containing the target pathogens was injected into the sample chamber, located in the center of the microdevice, and evenly distributed to the reaction chambers simultaneously via centrifugal force. For detection, fisetin, a plant-derived fluorophore, was used as the DNA-intercalating dye. Purified DNAs of Escherichia coli O157:H7 (E. coli O157:H7), Salmonella spp., Staphylococcus aureus (S. aureus), and Cochlodinium polykrikoides were successfully amplified and directly detected on the microdevice, where as low as 0.13 and 0.12 ng μL-1 of the DNA of E. coli O157:H7 and S. aureus, respectively, were identified. In addition, the potential of this microdevice for point-of-care testing was further examined by incorporating on-chip sample purification module and testing using a real sample - milk spiked with Salmonella spp. The thermally lysed milk sample was filtered using polydopamine-coated paper embedded inside a sample chamber and seamlessly transported into the reaction chambers by centrifugal force for subsequent LAMP followed by direct on-chip detection inside the reaction chambers in which fisetin-soaked papers were embedded. The limit of detection for Salmonella spp. was determined to be approximately 1.7 × 102 CFU mL-1 using the microdevice. This microdevice is safe, easy to use, selective, and sensitive enough for point-of-care testing to identify foodborne pathogens as well as environmentally harmful microorganisms.


Early divergence in lymphoid tissue apoptosis between pathogenic and nonpathogenic simian immunodeficiency virus infections of nonhuman primates.
The events that contribute to the progression to AIDS during the acute phase of a primate lentiviral infection are still poorly understood. In this study, we used pathogenic and nonpathogenic simian models of simian immunodeficiency virus (SIV) infection of rhesus macaques (RMs) and African green monkeys (AGMs), respectively, to investigate the relationship between apoptosis in lymph nodes and the extent of viral replication, immune activation, and disease outcome. Here, we show that, in SIVmac251-infected RMs, a marked increased in lymphocyte apoptosis is evident during primary infection at the level of lymph nodes. Interestingly, the levels of apoptosis correlated with the extent of viral replication and the rate of disease progression to AIDS, with higher apoptosis in RMs of Indian genetic background than in those of Chinese origin. In stark contrast, no changes in the levels of lymphocyte apoptosis were observed during primary infection in the nonpathogenic model of SIVagm-sab infection of AGMs, despite similarly high rates of viral replication. A further and early divergence between SIV-infected RMs and AGMs was observed in terms of the dynamics of T- and B-cell proliferation in lymph nodes, with RMs showing significantly higher levels of cycling cells (Ki67(+)) in the T-cell zones in association with relatively low levels of Ki67(+) in the B-cell zones, whereas AGMs displayed a low frequency of Ki67(+) in the T-cell area but a high proportion of Ki67(+) cells in the B-cell area. As such, this study suggests that species-specific host factors determine an early immune response to SIV that predominantly involves either cellular or humoral immunity in RMs and AGMs, respectively. Taken together, these data are consistent with the hypotheses that (i) high levels of T-cell activation and lymphocyte apoptosis are key pathogenic factors during pathogenic SIV infection of RMs and (ii) low T-cell activation and apoptosis are determinants of the AIDS resistance of SIVagm-infected AGMs, despite high levels of SIVagm replication.


Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq.
Plasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-h blood stages of the major human malaria parasite Plasmodium falciparum have been described using cDNA microarrays and RNA-seq, but these assays have not always performed well within non-coding regions, where the AT-content is often 90-95%. We developed a directional, amplification-free RNA-seq protocol (DAFT-seq) to reduce bias against AT-rich cDNA, which we have applied to three strains of P. falciparum (3D7, HB3 and IT). While strain-specific differences were detected, overall there is strong conservation between the transcriptional profiles. For the 3D7 reference strain, transcription was detected from 89% of the genome, with over 78% of the genome transcribed into mRNAs. We also find that transcription from bidirectional promoters frequently results in non-coding, antisense transcripts. These datasets allowed us to refine the 5' and 3' untranslated regions (UTRs), which can be variable, long (> 1000 nt), and often overlap those of adjacent transcripts. The approaches applied in this study allow a refined description of the transcriptional landscape of P. falciparum and demonstrate that very little of the densely packed P. falciparum genome is inactive or redundant. By capturing the 5' and 3' ends of mRNAs, we reveal both constant and dynamic use of transcriptional start sites across the intraerythrocytic developmental cycle that will be useful in guiding the definition of regulatory regions for use in future experimental gene expression studies.


