A-1 Monthly Public Assistance Statistical Report Family Investment Program, February 2005

Monthly Public Assistance Statistical Report Family Investment Program

HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm.

Gender inequality in health among elderly people in a combined framework of socioeconomic position, family characteristics and social support

This study analyses gender inequalities in health among elderly people in Catalonia (Spain) by adopting a conceptual framework that globally considers three dimensions of health determinants : socio-economic position, family characteristics and social support. Data came from the 2006 Catalonian Health Survey. For the purposes of this study a sub-sample of people aged 65–85 years with no paid job was selected (1,113 men and 1,484 women). The health outcomes analysed were self-perceived health status, poor mental health status and long-standing limiting illness. Multiple logistic regression models separated by sex were fitted and a hierarchical model was fitted in three steps. Health status among elderly women was poorer than among the men for the three outcomes analysed. Whereas living with disabled people was positively related to the three health outcomes and confidant social support was negatively associated with all of them in both sexes, there were gender differences in other social determinants of health. Our results emphasise the importance of using an integrated approach for the analysis of health inequalities among elderly people, simultaneously considering socio-economic position, family characteristics and social support, as well as different health indicators, in order fully to understand the social determinants of the health status of older men and women.

Strength of family history in predicting levels of blood pressure, plasma glucose and cholesterol

Rapport de synthèse : L'histoire familiale reflète non seulement la susceptibilité génétique d'un individu à certaines maladies mais également ses comportements et habitudes, notamment partagées au sein d'une famille. L'hypertension artérielle, le diabète et l'hypercholestérolémie sont des facteurs de risque cardio-vasculaire modifiables hautement prévalent. L'association entre l'histoire familiale d'hypertension artérielle ou de diabète et le risque accru de développer de l'hypertension artérielle ou du diabète, respectivement, a été préalablement établie. Par contre, le lien entre l'histoire familiale de facteurs de risque cardio-vasculaire et les traits continus correspondants n'avaient jamais été mis clairement en évidence. De même, la signification d'une histoire familiale inconnue n'avait jusqu'alors pas été décrite. Ce travail, effectué dans le cadre de l'étude Colaus (Cohorte Lausannoise), une cohorte regroupant un échantillon composé de 6102 participants âgés de 35 à 75 ans sélectionnés au hasard dans la population lausannoise, a permis de décrire en détail la relation entre l'histoire familiale des facteurs de risque cardio-vasculaires et les trait correspondants dans la population étudiée. Les différentes analyses statistiques ont permis de mettre en évidence une relation forte entre l'histoire familiale d'hypertension artérielle, de diabète ainsi que de l'hypercholestérolémie et leurs traits dichotomique et continu correspondants. Les anamnèses des frères et soeurs avaient des valeurs prédictives positives plus élevées que les anamnèses parentales. Ceci signifie que les programmes de dépistage ne prenant en compte que l'histoire familiale des frères et soeurs seraient probablement plus efficaces que ceux qui comportent l'évaluation des anamnèses paternelle et maternelle. Plus de 40% des participants ignoraient l'histoire familiale d'hypertension d'au moins un des membres de leur famille. Ceux-ci avaient des valeurs de tension artérielle systolique plus élevées que ceux dont l'histoire familiale était négative, permettant de souligner la valeur prédictive du fait de ne pas connaître l'histoire familiale d'hypertension artérielle. Ces résultats montrent également que, lors d'analyses de la relation entre l'anamnèse familiale de facteurs de risque cardiovasculaires et leurs traits correspondants, les participants donnant des réponses négatives doivent être distingués de ceux qui ne connaissent pas leur anamnèse familiale. Les résultats de cette étude confirment la place centrale qu'occupe l'anamnèse familiale dans l'évaluation du risque cardio-vasculaire auprès de la population générale. L'importance de cet outil prédictif simple et bon marché ne va cesser d'augmenter avec la disponibilité croissante d'information génétique détaillée pour les maladies cardiovasculaires communes.

The evolutionary history of the CD209 (DC-SIGN) family in humans and non-human primates

The CD209 gene family that encodes C-type lectins in primates includes CD209 (DC-SIGN), CD209L (L-SIGN) and CD209L2. Understanding the evolution of these genes can help understand the duplication events generating this family, the process leading to the repeated neck region and identify protein domains under selective pressure. We compiled sequences from 14 primates representing 40 million years of evolution and from three non-primate mammal species. Phylogenetic analyses used Bayesian inference, and nucleotide substitutional patterns were assessed by codon-based maximum likelihood. Analyses suggest that CD209 genes emerged from a first duplication event in the common ancestor of anthropoids, yielding CD209L2 and an ancestral CD209 gene, which, in turn, duplicated in the common Old World primate ancestor, giving rise to CD209L and CD209. K(A)/K(S) values averaged over the entire tree were 0.43 (CD209), 0.52 (CD209L) and 0.35 (CD209L2), consistent with overall signatures of purifying selection. We also assessed the Toll-like receptor (TLR) gene family, which shares with CD209 genes a common profile of evolutionary constraint. The general feature of purifying selection of CD209 genes, despite an apparent redundancy (gene absence and gene loss), may reflect the need to faithfully recognize a multiplicity of pathogen motifs, commensals and a number of self-antigens

