Thirteen dubious ways to detect conserved structural RNAs.

Covariation induced by compensatory base substitutions in RNA alignments is a great way to deduce conserved RNA structure, in principle. In practice, success depends on many factors, importantly the quality and depth of the alignment and the choice of covariation statistic. Measuring covariation between pairs of aligned positions is easy. However, using covariation to infer evolutionarily conserved RNA structure is complicated by other extraneous sources of covariation such as that resulting from homologous sequences having evolved from a common ancestor. In order to provide evidence of evolutionarily conserved RNA structure, a method to distinguish covariation due to sources other than RNA structure is necessary. Moreover, there are several sorts of artifactually generated covariation signals that can further confound the analysis. Additionally, some covariation signal is difficult to detect due to incomplete comparative data. Here, we investigate and critically discuss the practice of inferring conserved RNA structure by comparative sequence analysis. We provide new methods on how to approach and decide which of the numerous long non-coding RNAs (lncRNAs) have biologically relevant structures.

Program assessment of efforts to improve the quality of postpartum counselling in health centers in Morogoro region, Tanzania.

BACKGROUND: The postpartum period represents a critical window where many maternal and child deaths occur. We assess the quality of postpartum care (PPC) as well as efforts to improve service delivery through additional training and supervision in Health Centers (HCs) in Morogoro Region, Tanzania. METHODS: Program implementers purposively selected nine program HCs for assessment with another nine HCs in the region remaining as comparison sites in a non-randomized program evaluation. PPC quality was assessed by examining structural inputs; provider and client profiles; processes (PNC counselling) and outcomes (patient knowledge) through direct observations of equipment, supplies and infrastructure (n = 18) and PPC counselling (n = 45); client exit interviews (n = 41); a provider survey (n = 62); and in-depth provider interviews (n = 10). RESULTS: While physical infrastructure, equipment and supplies were comparable across study sites (with water and electricity limitations), program areas had better availability of drugs and commodities. Overall, provider availability was also similar across study sites, with 63% of HCs following staffing norms, 17% of Reproductive and Child Health (RCH) providers absent and 14% of those providing PPC being unqualified to do so. In the program area, a median of 4 of 10 RCH providers received training. Despite training and supervisory inputs to program area HCs, provider and client knowledge of PPC was low and the content of PPC counseling provided limited to 3 of 80 PPC messages in over half the consultations observed. Among women attending PPC, 29 (71%) had delivered in a health facility and sought care a median of 13 days after delivery. Barriers to PPC care seeking included perceptions that PPC was of limited benefit to women and was primarily about child health, geographic distance, gaps in the continuity of care, and harsh facility treatment. CONCLUSIONS: Program training and supervision activities had a modest effect on the quality of PPC. To achieve broader transformation in PPC quality, client perceptions about the value of PPC need to be changed; the content of recommended PPC messages reviewed along with the location for PPC services; gaps in the availability of human resources addressed; and increased provider-client contact encouraged.

Program synergies and social relations: implications of integrating HIV testing and counselling into maternal health care on care seeking.