Practices and Perceived Value of Proficiency Testing in Clinical Laboratories.
Proficiency testing (PT) can have regulatory and nonregulatory uses, providing an effective tool for quality improvement. Clinical laboratories were surveyed to determine how they perceive PT and how they use PT results and materials to improve laboratory testing quality. All laboratories certified to perform nonwaived testing under the CLIA regulations expected to perform required PT were invited to participate in the survey. We examined respondents' use of PT from 5 laboratory types: hospital, independent, public health, physician office, and "all other." Respondents' awareness of resources about PT was also examined. Several questions allowed responses on a categorical scale. Varying proportions of the respondents (n = 769) used PT to identify problems in the preanalytic (48%), analytic (86%), and postanalytic (76%) phases of testing. Responses also showed that PT was important for demonstrating personnel competency (93%), inappropriate specimen handling (80%), incorrect result interpretation (84%), and other uses. Respodents purchased PT even when not required to do so (77%). Based on all responses, most considered PT worth the cost (65%). Laboratories, regardless of type, have found ways of using leftover PT samples and the information from PT event summaries to help improve laboratory quality. Our findings suggest many laboratories are not taking full advantage of PT to improve testing quality. Additionally, the study suggests a need to improve awareness of resources about PT.


Self-reported priorities and resources of academic emergency physicians for the maintenance of clinical competence: a pilot study.
Medical licensing bodies and professional colleges require their members to maintain a broad spectrum of knowledge, skills and attitudes, which, when taken together, define a competent emergency physician (EP). The objectives of this pilot study were: 1) to determine the resources used by academic EPs to maintain competence and 2) to determine academic EPs' learning priorities. Using a modified Dillman method, we surveyed EPs from 2 Canadian academic tertiary health sciences centres. Thirty-seven (68.5%) of 54 EPs responded. Of those responding, 14 (37.8%) attended grand rounds 3 times or more annually, and 34 (91.7%) attended a medical conference or course at least once annually. Thirty-three (89.2%) respondents read journal articles at least once monthly, with 22 (59.5%) of those reading synopses of original articles. Twenty-three (62.1%) received clinical updates via email, and 11 (29.7%) subscribed to an audio journal or podcast of reviews of original research. Among the CanMEDS roles, Medical Expert, Scholar and Manager were selected as top professional development priorities by more than one-third of respondents. The topics that were not selected as priorities by respondents included patient communication and charting (Communicator); conflict resolution skills and teamwork abilities (Collaborator); advocate for patient and promote health in emergency department populations (Health Advocate) and ethical conflict resolution (Professional). The results of this pilot study suggest that in order to maintain clinical competence in emergency medicine, traditional formats of professional development (e.g., grand rounds, print media and original research) are being substituted for independent study, online media and reviews of original research. This study also suggests a strong preference for Medical Expert topics, while Professional, Health Advocate, Collaborator and Communicator topics are not a reported priority for professional development.


2',5'-Oligoadenylate synthetase levels in patients with multiple myeloma receiving maintenance therapy with interferon alpha 2b do not correlate with clinical response.
In clinical trials with interferon alpha 2b (IFN-alpha 2b) as maintenance therapy for multiple myeloma, the therapeutic benefit is inconclusive. Although the mechanism(s) by which IFN-alpha 2b prolongs remission in some patients is unknown, 2',5'-oligoadenylate synthetase (2,5-A synthetase) has been used as an objective indicator that IFN-alpha 2b is active in vivo. The enzyme was assayed in cytosol preparations of peripheral blood mononuclear cells (MNCs) from 111 patients who were receiving IFN-alpha 2b and 54 patients who were not, using an assay which measures the conversion of [alpha-32P]ATP to triphospho(adenylyl 2',5')adenosine. 2,5-A synthetase activity was compared with response to intensive therapy and with duration of maintenance therapy. Seventy-three per cent of patients had measurable amounts of 2,5-A synthetase during the first 6 months of maintenance therapy. This percentage decreased with longer follow-up but not significantly. There was no difference between the magnitude of enzyme induction amongst patients who were in complete remission, partial response or who had no change in disease status following intensive therapy. Peripheral blood T cells were a major source of 2,5-A synthetase activity in patients receiving the cytokine. However, both T and B cells produced the enzyme following exposure to IFN-alpha in vitro. The data show that the level of 2,5-A synthetase in patients with multiple myeloma is not indicative of clinical response to IFN-alpha 2b.


