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PubMed2026

Environmental coupling between metal resistance genes and bacterial communities in Beijing urban green-space soils.

Urban green spaces are intensively managed ecosystems exposed to chronic, multisource, low-intensity anthropogenic inputs. These inputs may alter soil microbial communities and influence the distribution of metal resistance genes (MRGs). However, MRG distributions and their relationships with environmental conditions and bacterial communities remain unclear under the complex, non-extreme pollution conditions typical of these ecosystems. We investigated Beijing urban green spaces as a representative system using metagenomic sequencing and metagenome-assembled genome (MAG) analysis. We characterized soil MRG composition, its environmental associations, and the distribution of potential hosts. MRG composition differed significantly among ecological conservation (EC), transitional urban (TU), and central urban (CU) zones. These differences were closely associated with soil physicochemical properties and bacterial community structure. Available phosphorus (AP) was significantly associated with variation in both bacterial community structure and MRG composition. MAG-based analysis identified distinct potential-host compositions across the three functional zones. Proteobacteria were more frequently represented among dereplicated MAGs from EC soils, whereas Actinobacteria were more frequent in TU and CU soils. Heavy metal concentrations correlated with MRG composition. However, variation partitioning analysis did not identify an independent contribution from heavy metals after accounting for soil physicochemical properties and bacterial community structure. These findings indicate that urban green-space soil monitoring should incorporate environmental conditions and microbial community characteristics rather than rely solely on total metal concentrations.

Soil Microbiology↗

PubMed1998

A technique To quantify the population size and composition of the biofilm component in communities of bacteria in the phyllosphere

The presence of microbial biofilms in the phyllosphere of terrestrial plants has recently been demonstrated, but few techniques to study biofilms associated with living plant tissues are available. Here we report a technique to estimate the proportion of the bacterial population on leaves that is assembled in biofilms and to quantitatively isolate bacteria from the biofilm and nonbiofilm (solitary) components of phyllosphere microbial communities. This technique is based on removal of bacteria from leaves by gentle washing, separation of biofilm and solitary bacteria by filtration, and disintegration of biofilms by ultrasonication. The filters used for this technique were evaluated for their nonspecific retention rates of solitary bacteria and for the efficiency of filtration for different concentrations of solitary bacteria in the presence of biofilms and other particles. The lethality and efficiency of disintegration of the sonication conditions used here were also evaluated. Isolation and quantification of bacteria by this technique is based on use of culture media. However, oligonucleotide probes, sera, or epifluorescent stains could also be used for direct characterization of the biofilm and solitary bacteria in the suspensions generated by this technique. Preliminary results from estimates of biofilm abundance in phyllosphere communities show that bacteria in biofilms constitute between about 10 and 40% of the total bacterial population on broad-leaf endive and parsley leaves.

Journal Article↗

PubMed2005

Comparative rates of violence in chimpanzees and humans.

This paper tests the proposal that chimpanzees (Pan troglodytes) and humans have similar rates of death from intraspecific aggression, whereas chimpanzees have higher rates of non-lethal physical attack (Boehm 1999, Hierarchy in the forest: the evolution of egalitarian behavior. Harvard University Press). First, we assembled data on lethal aggression from long-term studies of nine communities of chimpanzees living in five populations. We calculated rates of death from intraspecific aggression both within and between communities. Variation among communities in mortality rates from aggression was high, and rates of death from intercommunity and intracommunity aggression were not correlated. Estimates for average rates of lethal violence for chimpanzees proved to be similar to average rates for subsistence societies of hunter-gatherers and farmers. Second, we compared rates of non-lethal physical aggression for two populations of chimpanzees and one population of recently settled hunter-gatherers. Chimpanzees had rates of aggression between two and three orders of magnitude higher than humans. These preliminary data support Boehm's hypothesis.

Aggression↗

PubMedDate not supplied

Organ transplantation from living donors, between bioethics and the law.