BACKGROUND: Women and children in sub-Saharan Africa bear a disproportionate burden of HIV/AIDS. Integration of HIV with maternal and child services aims to reduce the impact of HIV/AIDS. To assess the potential gains and risks of such integration, this paper considers pregnant women's and providers' perceptions about the effects of integrated HIV testing and counselling on care seeking by pregnant women during antenatal care in Tanzania. METHODS: From a larger evaluation of an integrated maternal and newborn health care program in Morogoro, Tanzania, this analysis included a subset of information from 203 observations of antenatal care and interviews with 57 providers and 190 pregnant women from 18 public health centers in rural and peri-urban settings. Qualitative data were analyzed manually and with Atlas.ti using a framework approach, and quantitative data of respondents' demographic information were analyzed with Stata 12.0. RESULTS: Perceptions of integrating HIV testing with routine antenatal care from women and health providers were generally positive. Respondents felt that integration increased coverage of HIV testing, particularly among difficult-to-reach populations, and improved convenience, efficiency, and confidentiality for women while reducing stigma. Pregnant women believed that early detection of HIV protected their own health and that of their children. Despite these positive views, challenges remained. Providers and women perceived opt out HIV testing and counselling during antenatal services to be compulsory. A sense of powerlessness and anxiety pervaded some women's responses, reflecting the unequal relations, lack of supportive communications and breaches in confidentiality between women and providers. Lastly, stigma surrounding HIV was reported to lead some women to discontinue services or seek care through other access points in the health system. CONCLUSION: While providers and pregnant women view program synergies from integrating HIV services into antenatal care positively, lack of supportive provider-patient relationships, lack of trust resulting from harsh treatment or breaches in confidentiality, and stigma still inhibit women's care seeking. As countries continue rollout of Option B+, social relations between patients and providers must be understood and addressed to ensure that integrated delivery of HIV counselling and services encourages women's care seeking in order to improve maternal and child health.

Supply-side dimensions and dynamics of integrating HIV testing and counselling into routine antenatal care: a facility assessment from Morogoro Region, Tanzania.

BACKGROUND: Integration of HIV into RMNCH (reproductive, maternal, newborn and child health) services is an important process addressing the disproportionate burden of HIV among mothers and children in sub-Saharan Africa. We assess the structural inputs and processes of care that support HIV testing and counselling in routine antenatal care to understand supply-side dynamics critical to scaling up further integration of HIV into RMNCH services prior to recent changes in HIV policy in Tanzania. METHODS: This study, as a part of a maternal and newborn health program evaluation in Morogoro Region, Tanzania, drew from an assessment of health centers with 18 facility checklists, 65 quantitative and 57 qualitative provider interviews, and 203 antenatal care observations. Descriptive analyses were performed with quantitative data using Stata 12.0, and qualitative data were analyzed thematically with data managed by Atlas.ti. RESULTS: Limitations in structural inputs, such as infrastructure, supplies, and staffing, constrain the potential for integration of HIV testing and counselling into routine antenatal care services. While assessment of infrastructure, including waiting areas, appeared adequate, long queues and small rooms made private and confidential HIV testing and counselling difficult for individual women. Unreliable stocks of HIV test kits, essential medicines, and infection prevention equipment also had implications for provider-patient relationships, with reported decreases in women's care seeking at health centers. In addition, low staffing levels were reported to increase workloads and lower motivation for health workers. Despite adequate knowledge of counselling messages, antenatal counselling sessions were brief with incomplete messages conveyed to pregnant women. In addition, coping mechanisms, such as scheduling of clinical activities on different days, limited service availability. CONCLUSION: Antenatal care is a strategic entry point for the delivery of critical tests and counselling messages and the framing of patient-provider relations, which together underpin care seeking for the remaining continuum of care. Supply-side deficiencies in structural inputs and processes of delivering HIV testing and counselling during antenatal care indicate critical shortcomings in the quality of care provided. These must be addressed if integrating HIV testing and counselling into antenatal care is to result in improved maternal and newborn health outcomes.

Evidence of transmission of New Delhi metallo-ß-lactamase-producing Klebsiella pneumoniae through a gastrointestinal endoscope without an elevator channel.

OBJECTIVE: To investigate the source and transmission dynamics of an endoscope-associated New Delhi metallo-ß-lactamase-producing Klebsiella pneumonia (NDM-KP) outbreak. DESIGN: Epidemiological and genomic investigation. SETTING: Academic acute care hospital in New Jersey. PATIENTS: Five patients with active NDM-KP infection identified on clinical isolates, and four NDM-KP colonized patients identified via rectal swab screening. RESULTS: Over a twelve-month period, nine patients were identified with NDM-KP infection or colonization. Whole-genome sequencing (WGS) revealed that all of the identified cases were related by 25 mutational events or less. Seven of the cases were linked to gastrointestinal endoscopic procedures (four clinical cases and three positive screens among patients exposed to endoscopes suspected of transmission). Two cases demonstrated delayed transmission that occurred five months after the initial outbreak, likely through shared usage of a non-therapeutic gastroscope without an elevator channel. CONCLUSIONS: Although all endoscope cultures in our investigation were negative, the epidemiological link to gastrointestinal endoscopes, the high degree of relatedness via WGS, and the identification of asymptomatic NDM-KP colonization among patients exposed to shared endoscopes make the endoscopic mode of transmission most likely. This investigation highlights the probable transmission of NDM-KP via a gastroscope without an elevator channel, observed several months after an initial outbreak. We hypothesize that persistent mechanical defects may have contributed to the delayed device-related transmission of NDM-KP.