Genetic structure in the Amazonian catfish Brachyplatystoma rousseauxii: influence of life history strategies.
The Dorado or Plateado (Gilded catfish) Brachyplatystoma rousseauxii (Pimelodidae, Siluriformes) is a commercially valuable migratory catfish performing the largest migration in freshwaters: from the Amazonian headwaters in the Andean foothills (breeding area) to the Amazon estuary (nursery area). In spite of its importance to inform management and conservation efforts, the genetic variability of this species has only recently begun to be studied. The aim of the present work was to determine the population genetic structure of B. rousseauxii in two regions: the Upper Madera Basin (five locations in the Bolivian Amazon) and the Western Amazon Basin (one regional sample from the Uyucalí-Napo-Marañon-Amazon basin, Peru). Length polymorphism at nine microsatellite loci (284 individuals) was used to determine genetic variability and to identify the most probable panmictic units (using a Bayesian approach), after a significant departure from Hardy-Weinberg equilibrium was observed in the overall dataset (Western Amazon + Upper Madera). Bayesian analyses revealed at least three clusters in admixture in the five locations sampled in the Bolivian Amazon, whereas only two of these clusters were observed in the Western Amazon. Considering the migratory behaviour of B. rousseauxii, different life history strategies, including homing, are proposed to explain the cluster distribution. Our results are discussed in the light of the numerous threats to the species survival in the Madera basin, in particular dam and reservoir construction.


Urban-rural differences in amitriptyline use among nursing facility residents.
To characterize patterns of amitriptyline use across the urban-rural continuum. Retrospective analysis of antidepressant drug codes and demographic and clinical data from the Minimum Data Set (MDS), 1994 to 1997. Kansas nursing facilities. Facility residents aged 65 and older. A four-strata system was used to classify nursing facility location by county, from urban to frontier. We examined admission use and after-admission use of amitriptyline across strata for each year separately. Unadjusted and adjusted odds ratios were determined for each stratum, using the urban stratum as the point of reference. Admission use of amitriptyline occurred in 2.3 to 4% of all admissions, and although such use was highest in the most rural stratum, no clear urban-rural gradient was found. In contrast, amitriptyline use 30 days or more after admission demonstrated modest urban-rural gradients in unadjusted and adjusted analyses. In 1997, when adjusted for demographic factors, odds ratios for amitriptyline use were 2.10 (1.54-2.87), 1.68 (1.33-2.13), and 1.49 (1.17-1.90) for the Frontier, Rural, and Densely Settled Rural categories as compared with the Urban reference group. After admission to Kansas nursing facilities, rural practice patterns for amitriptyline use are less favorable than those in urban areas, and an urban-rural gradient is identified. Further work is needed to identify explanatory patient, facility, and prescriber factors.


Causal assessment of pharmaceutical treatments: why standards of evidence should not be the same for benefits and harms?
It is increasingly acknowledged both among epidemiologists and regulators that the assessment of pharmaceutical harm requires specific methodological approaches that cannot simply duplicate those developed for testing efficacy. However, this intuition lacks sound epistemic bases and delivers ad hoc advice. This paper explains why the same methods of scientific inference do not fare equally well for efficacy and safety assessment by tracing them back to their epistemic foundations. To illustrate this, Cartwright's distinction into clinching and vouching methods is adopted and a series of reasons is provided for preferring the latter to the former: (1) the need to take into account all available knowledge and integrate it with incoming data; (2) the awareness that a latent unknown risk may always change the safety profile of a given drug (precautionary principle); (3) cumulative learning over time; (4) requirement of probabilistic causal assessment to allow decision under uncertainty; (5) impartiality; and (6) limited and local information provided by randomised controlled trials. Subsequently, the clinchers/vouchers distinction is applied to a case study concerning the debated causal association between paracetamol and asthma. This study illustrates the tension between implicit epistemologies adopted in evaluating evidence and causality; furthermore, it also shows that discounting causal evidence may be a result of unacknowledged low priors or lack of valid alternative options. We conclude with a presentation of the changing landscape in pharmacology and the trend towards an increased use of Bayesian tools for assessment of harms.