The lack of cadaver donors and the high requirements for organs cannot be met by present sources, leading to the need for xenoorgans or stem cell-derived tissues/organs. Actually, despite experimental suggestions, scientific and ethical doubts have been raised by both the scientific community and international organizations (World Health Organization, 1998; European Council of Parliamentary Assembly, 1999). Thus, to balance the shortage of organs, laws allowing living organ donations have been issued in several countries, including Italy, where there is an increasingly favorable attention to organ transplantation from living donors. Because of the prohibition of body commercialization issued by the Oviedo Convention (1997), the bioethics and legal debate as well as issued laws concern 2 major closely related aspects: the health-defense of the donor who accepts a decreased well-being and the counterbalanced possibility of an economic advantage/indemnity.

Animals↗

PubMedDate not supplied

Lessons learned. What these seven studies teach us.

Seven evaluation studies of American Cancer Society programs offer findings useful for improving the programs studied and have larger implications for public health initiatives that rely on volunteers, the training of trainers, professional referral agents, and outreach through faith organizations or other indigenous community groups. Studies documented the following, for example: higher levels of productivity among volunteers who are cancer survivors, have health-related backgrounds, have college degrees, or both; the value of using existing organizations to recruit volunteers; the need for improved selection methods to reduce attrition in programs using "train the trainer" models; and the outreach potential of faith organizations as nodes in social networks within communities. The studies demonstrate to all voluntary health organizations the importance of assembling an accurate database to describe their activities and to enable them to answer important management questions. Lessons from these studies also can contribute to the development of better methods for the study of public health programs and for the incorporation of evaluation into the process of continuous program improvement within voluntary health organizations.

Humans↗

PubMed1994

Laboratory assessment of a user-assembled oxygen generation kit.

A laboratory assessment was made of a user-assembled oxygen generation kit designed for use in medical emergencies in the community. Twenty-five kits were studied at five different water temperatures and the rate of oxygen generation and its concentration were measured. The apparatus produced a mean (SD) oxygen volume of 37 (1.98) l which was not affected by the starting water temperature. The mean (SD) rate of flow varied from 2.2 (0.04) l.min-1 at 16 degrees C to 10.3 (2.74) l.min-1 at 40 degrees C but the duration of flow varied inversely. Oxygenation concentrations ranging from 30-51% were produced at starting water temperatures from 22 degrees C-40 degrees C, respectively.

Ambulatory Care↗

PubMed1998

Ossification of the posterior longitudinal ligament in three geographically and genetically different populations of ankylosing spondylitis and other spondyloarthropathies.

STUDY DESIGN: Cross sectional. RESEARCH QUESTIONS: (a) Is any clinical variable of ankylosing spondylitis (AS) associated with the presence of ossification of the posterior longitudinal ligament (OPLL)? and (b) Is OPLL present in patients with AS from different geographical or genetic backgrounds? METHODS: Three groups were assembled: (1) a prospective group of 103 consecutive AS patients from two community based rheumatology clinics from Guadalajara, who were evaluated using: a questionnaire with disease characteristics variables; clinical assessment by a neurologist; lateral radiographic views of the cervical spine and somatosensory evoked potentials (SSEP). (2) Fifty one spondyloarthropathies (SpA) patients from Mexico city whose cervical spine films were retrospectively reviewed. (3) Thirty nine AS patients from Edmonton, Canada whose cervical spine films were retrospectively reviewed and compared with 72 controls. RESULTS: Group 1: 74% of the 103 patients were men and 86% were HLA-B27 positive. The mean age was 35 years, and mean (SD) disease duration 10 (8) years. OPLL was reported in 16 patients (15.5%; 95% CI 9, 22). OPLL was statistically associated with older age (p = 0.001), longer disease duration (p = 0.001), clinical myelopathy (p = 0.03), worst functional index (p = 0.042), restricted axial movement measurements (all p < 0.001), radiological sacroilitis (p < 0.001 for linear association), osteitis pubis (p = 0.009), hip involvement (p = 0.006 for linear association), and abnormal SSEP (p = 0.008). Group 2: 92% of 51 patients were men; the mean age was 30 years and the mean (SD) disease duration 11 (7) years. OPLL was reported in 15 (29%, 95% CI 17, 41) patients (nine AS, two psoriatic arthritis, three juvenile AS, and one Reiter's syndrome). Group 3: 95% of the 39 patients were men; the mean of age was 46 years and disease duration of 18 (10) years. OPLL was reported in nine (23%; 95% CI 10, 36) patients, including one with psoriatic arthritis, and two with Crohn's disease. OPLL was observed in two of the control group. CONCLUSIONS: The prevalence of OPLL in AS and SpA is higher than previously recognised and seems to be associated with variables identifying more severe axial disease.

