Pseudoalignment for metagenomic read assignment.

MOTIVATION: Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains. RESULTS: We find that the recent idea of pseudoalignment introduced in the RNA-Seq context is highly applicable in the metagenomics setting. When coupled with the Expectation-Maximization (EM) algorithm, reads can be assigned far more accurately and quickly than is currently possible with state of the art software, making it possible and practical for the first time to analyze abundances of individual genomes in metagenomics projects. AVAILABILITY AND IMPLEMENTATION: Pipeline and analysis code can be downloaded from http://github.com/pachterlab/metakallisto. CONTACT: lpachter@math.berkeley.edu.

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies.

We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.

Domestic violence and the trauma surgeon.

BACKGROUND: Domestic violence has become increasingly recognized as a public health problem, and was declared a national epidemic by C. Everett Koop in 1992. In the United States, 1 to million women yearly suffer injuries due to domestic violence, and 30% to 50% of female homicides are committed by a present or former partner. The majority of these murder victims had either been seen in emergency rooms for prior domestic violence-related injuries, or had reported these injuries to the police. It is estimated that 50% of all acute injuries and 21% of all injuries in women requiring urgent surgery ar the result of partner abuse. DATA SOURCE: Medline and current literature review. CONCLUSIONS: Health care professionals in the emergency room are an important contact with the victims of domestic violence, and timely identification and intervention can save lives. Overall, upwards of 35% of all emergency room visits by women are the result of domestic violence, whether due to acute injury, problems during pregnancy, or stress-related complaints. Unfortunately, domestic abuse is infrequently disclosed voluntarily by the patient, and often overlooked by the treating physician. Thus, the purpose of this review is to familiarize surgeons with the presentation and management of victims of this hidden epidemic.

Active conservation of noncoding sequences revealed by three-way species comparisons.

Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human-mouse DNA comparison studies have discovered numerous conserved noncoding sequences of which only a fraction has been functionally investigated A question therefore remains as to whether most of these noncoding sequences are conserved because of functional constraints or are the result of a lack of divergence time.

Human and mouse gene structure: comparative analysis and application to exon prediction.

We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of similarity in the number, size and sequence of exons and introns. We then developed an approach for recognizing genes within such orthologous regions by first aligning the regions using an iterative global alignment system and then identifying genes based on conservation of exonic features at aligned positions in both species. The alignment and gene recognition are performed by new programs called and, respectively. performed well at exact identification of coding exons in 117 orthologous pairs tested.

VISTA : visualizing global DNA sequence alignments of arbitrary length.

SUMMARY: VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has a clean output, allowing for easy identification of similarity, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is currently available on the web, thus allowing for easy access by all researchers. AVAILABILITY: VISTA server is available on the web at http://www-gsd.lbl.gov/vista. The source code is available upon request. CONTACT: vista@lbl.gov

A dictionary-based approach for gene annotation.

This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.

Consensus theory model of AIDS/SIDA beliefs in four Latino populations.

To describe Latino beliefs about AIDS (SIDA), Latino adults were sampled at two U.S. sites (Connecticut and Texas) and two international sites (Mexico and Guatemala). A 125-item questionnaire covered risk factors, symptoms, treatments, and sequellae of AIDS. The cultural consensus model was used to determine the cultural beliefs for each sample. Responses from 161 people indicated that a single set of beliefs was present at each site and that beliefs were shared across sites. Comparison of answers between samples indicated high agreement (p < .0007). The proportion of shared beliefs, however, decreased significantly between samples: .68 in Connecticut, .60 in Texas, .51 in Mexico, and .41 in Guatemala (p < .05). The proportion of positive answers similarly decreased from Connecticut to Guatemala (p < .001). Beliefs were stronger and more detailed in the higher prevalence areas. Furthermore, Latino beliefs tended to converge on biomedical beliefs about the disease.

Latino beliefs about diabetes.