The effect of disease-modifying therapies on brain atrophy in patients with clinically isolated syndrome: a systematic review and meta-analysis.
Brain atrophy is associated with cognitive deficits in patients with clinically isolated syndrome (CIS) and can predict conversion to clinical definite multiple sclerosis. The aim of the present meta-analysis was to evaluate the effect of disease-modifying drugs (DMDs) on brain atrophy in patients with CIS. Eligible placebo-control randomized clinical trials of patients with CIS that had reported changes in brain volume during the study period were identified by searching the MEDLINE, SCOPUS, and Cochrane Central Register of Controlled Trials (CENTRAL) databases. This meta-analysis adopted the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews and meta-analyses. Three eligible studies were identified, comprising 1362 patients. The mean percentage change in brain volume was found to be significantly lower in DMD-treated patients versus placebo-treated subgroups (standardized mean difference [SMD]: = -0.13, 95% confidence interval [CI]: -0.25, 0.01; p = 0.04). In the subgroup analysis of the two studies that provided data on brain-volume changes for the first (0-12 months) and second (13-24 months) year of treatment, DMD attenuated brain-volume loss in comparison with placebo during the second year (SMD = -0.25; 95% CI: -0.43, -0.07; p < 0.001), but not during the first year of treatment (SMD = -0.01; 95% CI: -0.27, 0.24; p = 0.93). No evidence of heterogeneity was found between estimates, while funnel-plot inspection revealed no evidence of publication bias. DMDs appear to attenuate brain atrophy over time in patients with CIS. The effect of DMDs on brain-volume loss is evident after the first year of treatment.


Effects of monocular visual deprivation on geniculocortical innervation of area 18 in cat.
The effects of long-term monocular visual deprivation (MD) on the structure of the terminal arborizations of individual Y-type geniculocortical axons was studied in the cat's cortical area 18. Physiologically classified axons were filled with HRP by intracellular injection, and the three-dimensional distribution of the axons' terminal arborizations was quantified. Individual boutons observed at the light microscope (LM) level were verified as sites of synaptic contact by correlated light and electron microscopy (EM). Single boutons were serially sectioned and reconstructed for subsequent three-dimensional analysis. The arborizations of 17 Y-axons [6 normal (N), 6 nondeprived (ND), and 5 deprived (D)] were analyzed at the LM level, and 372 boutons (104 N, 129 ND, and 139 D) were fully reconstructed from serial sections for analysis at the EM level. MD leads to an expansion in the size of ND arborizations and a variable reduction in the size of the D arbors, which also have a higher bouton density than ND arborizations. ND axons form ectopic synapses, contacting proportionally more dendritic shafts than N or D boutons, and form more synapses per bouton, on average, than either N or D boutons. Compared to ND and N boutons, boutons of D axons are smaller, have fewer mitochondria, generally form synapses on a single target (usually dendritic spines), and occasionally make no synaptic contacts. The structural changes in the extent of individual axon arborizations may be the basis for change in ocular dominance column size with MD. However, the higher bouton density and variable effect on the extent of D axon arborization size suggest that considerable geniculocortical innervation from the deprived eye remains intact. The change in target preference for ND axons suggests that instead of a direct competition for postsynaptic sites by the developing geniculocortical axons innervated by the two retinas, the ND axon arborizations expand to invade synaptic space not normally occupied in such high proportion in the normal cortex. The severe changes in individual boutons following MD indicate that arborization size alone is not the only structural substrate underlying the altered responses of cortical neurons; changes in synaptic distribution onto target neurons may also play a role.


Silica-nanoparticle-dispersed methacrylate photopolymers with net diffraction efficiency near 100%.
We demonstrate volume holographic recording in silica-nanoparticle-dispersed methacrylate photopolymers with reduced scattering loss as low as 2%. This is made possible by use of 13-nm silica nanoparticles. As a result a net diffraction efficiency near 100% is achieved for a transmission volume hologram of 45-microm thickness. Grating buildup dynamics are measured for various nanoparticle concentrations, and the effects of nanoparticle size on refractive-index modulation and polymerization shrinkage are also evaluated.