Multi-drug resistant Pseudomonas aeruginosa: a 2019-2020 single center retrospective case control study.

Multi-drug resistance in the post COVID-19 world is a growing concern. The objective of this study was to describe temporal trends and explore independent risk factors for the isolation of multi-drug resistant (MDR) P. aeruginosa. Methods: This was a retrospective case-control study of patients with P. aeruginosa isolates recovered from January 2019 to December 2020. MDR P. aeruginosa was defined as non-susceptibility to at least one agent in three or more anti-pseudomonal antimicrobial categories. Results: In total, 258 unique isolates were identified. Prolonged hospitalization (P<0.001), prior antibiotic use (P<0.001), and respiratory sources (P<0.001) were strongly associated with the presence of MDR P. aeruginosa. From 2019 to 2020, there was a decrease in the total number of P. aeruginosa isolates but a significant increase in the proportion of MDR P. aeruginosa isolates (P=0.015). Conclusions: Over a period that coincided with the COVID-19 pandemic, there was an increased proportion of MDR P. aeruginosa isolates from hospitalized patients. Improved identification of patients at risk for MDR P. aeruginosa could facilitate appropriate empiric antibiotic decisions like dual anti-pseudomonal therapy. The features of the COVID-19 outbreak that had a severe impact on patient care and that may have affected drug resistance in other respiratory pathogens should be explored.

Primary cilia on muscle stem cells are critical to maintain regenerative capacity and are lost during aging.

During aging, the regenerative capacity of muscle stem cells (MuSCs) decreases, diminishing the ability of muscle to repair following injury. We found that the ability of MuSCs to regenerate is regulated by the primary cilium, a cellular protrusion that serves as a sensitive sensory organelle. Abolishing MuSC cilia inhibited MuSC proliferation in vitro and severely impaired injury-induced muscle regeneration in vivo. In aged muscle, a cell intrinsic defect in MuSC ciliation was associated with the decrease in regenerative capacity. Exogenous activation of Hedgehog signaling, known to be localized in the primary cilium, promoted MuSC expansion, both in vitro and in vivo. Delivery of the small molecule Smoothened agonist (SAG1.3) to muscles of aged mice restored regenerative capacity leading to increased strength post-injury. These findings provide fresh insights into the signaling dysfunction in aged MuSCs and identify the ciliary Hedgehog signaling pathway as a potential therapeutic target to counter the loss of muscle regenerative capacity which accompanies aging.

Saving Lives Together: A Qualitative Evaluation of the Saving Mothers, Giving Life Public-Private Partnership.