Adult↗

PubMed2026

Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.

While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50-73%) compared to 14-21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.

Animals↗

PubMed1999

Clinical profile of hypertrophic cardiomyopathy identified de novo in rural communities.

OBJECTIVES: The purpose of this study was to assess the extent to which hypertrophic cardiomyopathy (HCM) exists unsuspected and undetected in the general population. BACKGROUND: Hypertrophic cardiomyopathy is a disease with diverse natural history for which the potential to produce adverse consequences has been emphasized. However, the possibility of this disease remaining clinically dormant for many years has not been as widely appreciated. Certainly, the clinical recognition of previously undiagnosed patients with HCM may be advantageous by permitting risk stratification for sudden cardiac death or for timely pharmacologic therapy when symptoms intervene. METHODS: We prospectively conducted an echocardiographic survey in 64 primarily rural communities within Minnesota (populations < 10,000) over a 33-month period. RESULTS: A total of 15,137 echocardiograms were performed at the request of primary care physicians for the purpose of excluding cardiovascular abnormalities. Hypertrophic cardiomyopathy was identified in 44 patients during the survey (0.29%), and 29 of these patients (0.19% of the 15,137 echocardiograms) had not been previously identified as having cardiac disease or HCM. At diagnosis, ages were 16 to 87 years (mean 57); 14 patients were > or = 60 years of age, and only two were < 30 years. Twenty-four patients (83%) had either no or only mild or transient symptoms; 5 (17%) evidenced severe functional limitation; in eight patients the onset of symptoms had been deferred until > or = 70 years of age. Basal left ventricular outflow obstruction (gradients 20 to 82 mm Hg) was evident in 11 patients (38%). Relatively mild phenotypic expression of the disease was substantiated by localized patterns of left ventricular wall thickening occurring more commonly than diffusely distributed hypertrophy (48% vs. 7%, respectively), and electrocardiograms that were frequently normal (about 25%) and rarely showed evidence of left ventricular hypertrophy (10%). CONCLUSIONS: These prospectively assembled data show that HCM may remain clinically dormant and undetected within community-based rural populations for many years (often to advanced ages) with a not inconsequential prevalence similar to that of HCM in the general population.

Adolescent↗

PubMed2005

Host specificity of insect herbivores in tropical forests.

Studies of host specificity in tropical insect herbivores are evolving from a focus on insect distribution data obtained by canopy fogging and other mass collecting methods, to a focus on obtaining data on insect rearing and experimentally verified feeding patterns. We review this transition and identify persisting methodological problems. Replicated quantitative surveys of plant-herbivore food webs, based on sampling efforts of an order of magnitude greater than is customary at present, may be cost-effectively achieved by small research teams supported by local assistants. Survey designs that separate historical and ecological determinants of host specificity by studying herbivores feeding on the same plant species exposed to different environmental or experimental conditions are rare. Further, we advocate the use of host-specificity measures based on plant phylogeny. Existing data suggest that a minority of species in herbivore communities feed on a single plant species when alternative congeneric hosts are available. Thus, host plant range limits tend to coincide with those of plant genera, rather than species or suprageneric taxa. Host specificity among tropical herbivore guilds decreases in the sequence: granivores > leaf-miners > fructivore > leaf-chewers = sap-suckers > xylophages > root-feeders, thus paralleling patterns observed in temperate forests. Differences in host specificity between temperate and tropical forests are difficult to assess since data on tropical herbivores originate from recent field studies, whereas their temperate counterparts derive from regional host species lists, assembled over many years. No major increase in host specificity from temperate to tropical communities is evident. This conclusion, together with the recent downward revisions of extremely high estimates of tropical species richness, suggest that tropical ecosystems may not be as biodiverse as previously thought.

Animals↗

PubMed2006

Morphological assembly mechanisms in Neotropical bat assemblages and ensembles within a landscape.