Insight, neurocognition, and schizophrenia: predictive value of the wisconsin card sorting test.
Lack of insight in schizophrenia is a key feature of the illness and is associated with both positive and negative clinical outcomes. Previous research supports that neurocognitive dysfunction is related to lack of insight, but studies have not examined how neurocognition relates to change in insight over time. Therefore, the current study sought to understand how performance on the Wisconsin Card Sorting Test (WCST) differed between participants with varying degrees of change in insight over a 6-month period. Fifty-two patients with schizophrenia or schizoaffective disorder were administered the WCST and Positive and Negative Syndrome Scale (PANSS) at baseline, and the PANSS was again administered at a 6-month follow-up assessment. Results indicated that while neurocognition was related to insight at baseline, it was not related to subsequent change in insight. The implications of findings for conceptualization and assessment of insight are discussed.


Reduced plant competition among kin can be explained by Jensen's inequality.
Plants often compete with closely related individuals due to limited dispersal, leading to two commonly invoked predictions on competitive outcomes. Kin selection, from evolutionary theory, predicts that competition between relatives will likely be weaker. The niche partitioning hypothesis, from ecological theory, predicts that competition between close relatives will likely be stronger. We tested for evidence consistent with either of these predictions by growing an annual legume in kin and nonkin groups in the greenhouse. We grew plant groups in treatments of symbiotic nitrogen fixing bacteria differing in strain identity and composition to determine if differences in the microbial environment can facilitate or obscure plant competition patterns consistent with kin selection or niche partitioning. Nonkin groups had lower fitness than expected, based on fitness estimates of the same genotypes grown among kin. Higher fitness among kin groups was observed in mixtures of N-fixing bacteria strains compared to single inoculations of bacteria strains present in the soil, which increased fitness differences between kin and nonkin groups. Lower fitness in nonkin groups was likely caused by increased competitive asymmetry in nonkin groups due to genetic differences in plant size combined with saturating relationships with plant size and fitness- i.e. Jensen's inequality. Our study suggests that microbial soil symbionts alter competitive dynamics among kin and nonkin. Our study also suggests that kin groups can have higher fitness, as predicted by kin selection theory, through a commonly heritable trait (plant size), without requiring kin recognition mechanisms.


COVID-19 pandemic and Farr's law: A global comparison and prediction of outbreak acceleration and deceleration rates.
The COVID-19 outbreak has forced most of the global population to lock-down and has put in check the health services all over the world. Current predictive models are complex, region-dependent, and might not be generalized to other countries. However, a 150-year old epidemics law promulgated by William Farr might be useful as a simple arithmetical model (percent increase [R1] and acceleration [R2] of new cases and deaths) to provide a first sight of the epidemic behavior and to detect regions with high predicted dynamics. Thus, this study tested Farr's Law assumptions by modeling COVID-19 data of new cases and deaths. COVID-19 data until April 10, 2020, was extracted from available countries, including income, urban index, and population characteristics. Farr's law first (R1) and second ratio (R2) were calculated. We constructed epidemic curves and predictive models for the available countries and performed ecological correlation analysis between R1 and R2 with demographic data. We extracted data from 210 countries, and it was possible to estimate the ratios of 170 of them. Around 42·94% of the countries were in an initial acceleration phase, while 23·5% already crossed the peak. We predicted a reduction close to zero with wide confidence intervals for 56 countries until June 10 (high-income countries from Asia and Oceania, with strict political actions). There was a significant association between high R1 of deaths and high urban index. Farr's law seems to be a useful model to give an overview of COVID-19 pandemic dynamics. The countries with high dynamics are from Africa and Latin America. Thus, this is a call to urgently prioritize actions in those countries to intensify surveillance, to re-allocate resources, and to build healthcare capacities based on multi-nation collaboration to limit onward transmission and to reduce the future impact on these regions in an eventual second wave.


Dietary saturated fat intake and atherosclerotic vascular disease mortality in elderly women: a prospective cohort study.
The reduction of saturated fatty acid (SFA) intake has been the basis of long-standing dietary recommendations. However, recent epidemiologic studies have reported conflicting evidence in the relation between SFA consumption and risk of atherosclerotic vascular disease (ASVD) mortality. We investigated the association of SFA intake with serum lipid profiles and ASVD mortality in a population-based 10-y cohort study. At baseline (1998) 1469 women living in Perth, Western Australia, with a mean ± SD age of 75.2 ± 2.7 y had SFA intake measured by using a validated food-frequency questionnaire. Outcome data were serum lipids at baseline and ASVD deaths over 10 y (13,649 person-years of follow-up), retrieved from the Western Australian Data Linkage System. Other risk factors for ASVD were assessed and adjusted for in multivariable analyses. ASVD deaths occurred in 9.1% (134) of participants. The highest quartile of SFA intake (>31.28 g/d) had an ~16% cumulative mortality risk compared with ~5% in the lowest quartile (<17.39 g/d) (HR: 3.07; 95% CI: 1.54, 6.11; P = 0.001). Baseline SFA intake was associated with baseline serum total and LDL cholesterol in multivariable-adjusted models (β: 0.199, SE: 0.056, P < 0.001 and β: 0.190, SE: 0.051, P < 0.001, respectively). However, baseline serum total and LDL cholesterol were not associated with ASVD mortality. High SFA intake was associated with the risk of ASVD mortality in this population of elderly women. Although there was a strong positive association between SFA intake and LDL cholesterol, LDL cholesterol was not associated with ASVD mortality in this cohort. Nevertheless, these data support dietary advice to reduce SFA intake.


