Cluster Analysis

Arsenic is one of the most common metalloid contaminants in groundwater and it has both acute and chronic toxicity affecting multiple organs. Details of the mechanism of arsenic toxicity are still lacking and profile studies at metabolic level are very limited. Using gas chromatography coupled with mass spectroscopy (GC/MS), we first generated metabolomic profiles from the livers of arsenic-treated zebrafish and identified 34 significantly altered metabolite peaks as potential markers, including four prominent ones: cholic acid, glycylglycine, glycine and hypotaurine. Combined results from GC/MS, histological examination and pathway analyses suggested a series of alterations, including apoptosis, glycogenolysis, changes in amino acid metabolism and fatty acid composition, accumulation of bile acids and fats, and disturbance in glycolysis related energy metabolism. The alterations in glycolysis partially resemble Warburg effect commonly observed in many cancer cells. However, cellula...

Some but not all models of obsessive–compulsive disorder (OCD) emphasize the role of dysfunctional beliefs in the etiology and maintenance of this disorder. Clinical observations suggest that some OCD patients have prominent dysfunctional beliefs associated with their obsessions and compulsions, while other patients do not show this pattern. It is possible that dysfunctional beliefs play a role in only a

Hepatocarcinogenesis is under polygenic control. We analyzed gene expression patterns of dysplastic liver nodules (DNs) and hepatocellular carcinomas (HCCs) chemically-induced in F344 and BN rats, respectively susceptible and resistant to hepatocarcinogenesis. Expression profiles were performed by microarray and validated by quantitative RT-PCR and Western blot. Cluster analysis revealed two distinctive gene expression patterns, the first of which included normal liver of both strains and BN nodules, and the second one F344 nodules and HCC of both strains. We identified a signature predicting DN and HCC progression, characterized by highest expression of oncosuppressors Csmd1, Dmbt1, Dusp1, and Gnmt, in DNs, and Bhmt, Dmbt1, Dusp1, Gadd45g, Gnmt, Napsa, Pp2ca, and Ptpn13 in HCCs of resistant rats. Integrated gene expression data revealed highest expression of proliferation-related CTGF, c-MYC, and PCNA, and lowest expression of BHMT, DMBT1, DUSP1, GADD45g, and GNMT, in more aggressi...

This study examines the relationship between a computerized neuropsychological assessment battery, the Automated Neuropsychological Assessment Metrics (ANAM) and a widely used ability measure, Woodcock-Johnson III Tests of Cognitive Ability (WJ-III). Results indicated substantial relationship between the ANAM throughput (accuracy/response time) scores and the WJ-III Cognitive Efficiency cluster. An unexpectedly strong relationship was evident between accuracy scores on the ANAM Logical Reasoning scale and the WJ-III General Intellectual Ability score, purporting to measure the g factor. The findings support the viability of the ANAM as a time- and cost-effective tool for appraisal of cognitive function.

The transcriptomic diversity of cell types in the human body can be analysed in unprecedented detail using single cell (SC) technologies. Unsupervised clustering of SC transcriptomes, which is the default technique for defining cell types, is prone to group cells by technical, rather than biological, variation. Compared to de-novo (unsupervised) clustering, we demonstrate using multiple benchmarks that supervised clustering, which uses reference transcriptomes as a guide, is robust to batch effects and data quality artifacts. Here, we present RCA2, the first algorithm to combine reference projection (batch effect robustness) with graph-based clustering (scalability). In addition, RCA2 provides a user-friendly framework incorporating multiple commonly used downstream analysis modules. RCA2 also provides new reference panels for human and mouse and supports generation of custom panels. Furthermore, RCA2 facilitates cell type-specific QC, which is essential for accurate clustering of d...

We aimed to summarize and map the existing global population-based data on active trachoma and trichiasis. Detailed distribution maps of various infectious diseases have proved a valuable tool in their control. Such maps play an important role in assessing the magnitude of the problem, defining priority areas for control, monitoring changes, and advocacy. Until now, information on trachoma prevalence at within country levels has not been systematically collated, analysed and reported. We gathered the last 18 years' worth of reported data on active trachoma in children aged less than 10 years, and the last 25 years of reported trichiasis in adults aged 15 years and over from 139 population-based surveys in 33 countries. We collated these data into one database using the "district" (second administrative level) as the standard unit of reporting. We used Geographical Information Systems as a database and cartographic tool to generate a global map of the prevalence of trac...

This paper discusses the application of an unsupervised text mining technique for the extraction of information from clinical records in Italian. The approach includes two steps. First of all, a metathesaurus is exploited together with natural language processing tools to extract the domain entities. Then, clustering is applied to explore relations between entity pairs. The results of a preliminary experiment, performed on the text extracted from 57 medical records containing more than 20,000 potential relations, show how the clustering should be based on the cosine similarity distance rather than the City Block or Hamming ones.