BACKGROUND: Public-private partnerships (PPPs) have garnered appeal among governments around the world, making impressive contributions to health resource mobilization and improved health outcomes. Saving Mothers, Giving Life (SMGL), a PPP aimed at reducing maternal deaths, was born out of the need to mobilize new actors, capitalize on diverse strengths, and marshal additional resources. A qualitative study was initiated to examine how the SMGL partnership functioned to achieve mortality reduction goals and foster country ownership and sustainability. METHODS: We purposively selected 57 individuals from U.S. and global public and private partner organizations engaged in SMGL in Uganda and Zambia for qualitative in-depth interviews. Representative selection was based on participant knowledge of partner activities and engagement with the partnership at various points in time. Of those invited, 46 agreed to participate. Transcripts were double-coded, and discordant codes were resolved by consensus. RESULTS: Several recurring themes emerged from our study. Perceived strengths of the partnership included goal alignment; diversity in partner expertise; high-quality monitoring, evaluation, and learning; and strong leadership and country ownership. These strengths helped SMGL achieve its goals in reducing maternal and newborn mortality. However, uncertainty in roles and responsibilities, perceived power inequities between partners, bureaucratic processes, a compressed timeline, and limited representation from ministries of health in the SMGL governance structure were reported impediments. CONCLUSION: While SMGL faced many of the same challenges experienced by other PPPs, local counterparts and the SMGL partners were able to address many of these issues and the partnership was ultimately praised for being a successful model of interagency coordination. Efforts to facilitate country ownership and short-term financial sustainability have been put in place for many elements of the SMGL approach; however, long-term financing is still a challenge for SMGL as well as other global health PPPs. Addressing key impediments outlined in this study may improve long-term sustainability of similar PPPs.

A collagen­chitosan hydrogel for endothelial differentiation and angiogenesis.

Cell therapy for the treatment of cardiovascular disease has been hindered by low cell engraftment, poor survival, and inadequate phenotype and function. In this study, we added chitosan to a previously developed injectable collagen matrix, with the aim of improving its properties for cell therapy and neovascularization. Different ratios of collagen and chitosan were mixed and chemically crosslinked to produce hydrogels. Swell and degradation assays showed that chitosan improved the stability of the collagen hydrogel. In culture, endothelial cells formed significantly more vascular-like structures on collagen­chitosan than collagen-only matrix. While the differentiation of circulating progenitor cells to CD31+ cells was equal on all matrices, vascular endothelial-cadherin expression was increased on the collagen­chitosan matrix, suggesting greater maturation of the endothelial cells. In addition, the collagen­chitosan matrix supported a significantly greater number of CD133+ progenitor cells than the collagen-only matrix. In vivo, subcutaneously implanted collagen­chitosan matrices stimulated greater vascular growth and recruited more von Willebrand factor (vWF+) and CXCR4+ endothelial/angiogenic cells than the collagen-only matrix. These results indicate that the addition of chitosan can improve the physical properties of collagen matrices, and enhance their ability to support endothelial cells and angiogenesis for use in cardiovascular tissue engineering applications.

Staphylococcus epidermidis forms biofilms under simulated platelet storage conditions.

BACKGROUND: Staphylococcus epidermidis grows slowly in platelet (PLT) preparations compared to other bacteria, presenting the possibility of missed detection by routine screening. S. epidermidis is a leading cause of nosocomial sepsis, with virulence residing in its ability to establish chronic infections through production of slime layers, or biofilms, on biomedical devices. This study aims to establish biofilm formation (BF) as a mode of growth by S. epidermidis in PLT preparations. STUDY DESIGN AND METHODS: Biofilm-positive (BFpos) and -negative (BFneg) S. epidermidis strains were grown in whole blood-derived PLTs (WBDPs) and in glucose-rich medium (TSBg). An assay for BF was adapted for cultures grown in WBDPs or filtered WBDPs in polystyrene culture plates. Bacterial attachment to polyvinylchloride PLT bags and PLTs was examined by scanning electron microscopy. RESULTS: Both strains display similar growth profiles in WBDPs and TSBg. Unexpectedly, evidence of BF was observed on PLT bags and on PLTs directly, not only by the BFpos strain but also by the BFneg strain. The BFpos strain displayed greater plastic adherence than the BFneg strain in WBDPs (p < 0.05). BF by the BFneg strain was approximately 10-fold greater in WBDPs compared to TSBg (p < 0.05), likely by use of PLTs as a scaffold. Furthermore, BF by S. epidermidis was significantly decreased when PLT concentration was reduced 1000-fold. CONCLUSIONS: S. epidermidis forms biofilms on PLT aggregates and on PLT bags under PLT storage conditions. Our results demonstrate that the PLT storage environment can promote a BF growth mechanism for contaminant bacteria.