A-1 Monthly Public Assistance Statistical Report Family Investment Program, March 2005

A-1 Monthly Public Assistance Statistical Report Family Investment Program

Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events

Genomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements is that REPP and REPD are not yet well characterized, probably due to their polymorphic status. Here, we describe a novel primate-specific gene family, named FAM90A (family with sequence similarity 90), found within these SDs. According to the current human reference sequence assembly, the FAM90A family includes 24 members along 8p23.1 region plus a single member on chromosome 12p13.31, showing copy number variation (CNV) between individuals. These genes can be classified into subfamilies I and II, which differ in their upstream and 5′-untranslated region sequences, but both share the same open reading frame and are ubiquitously expressed. Sequence analysis and comparative fluorescence in situ hybridization studies showed that FAM90A subfamily II suffered a big expansion in the hominoid lineage, whereas subfamily I members were likely generated sometime around the divergence of orangutan and African great apes by a fusion process. In addition, the analysis of the Ka/Ks ratios provides evidence of functional constraint of some FAM90A genes in all species. The characterization of the FAM90A gene family contributes to a better understanding of the structural polymorphism of the human 8p23.1 region and constitutes a good example of how SDs, CNVs and rearrangements within themselves can promote the formation of new gene sequences with potential functional consequences.

Impact of Ownership Structure on the Performance of China’s Feed Mill Sector, April 2005

In the decade of the 1990s, China’s feed sector became increasingly privatized, more feed mills opened, and the scale of operation expanded. Capacity utilization remained low and multi-ministerial supervision was still prevalent, but the feed mill sector showed a positive performance overall, posting a growth rate of 11 percent per year. Profit margin over sales was within allowable rates set by the government of China at 3 to 5 percent. Financial efficiency improved, with a 20 percent quicker turnover of working capital. Average technical efficiency was 0.805, as more efficient feed mills increasingly gained production shares. This study finds evidence that the increasing privatization explains the improved performance of the commercial feed mill sector. The drivers that shaped the feed mill sector in the 1990s have changed with China’s accession to the World Trade Organization. With the new policy regime in place, the study foresees that, assuming an adequate supply of soy meal and an excess capacity in the feed mill sector, it is likely that China will allow corn imports up to the tariff rate quota (TRQ) of 7.2 mmt since the in-quota rate is very low at 1 percent. However, when the TRQ is exceeded, the import duty jumps to a prohibitive out-quota rate of 65 percent. With an import duty for meat of only 10 to 12 percent, China would have a strong incentive to import meat products directly rather than bringing in expensive corn to produce meat domestically. This would be further reinforced if structural transformation in the swine sector would narrow the cost differential between domestic and imported pork.

A-1 Monthly Public Assistance Statistical Report Family Investment Program, April 2005

Monthly Public Assistance Statistical Report Family Investment Program

A-1 Monthly Public Assistance Statistical Report Family Investment Program, May 2005

Monthly Public Assistance Statistical Report Family Investment Program

The demands of family caregivers of elderly individuals with dementia

The purpose of this cross-sectional observational study was to identify characteristics of caregivers of elderly people with dementia, types of care demands and to relate demands to the stage of dementia. The study was carried out in 2004 with 104 older adults and 90 caregivers in Ribeirão Preto, state of São Paulo. The OARS instrument was utilized and a questionnaire answered by caregivers. Among older adults, 66.3% were female, aged 75.5 years in average and 86.5% had caregivers. Eighty percent of the caregivers were women family members, aged 52.3 years in average. They spent 15.10 hours/day with care, without help. An important relationship was observed between caregiver's burden, physical and emotional effort and stage of dementia. Emotional overburden was higher at dementia early and late stages, this difference was statistically non-significant. Results reveal the urgent need to plan formal and informal support strategies to caregivers of Brazilian elderly people with dementia.

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

A-1 Monthly Public Assistance Statistical Report Family Investment Program, June 2005

A-1 Monthly Public Assistance Statistical Report Family Investment Program, June 2005

Iowa Federal Family Education Loan Program Division, Iowa College Student Aid Commission, Independent Auditor's Reports, Basic Financial Statements and Supplementary Information, June 30, 2004

State Audit Reports