Effect of scent on comfort of aircraft passengers.
Scents may influence the perceived comfort of an environment. There are only a few studies conducted on the relationship between scent and comfort in aircraft cabin. The goal of this research is to explore whether relationships between scents and perceived comfort can be found for passengers in an aircraft cabin. 276 participants joined an experiment in a Boeing 737 fuselage. The participants were divided into nine groups and each joined a session for 60 minutes with the exposure to different scents. The effect of the odor was measured by a set of questionnaires at the beginning and at the end of the session. Results of questionnaires were analyzed regarding the effects on the completion time, of the type of scents, of the intensity of the scent and on gender. Significant differences were found at the beginning and at the end of the experiment regarding comfort and emotion, but sometimes no relations could be established. The influence of different scents on comfort/discomfort varied and changed over time. However, in all scenarios, participant' scores on emotion decreased. Additionally, the added scents influenced the linearity between the changes in comfort and discomfort. Smell could influence the perceived comfort/discomfort of aircraft passengers over time, and different types of smells have different effects on passengers. The preferences on scents are diverse, which highlights the need for personalization in aircraft cabin design.


The neurosurgical anatomy of the sphenoid sinus and sellar floor in endoscopic transsphenoidal surgery.
A considerable degree of variability exists in the anatomy of the sphenoid sinus, sella turcica, and surrounding skull base structures. The authors aimed to characterize neuroimaging and intraoperative variations in the sagittal and coronal surgical anatomy of healthy controls and patients with sellar lesions. Magnetic resonance imaging studies obtained in 100 healthy adults and 78 patients with sellar lesions were reviewed. The following measurements were made on midline sagittal images: sellar face, sellar prominence, sellar angle, tuberculum sellae angle, sellar-clival angle, length of planum sphenoidale, and length of clivus. The septal configuration of the sphenoid sinus was classified as either simple or complex, according to the number of septa, their symmetry, and their morphological features. The following measurements were made on coronal images: maximum width of the sphenoid sinus and sellar face, and the distance between the parasellar and midclivus internal carotid arteries. Neuroimaging results were correlated with intraoperative findings during endoscopic transsphenoidal surgery. Three sellar floor morphologies were defined in normal adults: prominent (sellar angle of < 90°) in 25%, curved (sellar angle 90-150°) in 63%, flat (sellar angle > 150°) in 11%, and no floor (conchal sphenoid) in 1%. In healthy adults, the following mean measurements were obtained: sellar face, 13.4 mm; sellar prominence, 3.0 mm; sellar angle, 112°; angle of tuberculum sellae, 112°; and sellar-clival angle, 117°. Compared with healthy adults, patients with sellar lesions were more likely to have prominent sellar types (43% vs 25%, p = 0.01), a more acute sellar angle (102° vs 112°, p = 0.03), a more prominent sellar floor (3.8 vs 3.0 mm, p < 0.005), and more acute tuberculum (105° vs 112°, p < 0.01) and sellar-clival (105° vs 117°, p < 0.003) angles. A flat sellar floor was more difficult to identify intraoperatively and more likely to require the use of a chisel or drill to expose (75% vs 25%, p = 0.01). A simple sphenoid sinus configuration (no septa, 1 vertical septum, or 2 symmetric vertical septa) was noted in 71% of studies, and the other 29% showed a complex configuration (2 or more asymmetrical septa, 3 or more septa of any kind, or the presence of a horizontal septum). Intraoperative correlation was more challenging in cases with complex sinus anatomy; the most reliable intraoperative midline markers were the vomer, superior sphenoid rostrum, and bilateral parasellar and clival carotid protuberances. Preoperative assessment of neuroimaging studies is critical for characterizing the morphological characteristics of the sphenoid sinus, sellar floor, tuberculum sellae, and clivus. The flat sellar type identified in 11% of people) or a complex sphenoid sinus configuration (in 29% of people) may make intraoperative correlation substantially more challenging. An understanding of the regional anatomy and its variability can improve the safety and accuracy of transsphenoidal and extended endoscopic skull base approaches.