Empirical studies on bat assemblages have shown that richness is not appreciably influenced by local processes such as ecological interactions. However, most of these studies have been done in large areas that include high heterogeneity, and they analyse all bat species within such areas, and thus they may be not reflecting local but supra-community conditions. We followed an ecomorphological approach to assess how bat assemblages of species from the families Phyllostomidae and Mormoopidae, and ensembles of frugivorous bats, are assembled in local habitats within a single landscape. We measured the volume of the space defined by wing morphology and quantified the average distance between species within such a volume. Then, we related these measures to local richness. Such relationships were contrasted against relationships with random assemblages to test for statistical differences. At the ensemble level of organization, we found that the frugivorous bat morphological assembly mechanism is different from random patterns, and it corresponds to the volume-increasing model. On the other hand, bat assembly mechanisms may be ubiquitous at the assemblage level, because groups of species coexisting in a local habitat and delimited only by phylogeny include more than one ecological group with no potential to interact. Assembling processes are crucial to an understanding of species diversity in local communities, and ecomorphological analyses are very promising tools that may help in their study.

Analysis of Variance↗

PubMed2026

StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

SUMMARY: Metagenomic workflows involve complex multi-step analyses, from quality control and assembly to binning, annotation, and strain-level profiling. Few existing metagenomic pipelines achieve the combination of flexibility, reproducibility, and hybrid assembly support within a unified workflow. We present StrainMake, a Snakemake-based workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data. StrainMake integrates widely used tools across all major steps-quality control, assembly, binning, dereplication, taxonomic and functional annotation-while also providing non-redundant gene catalogues, community-scale metabolic models, and strain-level microdiversity metrics. The modular design enables the use of alternative tools, scalable execution on HPC systems, and full reproducibility through Snakemake and Conda. RESULTS: Applied to the CAMI II strain-madness dataset, StrainMake produced high-quality assemblies and metagenome-assembled genomes (MAGs), while enabling strain-resolved comparisons across samples. Hybrid assemblies improved contiguity, whereas short-read assemblies offered faster runtimes, illustrating the workflow's benchmarking capacity. AVAILABILITY AND IMPLEMENTATION: StrainMake is open source and available at https://github.com/UMMISCO/strainmake, together with comprehensive documentation. Generated data are deposited in Zenodo (doi: 10.5281/zenodo.16950162).

Metagenomics↗

PubMed2026

Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.

Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.

Animals↗

PubMed1980

[Education of nursing personnel for community health care].

The article reviews the efforts that nursing has been making in Peru to adjust training to the health needs of the population, particularly in rural and marginal urban areas, and in keeping with the policy of extending coverage by the strategies of primary care and community participation. In particular, the program of the Professional Baccalaureate in Nursing is reviewed, and a detailed description of its planning is given on the basis of selected functions, the educational process, the curricular structure, and progress made since the program was launched. Noteworthy among the innovative aspects of this experiment is the imparting of professional training in discrete learning blocks, which take the place of subjects. These blocks center on the teaching-learning of functions, which are identified through the analysis of community problems and health needs. Each function or group of functions serves as a focus around which are assembled the knowledge and skills required to master them and thus for attainment of the educational objectives of each block.

Community Health Nursing↗

PubMed2026

Climate and soil shape Daqu wheat quality and seed microbiome via rhizosphere taxa and microbial assembly.

The grain quality and seed microbiome of Daqu wheat are fundamental determinants of Daqu fermentation performance; however, the mechanisms by which cultivation environments influence these traits via rhizosphere microbial communities remain unclear. Bacterial and fungal communities across the bulk soil-rhizosphere-seed continuum of three wheat cultivars grown in four ecoregions were characterized using absolute quantitative amplicon sequencing. The rhizosphere microbiome was treated as a central intermediary, while the response variables were seed microbial diversity and grain-quality traits, including starch content, protein content, and grain hardness. Twelve physicochemical properties of soil and 11 climatic factors were integrated into a multidimensional association framework. Environmental conditions exerted stronger influences on both seed quality traits and microbial diversity than cultivar identity. Distinct regional signatures were also evident in rhizosphere microbiomes, with environmental gradients explaining community variation more effectively than geographic distance. Bacterial communities exhibited greater sensitivity to environmental fluctuations than fungi. Mantel analyses identified available nitrogen, precipitation, and atmospheric pressure as significant drivers of core rhizosphere taxa (P < 0.05). iCAMP revealed that stochastic processes predominantly governed rhizosphere bacterial assembly, whereas stochastic and deterministic mechanisms jointly shaped fungal assembly. Partial least squares path modeling further uncovered a rhizosphere-mediated environment-seed cascade, wherein sunlight intensity and duration, atmospheric pressure, and soil nitrogen directly or indirectly affected seed wet gluten content, grain hardness, and seed microbial diversity through their influences on rhizosphere microbiota. Rhizosphere bacterial diversity was negatively associated with seed bacterial diversity (path coefficient = -0.118, P < 0.05), indicating that rhizosphere communities may shape seed endophytic bacterial assemblages via environmental filtering and competitive interactions. Collectively, these findings elucidate how environments shape the quality and seed microbiomes of Daqu wheat, providing scientific guidance for optimal site selection and the standardized production of high-quality brewing wheat for industrial Baijiu.