OBJECTIVE: To describe Latino beliefs about diabetes and assess heterogeneity in beliefs across different groups. RESEARCH DESIGN AND METHODS: This study comprised a survey of 161 representative Latino adults from four diverse communities: Hartford, Connecticut; Edinburg, Texas; Guadalajara, Mexico; and rural Guatemala. A 130-item questionnaire covered causes symptoms, and treatments for diabetes. Information on demographics and acquaintanceship with someone with diabetes was also collected. The cultural consensus model was used to analyze the variation in responses to determine whether the degree of consistency within and between samples was sufficient to warrant aggregation and description as a single set of beliefs. RESULTS: Homogeneous beliefs were present within each of the four samples. Although variability in responses increased significantly from Connecticut to Guatemala (P < 0.00005), there was significant agreement between samples on the answers (P < 0.0005). Answers tended to be concordant with the biomedical description of diabetes. Greater acculturation, higher educational attainment, and higher diabetes prevalence were associated with greater cultural knowledge about diabetes. In Connecticut, greater knowledge correlated with longer mainland U.S. residency (P < 0.05). In Mexico, those with average educational attainment knew more (P < 0.05). Finally, average knowledge levels were higher in communities with greater diabetes prevalence. CONCLUSIONS: The cultural consensus model facilitated assessment of cultural beliefs regarding diabetes and diabetes management. Overall, Latino cultural beliefs about diabetes were concordant with the biomedical model. Variation in responses tended to characterize less knowledge or experience with diabetes and not different beliefs.

Parent's participation and perspectives regarding clinical judgment and clinical guideline development.

Increasing parental participation in their child's health and health care is an important process by which the health care system can effectively address and service the needs of its patients. Clinicians need to have an appreciation of parental understanding, beliefs, and expectations. This paper reviews the recent literature regarding parental needs, concerns, decision-making strategies, and expectations for their children's health and health care.

Home-based therapies for the common cold among European American and ethnic minority families: the interface between alternative/complementary and folk medicine.

BACKGROUND: Most studies of alternative/complementary medicine use in children have focused on children with chronic illness and have not addressed the more common form of complementary medicine: popular home-based interventions and therapies for common low-morbidity sickness episodes. Also, there has often been a distinction between alternative/ complementary medical practices used by the general population and those used by members of ethnic minority groups and commonly referred to as folk medicine or ethnomedicine. OBJECTIVE: To describe the home-based therapies and practices that parents from diverse ethnocultural backgrounds use to treat the common cold in their children. METHOD: Interviews with mothers of children coming for care at a number of clinics and physicians' offices. Included were mothers from European American, African American, Puerto Rican, and West Indian-Caribbean heritages. RESULTS: Mean number of home-based remedies for the common cold did not differ among ethnic groups (controlling for maternal age, maternal education, number of children, and health insurance status). There were differences among groups regarding the frequency of use of specific remedies. CONCLUSIONS: Home-based remedies for colds in childhood are commonly used. Many of the treatments are complementary to biomedical treatment (ie, antipyretics, over-the-counter cold remedies, fluids). Very few are potentially hazardous if taken in moderation. Mothers from ethnic minorities use similar amounts of homebased interventions when compared with mothers from the majority culture.

Maternal expectations about normal child development in 4 cultural groups.

OBJECTIVE: To determine whether expectations about normal infant and child development are different among mothers from 4 ethnocultural groups. PARTICIPANTS: Two hundred fifty-five mothers (90 Puerto Rican, 59 African American, 69 European American, 37 West Indian-Caribbean) whose children received health care at hospital-based pediatric clinics and private pediatricians' and family practitioners' offices. DESIGN: Verbally administered questionnaire that included 25 questions in which mothers were asked to give their opinions about the age at which a normal child should begin to accomplish standard developmental milestones. ANALYSIS: Responses (mean ages at which mothers expected children to attain the milestones) from each group were compared after controlling for age of mother, number of children, level of education, and socioeconomic status. RESULTS: Significant differences among ethnic groups' responses were seen for 9 of 25 developmental milestones. Differences were mainly seen among personal and social milestones, and Puerto Rican mothers tended to expect children to attain these milestones at a later age than did other mothers. No differences in responses were seen between Spanish- and English-speaking Puerto Rican mothers. European-American mothers expected children to take first steps and become toilet trained at a later age. CONCLUSIONS: Developmental expectations differ among mothers from different ethnocultural groups. Many of these differences can be explained by underlying cultural beliefs and values and specific child-rearing practices. Clinicians should ask about maternal expectations during child health visits to interpret mothers' concerns and opinions about their children's development.

Culture and child behavior and psychosocial development.

