K-meson nucleon scattering

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Emergence, ecology and dispersal of the pandemic generating Vibrio cholerae lineage

Although cholera is an ancient disease that first arose at least half a millennium ago, it remains a major health threatglobally. Its pandemic form is caused by strains from a single lineage of the bacterium Vibrio cholerae. The ancestor of this lineageharbored several distinctive characteristics, the most notable being the O1 antigen polysaccharide. This lineage generatedtwo biotypes, first Classical, responsible for six pandemics, and later El Tor, responsible for the seventh and ongoing pandemic.Just as El Tor replaced Classical as the main cause of outbreaks in the last fifty years, several variants of El Tor have evolved anddisplaced their predecessors worldwide. Understanding the ecology, evolution and dispersal of pandemic V. cholerae is centralto studying this complex disease with environmental reservoirs. Here, we present recent advancements of our knowledge on theemergence and spread of the pandemic generating lineage of V. cholerae in the light of established eco-evolutionary observations.Specific ecological interactions shape seasonal cholera, playing a role in the abundance and distribution of its causative agent.Both species-specific and lineage-specific genetic determinants play a role in the ability of V. cholerae strains to cause pandemicswith seasonal outbreaks, having evolved gradually over centuries. On the basis of the current understanding, we outline futurethreats and changes in biogeographical and genomic-based investigation strategies to combat this global problem

Mother’s dietary diversity and association with stunting among children <2 years old in a low socio‐economic environment: A case–control study in an urban care setting in Dhaka, Bangladesh

Mothers are often responsible for preparing nutritious foods in their households. However, the quality of mother’s diets is often neglected, which may affect both mother’s and child’s nutrition. Because no single food contains all necessary nutrients, diversity in dietary sources is needed to ensure a quality diet. We aimed to study the association between mother’s dietary diversity and stunting in children <2 years attending Dhaka Hospital of icddr,b, a diarrhoeal disease hospital in Dhaka, Bangladesh. A case–control study (n = 296) was conducted from November 2016 to February 2017. Data were collected from mothers of stunted children <2 years (length‐for‐age z score [LAZ] < −2) as “cases” and nonstunted (LAZ ≥ −1) children <2 years as “controls.” Mothers were asked to recall consumption of 10 defined food groups 24 hr prior to the interview as per Guidelines for Minimum Dietary Diversity for Women. Among the mothers of cases, 58% consumed <5 food groups during the last 24 hr, compared with 45% in control mothers (P = 0.03). Children whose mothers consumed <5 food groups were 1.7 times more likely to be stunted than children whose mothers consumed ≥5 food groups (P = 0.04). Intake of food groups such as pulses, dairy, eggs, and vitamin A rich fruit was higher in control mothers. Proportion of mother’s illiteracy, short stature, monthly family income <BDT 11,480, absence of bank account, and poor sanitation was also found to be higher in stunted group. Further study particularly intervention or longitudinal study to see the causality of mother’s dietary diversity with child stunting is recommended.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148421/1/mcn12665.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148421/2/mcn12665_am.pd

OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

<p>Abstract</p> <p>Background</p> <p>Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.</p> <p>Results</p> <p>Here we report an online codon-preserved alignment tool (OCPAT) that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s) from at least one species; however, functional annotation clustering of the ~1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved.</p> <p>Conclusion</p> <p>The OCPAT program facilitates large-scale evolutionary and phylogenetic analyses of entire biological processes, pathways, and diseases.</p

Perceptions of Acute Malnutrition and Its Management in Infants Under 6 Months of Age: A Qualitative Study in Rural Bangladesh.

BACKGROUND: World Health Organization guidelines advise community-based care (CBC) for "uncomplicated" severe acute malnutrition (SAM) infants <6 months old (u6m), whereas current national protocols refer to inpatient care. Our aim was to inform and shape future management strategies by understanding caregivers' and different stakeholders' perceptions on malnutrition among infants u6m on barriers/facilitators to future CBC. METHODS: The methods used in this study are as follows: in-depth interviews and focus group discussions (FGDs) in southern Bangladesh, thematic analysis of transcripts, and sample size by data saturation. RESULTS: We conducted 5 FGDs with 29 caregivers, 4 with 29 health care workers, 4 key informant interviews each with community leaders and health supervisors. Five themes emerged. 1) Identification of SAM infants and care-seeking behavior: malnutrition was not noticed until severe, caregivers focused on clinical symptoms. Both allopathic and traditional healers were consulted. (2) Perceived causes of infant malnutrition: underlying illness, poor feeding practices, poverty, and local superstitions. (3) Views and preferences on treatment: hospitals and doctors were perceived as offering the best treatment, health care workers were also important, and respondents highlighted the need care of the caregiver/mother along with the infant. (4) Perceived benefits and risks of CBC: lower cost and greater accessibility were appreciated but worried about quality. (5) Community networks: wider family and social support networks were considered important aspects of care. CONCLUSIONS: There is considerable potential for CBC but needs to be better and earlier identification of at-risk infants, strengthening of health systems to avoid community options being perceived as "second best," engagement with families and communities to tackle "upstream" determinants of SAM, and care for mother-infant pairs

Severe malnutrition in infants aged <6 months-Outcomes and risk factors in Bangladesh: A prospective cohort study.