A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans.
Eukaryotic DNA is highly organized within nuclei and this organization is important for genome function. Fluorescent in situ hybridization (FISH) approaches allow 3D architectures of genomes to be visualized. Scalable FISH technologies, which can be applied to whole animals, are needed to help unravel how genomic architecture regulates, or is regulated by, gene expression during development, growth, reproduction, and aging. Here, we describe a multiplexed DNA FISH Oligopaint library that targets the entire Caenorhabditis elegans genome at chromosome, three megabase, and 500 kb scales. We describe a hybridization strategy that provides flexibility to DNA FISH experiments by coupling a single primary probe synthesis reaction to dye conjugated detection oligos via bridge oligos, eliminating the time and cost typically associated with labeling probe sets for individual experiments. The approach allows visualization of genome organization at varying scales in all/most cells across all stages of development in an intact animal model system.


Phloretin either alone or in combination with duloxetine alleviates the STZ-induced diabetic neuropathy in rats.
Diabetic neuropathy (DN) is one of most disabling disorder complicating diabetes mellites (DM), which affects more than 50% of the all diabetic patients during the disease course. Duloxetine (DX) is one of the first-line medication that approved by FDA for management of DN, nevertheless, it is too costly and has many adverse effects. Recently, phloretin (PH) exhibited powerful euglycemic, antihyperlipidemic, antioxidant, and anti-inflammatory activities. Therefore, we investigated the in vivo possible antineuropathic activity of phloretin, besides, its modulating effects on duloxetine potency, in a rat model of DN. Twelve-week-old male Wistar rats received a single intraperitoneal injection of 55 mg/kg STZ to induce DM. Either DX (30 or 15 mg/kg dissolved in distilled water), PH (50 0r 25 mg/kg dissolved in 0.5% DMSO) or a combination of 15 mg/kg DX and 25 mg/kg PH, used daily orally for 4 weeks to treat DN, starting from the end of the 4th week of DM development, when DN confirmed. Our finding showed that both DX and PH dose-dependently improved behavioral parameters (with the superiority of DX), sciatic nerve tissue antioxidant state, and suppressed tissue inflammatory cytokine, besides, they abrogated the tissue histopathological changes (with the superiority of PH). Moreover, DX augmented the DM metabolic disturbance and hepatic dysfunction, however, PH effectively amended these disorders. Furthermore, the low-dose combination of both, had the merits of both medications, with the alleviation of their disadvantages. Therefore, phloretin could be a promising agent in the management of DN either alone or in combination with duloxetine.


Gonadotropin-inhibitory hormone reduces sexual motivation but not lordosis behavior in female Syrian hamsters (Mesocricetus auratus).
Reproductive success is maximized when female sexual motivation and behavior coincide with the time of optimal fertility. Both processes depend upon coordinated hormonal events, beginning with signaling by the gonadotropin-releasing hormone (GnRH) neuronal system. Two neuropeptidergic systems that lie upstream of GnRH, gonadotropin-inhibitory hormone (GnIH; also known as RFamide related peptide-3) and kisspeptin, are potent inhibitory and excitatory modulators of GnRH, respectively, that participate in the timing of the preovulatory luteinizing hormone (LH) surge and ovulation. Whether these neuropeptides serve as neuromodulators to coordinate female sexual behavior with the limited window of fertility has not been thoroughly explored. In the present study, either intact or ovariectomized, hormone-treated female hamsters were implanted for fifteen days with chronic release osmotic pumps filled with GnIH or saline. The effect of GnIH on sexual motivation, vaginal scent marking, and lordosis was examined. Following mating, FOS activation was quantified in brain regions implicated in the regulation of female sexual behavior. Intracerebroventricular administration of GnIH reduced sexual motivation and vaginal scent marking, but not lordosis behavior. GnIH administration altered FOS expression in key neural loci implicated in female reproductive behavior, including the medial preoptic area, medial amygdala and bed nucleus of the stria terminalis, independent of changes in circulating gonadal steroids and kisspeptin cell activation. Together, these data point to GnIH as an important modulator of female proceptive sexual behavior and motivation, independent of downstream alterations in sex steroid production.