This paper provides an overview of the relationship between cultural beliefs, values, practices, behavior, and psychosocial development. A framework for analyzing this relationship is presented, illustrated with studies from the cross-cultural literature. We then present a review of the literature concerning the cultural influences on one specific behavioral issue, temperament. We conclude with a critical discussion of the unique methodological issues encountered in the study of child behavior and psychosocial development in a cross-cultural and/or culturally diverse perspective.

Ethnomedical (folk) remedies for childhood asthma in a mainland Puerto Rican community.

BACKGROUND: Childhood asthma is the most common chronic illness of childhood. The highest prevalence of childhood asthma in the United States occurs in the Puerto Rican community, and there are many traditional beliefs and practices regarding asthma that coexist with biomedical therapies. OBJECTIVES: To describe the ethnomedical treatment practices for childhood asthma in one mainland United States Puerto Rican community and to determine whether any of these practices are effective or potentially harmful. METHOD: Home interview with caretakers of 118 Puerto Rican children with asthma who seek care at two community health clinics in an inner city in the eastern United States. RESULTS: Common home-based ethnomedical practices include attempts to maintain physical and emotional balance and harmony, religious practices, and ethnobotanical and other therapies. Potentially harmful practices are uncommon, and other remedies are only harmful if not taken as directed. Many remedies are not effective from a biomedical standpoint (ie, bronchodilation or antiinflammation), but if analyzed within the ethnomedical explanatory model--which includes the belief that expulsion of mucus and phlegm from the body is beneficial for the treatment of asthma--these remedies bring about the desired effect and are therefore considered effective to the user. CONCLUSIONS: Ethnomedical therapies for asthma in the mainland Puerto Rican community are well known and commonly used. Most practices are not idiosyncratic but fit within a coherent ethnocultural belief system. The health care practitioner can lower the risk for potentially toxic effects of some treatments by discussing these practices with patients and families. Some ethnomedical practices are not discordant with biomedical therapy. Incorporation of these practices into the biomedical plan may help to fit the biomedical therapy into the lifestyle of the patient.

Culture and clinical care. Folk illness beliefs and behaviors and their implications for health care delivery.

This article presents an approach to the evaluation of patient-held beliefs and behaviors that may not be concordant with those of biomedicine. Physicians and patients often hold discrepant models of health and illness that may affect the effectiveness of communication during the clinical visit. An extreme example of such a discrepancy exists when the patient feels that he or she has an illness that is not defined within the biomedical paradigm. These are commonly referred to as folk illnesses. An example of such an illness is provided in order to discuss the effects of folk beliefs on patient-held perceptions of health and sickness, treatment-seeking behavior, clinical care, and physician-patient communication. Guidelines for addressing clinical issues surrounding folk beliefs and behaviors in a culturally sensitive way are discussed.

Acculturation and compliance with medical therapy.

Lack of compliance with medical therapy is a major clinical problem. We undertook a study to determine whether degree of acculturation to mainland U.S. culture was predictive of compliance in Puerto Rican families having a child with asthma. A questionnaire was administered to parents of Puerto Rican asthmatic children attending an asthma clinic and taking oral theophylline as part of their medical management. The questionnaire included items concerning medical, socioeconomic, and cultural variables, as well as a standardized instrument devised to measure degree of acculturation. Compliance was measured by a serum theophylline level obtained at the time of the visit. Families were divided into compliant (n = 15) and noncompliant (n = 13) groups based on their child's serum theophylline determination. There was a significant difference in mean acculturation scores between compliant and noncompliant groups (p = .008). Those in the complaint group had scores indicative of a style of acculturation that integrated aspects of both "Anglo" and Puerto Rican lifestyles. Those in the noncompliant group had scores indicative of a less acculturated lifestyle. The findings of this study show that degree of acculturation is a predictor of compliance with medical therapy in mainland Puerto Ricans. Additional studies with other cultural groups are needed, as well as other studies incorporating acculturation into a multivariate model of compliance.

Empacho in four Latino groups: a study of intra- and inter-cultural variation in beliefs.

It is usually impossible to know if reported differences between cultures are due to cultural differences or due to a difference in the methods used to study the cultures. This paper describes a collaborative, multisite study using a shared methodology to study intra- and inter-cultural variation in beliefs. A series of standard interview schedules were used to study Latin American beliefs about empacho in Guatemala, Mexico, and in the United States (Mexican-Americans and Puerto Ricans). Results showed consistency in beliefs about empacho both within and between the four samples.