Triticum↗

PubMed2004

Recruitment for a community-based study of early pregnancy: the Right From The Start study.

Despite the high incidence of spontaneous abortion, little is known about its causes, in part because of the challenge of assembling a large cohort of women in early pregnancy for prospective study. We describe the effectiveness of recruitment strategies used in Right From The Start (RFTS), a prospective, community-based study of spontaneous abortion. Between December 2000 and September 2002, 803 pregnant women enrolled in RFTS, 103 of whom were recruited while trying to conceive. The mean gestational age at enrollment was 52 days, with 25% of the cohort enrolling before 6 completed weeks' gestation. Participants recruited directly from the community typically enrolled earlier in their pregnancies (mean of 44 days) and accounted for 24% of the total cohort and 83% of all participants who were recruited while trying to conceive. Posting brochures in drug stores and targeted mailings to new homeowners were the most effective community recruitment strategies. Recruitment at private and public prenatal care sites accounted for 57% and 19% of the participants respectively. Recruitment from public clinics required direct contact by RFTS staff and yielded women who enrolled at later gestational ages (mean of 58 days), but was valuable for inclusion of minorities and lower income women with less favourable health behaviours. Although intensive, diverse efforts were required, when recruitment efforts were maximised, we successfully recruited over 10% of the estimated number of pregnant women in the community.

Abortion, Spontaneous↗

PubMedDate not supplied

Understanding communities today: using matching needs and services to assess community needs and design community-based services.

Matching Needs and Services (MNS) is a practice tool intended to help people who work with vulnerable children use rigorously assembled information on needs as a guide to design, implement, and evaluate more-effective services. To do this, MNS focuses on needs but links them to outcomes and thresholds before dealing with the services to achieve those outcomes.

Child↗

PubMed2004

Assembly and analysis of the mouse immunoglobulin kappa gene sequence.

The mechanisms regulating V gene usage leading to the immunoglobulin (Ig) repertoire have been of interest for many years but are only partially defined. To gain insight into these processes, we have assembled the nucleotide sequence of the Mus musculus Igkappa locus using data recently made available from genome-wide sequencing efforts. We found the locus to be 3.21 Mb in length and mapped all known functional, pseudo- and relic V gene segments onto the sequence, along with known regulatory elements. We corrected errors in former gene assignments, positions and orientations and identified a novel Vkappa4 gene segment. This assembly allowed the establishment of a unified nomenclature for the V genes based on their relative positions similar to the nomenclature system adopted for the human Ig loci. The 5' boundary of the locus is defined by the presence of the tumor-associated calcium-signal transducer-2 gene located 19 kb upstream of Vkappa24-140, the most distal V gene. No non- Vkappa genes were found in the sequence of the locus. Detailed analysis of the sequences 0.5 kb upstream, within, and 0.5 kb downstream of each potentially functional V gene revealed interesting patterns of statistically significant clustering of transcription factor consensus binding sites, generally specific to a particular family. We found E boxes were clustered not only in promoter regions, but also nearby recombination signal sequences. Family members of Vkappa4/5 genes exhibit a conserved pattern of octamer sites in their downstream regions, as well as Ebf sites in their introns, and Lef-1 sites in their upstream regions. We discuss potential functional implications of these findings in the context of possible combinatorial mechanisms for targeting V genes for rearrangement. The assembled sequence and its analyses are available as a resource to the scientific community.

Animals↗