Topological Magnetic Phase in the Candidate Weyl Semimetal CeAlGe.
We report the discovery of topological magnetism in the candidate magnetic Weyl semimetal CeAlGe. Using neutron scattering we find this system to host several incommensurate, square-coordinated multi-k[over →] magnetic phases below T_{N}. The topological properties of a phase stable at intermediate magnetic fields parallel to the c axis are suggested by observation of a topological Hall effect. Our findings highlight CeAlGe as an exceptional system for exploiting the interplay between the nontrivial topologies of the magnetization in real space and Weyl nodes in momentum space.


High-resolution laser ablation inductively coupled plasma mass spectrometry used to study transport of metallic nanoparticles through collagen-rich microstructures in fibroblast multicellular spheroids.
We have efficiently produced collagen-rich microstructures in fibroblast multicellular spheroids (MCSs) as a three-dimensional in vitro tissue analog to investigate silver (Ag) nanoparticle (NP) penetration. The MCS production was examined by changing the seeding cell number (500 to 40,000 cells) and the growth period (1 to 10 days). MCSs were incubated with Ag NP suspensions with a concentration of 5 μg mL-1 for 24 h. For this study, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was used to visualize Ag NP localization quantitatively. Thin sections of MCSs were analyzed by LA-ICP-MS with a laser spot size of 8 μm to image distributions of 109Ag, 31P, 63Cu, 66Zn, and 79Br. A calibration using a NP suspension was applied to convert the measured Ag intensity into the number of NPs present. The determined numbers of NPs ranged from 30 to 7200 particles in an outer rim of MCS. The particle distribution was clearly correlated with the presence of 31P and 66Zn and was localized in the outer rim of proliferating cells with a width that was equal to about twice the diameter of single cells. Moreover, abundant collagens were found in the outer rim of MCSs. For only the highest seeding cell number, NPs were completely captured at the outer rim, in a natural barrier reducing particle transport, whereas Eosin (79Br) used as a probe of small molecules penetrated into the core of MCSs already after 1 min of exposure. Graphical abstract Fibroblast MCS could build up the barrier only for nanoparticles.


Thermal and Herbicide Tolerances of Chromerid Algae and Their Ability to Form a Symbiosis With Corals.
Reef-building corals form an obligate symbiosis with photosynthetic microalgae in the family Symbiodiniaceae that meet most of their energy requirements. This symbiosis is under threat from the unprecedented rate of ocean warming as well as the simultaneous pressure of local stressors such as poor water quality. Only 1°C above mean summer sea surface temperatures (SSTs) on the Great Barrier Reef (GBR) can trigger the loss of Symbiodiniaceae from the host, and very low concentrations of the most common herbicide, diuron, can disrupt the photosynthetic activity of microalgae. In an era of rapid environmental change, investigation into the assisted evolution of the coral holobiont is underway in an effort to enhance the resilience of corals. Apicomplexan-like microalgae were discovered in 2008 and the Phylum Chromerida (chromerids) was created. Chromerids have been isolated from corals and contain a functional photosynthetic plastid. Their discovery therefore opens a new avenue of research into the use of alternative/additional photosymbionts of corals. However, only two studies to-date have investigated the symbiotic nature of Chromera velia with corals and thus little is known about the coral-chromerid relationship. Furthermore, the response of chromerids to environmental stressors has not been examined. Here we tested the performance of four chromerid strains and the common dinoflagellate symbiont Cladocopium goreaui (formerly Symbiodinium goreaui, ITS2 type C1) in response to elevated temperature, diuron and their combined exposure. Three of the four chromerid strains exhibited high thermal tolerances and two strains showed exceptional herbicide tolerances, greater than observed for any photosynthetic microalgae, including C. goreaui. We also investigated the onset of symbiosis between the chromerids and larvae of two common GBR coral species under ambient and stress conditions. Levels of colonization of coral larvae with the chromerid strains were low compared to colonization with C. goreaui. We did not observe any overall negative or positive larval fitness effects of the inoculation with chromerid algae vs. C. goreaui. However, we cannot exclude the possibility that chromerid algae may have more important roles in later coral life stages and recommend this be the focus of future studies.