At academic medical centers, attending rounds (AR) serve to coordinate patient care and educate trainees, yet variably involve patients. To determine the impact of standardized bedside AR on patient satisfaction with rounds. Cluster randomized controlled trial. 500-bed urban, quaternary care hospital. 1200 patients admitted to the medicine service. Teams in the intervention arm received training to adhere to 5 AR practices: 1) pre-rounds huddle; 2) bedside rounds; 3) nurse integration; 4) real-time order entry; 5) whiteboard updates. Control arm teams continued usual rounding practices. Trained observers audited rounds to assess adherence to recommended AR practices and surveyed patients following AR. The primary outcome was patient satisfaction with AR. Secondary outcomes were perceived and actual AR duration, and attending and trainee satisfaction. We observed 241 (70.1%) and 264 (76.7%) AR in the intervention and control arms, respectively, which included 1855 and 1903 patient ro...

Reducing youth suicide in the United States (U.S.) is a national public health priority, and lesbian, gay, bisexual, transgender, and queer or questioning (LGBTQ) youth are at elevated risk. The Centers for Disease Control and Prevention (CDC) endorses six evidence-based (EB) strategies that center on meeting the needs of LGBTQ youth in schools; however, fewer than 6 % of U.S. schools implement all of them. The proposed intervention model, "RLAS" (Implementing School Nursing Strategies to Reduce LGBTQ Adolescent Suicide), builds on the Exploration, Preparation, Implementation, and Sustainment (EPIS) conceptual framework and the Dynamic Adaptation Process (DAP) to implement EB strategies in U.S. high schools. The DAP accounts for the multilevel context of school settings and uses Implementation Resource Teams (IRTs) to facilitate appropriate expertise, advise on acceptable adaptations, and provide data feedback to make schools implementation ready and prepared to sustain ch...

New approaches are needed to enhance implementation of complex interventions for geriatric syndromes such as falls. To test whether a complexity science-based staff training intervention (CONNECT) promoting high-quality staff interactions improves the impact of an evidence-based falls quality improvement program (FALLS). Cluster-randomized trial in 24 nursing homes receiving either CONNECT followed by FALLS (intervention), or FALLS alone (control). Nursing home staff in all positions were asked to complete surveys at baseline, 3, 6, and 9 months. Medical records of residents with at least 1 fall in the 6-month pre- and postintervention windows (n = 1794) were abstracted for fall risk reduction measures, falls, and injurious falls. CONNECT taught staff to improve their connections with coworkers, increase information flow, and use cognitive diversity in problem solving. Intervention components included 2 classroom sessions, relationship mapping, and self-monitoring. FALLS provided in...

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatel...

Maternal undernutrition and low macro- and micronutrient intake and weight gain during pregnancy have been reported in Bangladesh. We aimed to determine the effects of lipid-based nutrient supplements for pregnant and lactating women (LNS-PL) on weight gain and midupper arm circumference (MUAC) during pregnancy. The Rang-Din Nutrition Study, a cluster-randomized effectiveness trial conducted in Bangladesh, enrolled 4011 pregnant women at ≤20 wk gestation who received either 60 mg Fe + 400 μg folic acid/d or 20 g LNS-PL/d (118 kcal) containing essential fatty acids and vitamins and minerals until delivery. At 36 wk gestation, women were interviewed at home and then attended a follow-up examination at local clinics (n = 2877), where anthropometric measurements were taken. No significant differences between intervention groups in maternal weight gain per week, low weight gain per week, or MUAC at 36 wk gestation were observed in the full sample. However, among multiparous women aged ≥2...

Genes involved in the reproductive isolation are particularly useful as molecular markers in speciation studies. Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae), a putative species complex, is a vector of visceral leishmaniasis in Latin America. We isolated from this species a fragment homologous to cacophony, a Drosophila gene that encodes features of the lovesong, an acoustic signal that is important in the sexual isolation of closely related species and known to vary considerably among L. longipalpis putative siblings species. Using an intron of the sandfly cacophony as a marker, we analyzed the molecular variation and sequence divergence among five populations of L. longipalpis from Brazil, three allopatric (Jacobina, Lapinha and Natal) and two putative sympatric sibling species from the locality of Sobral. A high level of polymorphism was found and analysis of the data indicates that very little gene flow is occurring among the populations of Jacobina, Lapinha, and Natal. A high level of differentiation was also observed between the two putative sympatric species of Sobral, one of which seems to be the same sibling species found in Natal, while the other is somewhat more related to Jacobina and Lapinha. However, the amount of estimated gene flow among the Sobral siblings is about seven times higher than the previously estimated for period, another lovesong gene, perhaps indicating that introgression might be affecting cacophony more than period. The results suggest that L. longipalpis is not a single species in Brazil, but it is yet not clear whether the different populations studied deserve species status rather than representing an incipient speciation process.