Severe acute malnutrition (SAM) affects ~4 million infants under 6 months (u6m) worldwide, but evidence underpinning their care is "very low" quality. To inform future research and policy, the objectives of our study were to identify risk factors for infant u6m SAM and describe the clinical and anthropometric outcomes of treatment with current management strategies. We conducted a prospective cohort study in infants u6m in Barisal district, Bangladesh. One group of 77 infants had SAM (weight-for-length Z-score [WLZ] <-3 and/or bipedal oedema); 77 others were "non-SAM" (WLZ ≥-2 to <+2, no oedema, mid-upper-arm circumference ≥125 mm). All were enrolled at 4-8 weeks of age and followed up at 6 months. Maternal education and satisfaction with breastfeeding were among factors associated with SAM. Duration of exclusive breastfeeding was shorter at enrolment (3·9 ± 2.1 vs. 5.7 ± 2.2 weeks, P < 0.0001) and at age 6 months (13.2 ± 8.9 vs. 17.4 ± 7.9 weeks; P = 0.003) among SAM infants. Despite referral, only 13 (17%) reported for inpatient care, and at 6 months, 18 (23%) infants with SAM still had SAM, and 3 (3.9%) died. In the non-SAM group, one child developed SAM, and none died. We conclude that current treatment strategies have limited practical effectiveness: poor uptake of inpatient referral being the main reason. World Health Organization recommendations and other intervention strategies of outpatient-focused care for malnourished but clinically stable infants u6m need to be tested. Breastfeeding support is likely central to future treatment strategies but may be insufficient alone. Better case definitions of nutritionally at-risk infants are also needed

Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition

BACKGROUND: Childhood undernutrition remains a significant global health challenge accounting for over half of all under 5 child mortality. Moderate acute malnutrition (MAM), which leads to wasting [weight-for-length z-scores (WLZ) between - 2 and - 3], affects 33 million children under 5 globally and more than 2 million in Bangladesh alone. We have previously reported that acute malnutrition in this population is associated with gut microbiota immaturity, and in a small, 1-month pre-proof-of-concept (POC) study demonstrated that a microbiota-directed complementary food formulation (MDCF-2) was able to repair this immaturity, promote weight gain and increase plasma biomarkers and mediators of healthy growth. Here we describe the design controlled feeding study that tests whether MDCF-2 exhibits superior efficacy (ponderal growth, host biomarkers of a biological state) than a conventional Ready-to-use Supplementary Food (RUSF) in children with MAM over intervention period of 3 months. METHODS: Two separate cohorts of 12-18-month-old children will be enrolled: 124 with primary MAM, and 124 with MAM after having been treated for severe acute malnutrition (post-SAM MAM). We have established several field sites in an urban slum located in the Mirpur district of Dhaka, Bangladesh and at a rural site, Kurigram in the north of Bangladesh. The two groups of children receiving MDCF-2 and RUSF will be compared at baseline (pre-intervention), after 1 month, at the end of intervention (3 months), 1 month after cessation of intervention, and every 6 months thereafter for 4 years. DISCUSSION: This study will determine whether daily, controlled administration of MDCF-2 for 3 months provides superior improvements in weight gain, microbiota repair, and elevated levels of key plasma biomarkers/mediators of healthy growth compared to the control RUSF formulation. The pathogenesis of MAM is poorly defined and there are currently no WHO-approved treatments; results from the current study of children with primary MAM and post-SAM MAM will shed light on the effects of the gut microbiota on childhood growth/development and will provide a knowledge base that may help improve complementary feeding practices. TRIAL REGISTRATION: The primary MAM and post-SAM MAM trials are registered in Clintrials.gov (NCT04015999 and NCT04015986, registered on July 11, 2019, retrospectively registered)

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

Abstract Background Cross-species gene expression analyses using oligonucleotide microarrays designed to evaluate a single species can provide spurious results due to mismatches between the interrogated transcriptome and arrayed probes. Based on the most recent human and chimpanzee genome assemblies, we developed updated and accessible probe masking methods that allow human Affymetrix oligonucleotide microarrays to be used for robust genome-wide expression analyses in both species. In this process, only data from oligonucleotide probes predicted to have robust hybridization sensitivity and specificity for both transcriptomes are retained for analysis. Results To characterize the utility of this resource, we applied our mask protocols to existing expression data from brains, livers, hearts, testes, and kidneys derived from both species and determined the effects probe numbers have on expression scores of specific transcripts. In all five tissues, probe sets with decreasing numbers of probes showed non-linear trends towards increased variation in expression scores. The relationships between expression variation and probe number in brain data closely matched those observed in simulated expression data sets subjected to random probe masking. However, there is evidence that additional factors affect the observed relationships between gene expression scores and probe number in tissues such as liver and kidney. In parallel, we observed that decreasing the number of probes within probe sets lead to linear increases in both gained and lost inferences of differential cross-species expression in all five tissues, which will affect the interpretation of expression data subject to masking. Conclusion We introduce a readily implemented and updated resource for human and chimpanzee transcriptome analysis through a commonly used microarray platform. Based on empirical observations derived from the analysis of five distinct data sets, we provide novel guidelines for the interpretation of masked data that take the number of probes present in a given probe set into consideration. These guidelines are applicable to other customized applications that involve masking data from specific subsets of probes