Ancient genomes reveal a deep history of treponemal disease in the Americas.

Human treponemal infections are caused by a family of closely related Treponema pallidum that give rise to the diseases yaws, bejel, pinta and, most famously, syphilis. Debates on both a common origin for these pathogens and the history of syphilis itself has weighed evidence for the "Columbian hypothesis", which argues for an American origin, against that for the "pre-Columbian hypothesis", which argues for presence of the disease in Eurasia in the Medieval period and possibly earlier. While molecular data has provided a genetic basis for distinction of the typed subspecies, deep evolution of the complex has remained unresolved due to limitations in the conclusions that can be drawn from the sparse paleogenomic data currently available.

CHARTING THE EVOLUTION AND TRANSFORMATIVE IMPACT OF THE PACIFIC SYMPOSIUM ON BIOCOMPUTING THROUGH A 30-YEAR RETROSPECTIVE ANALYSIS OF COLLABORATIVE NETWORKS AND THEMES USING MODERN COMPUTATIONAL TOOLS.

Founded nearly 30 years ago, the Pacific Symposium on Biocomputing (PSB) has continually promoted collaborative research in computational biology, annually highlighting emergent themes that reflect the expanding interdisciplinary nature of the field. This study aimed to explore the collaborative and thematic dynamics at PSB using topic modeling and network analysis methods. We identified 14 central topics that have characterized the discourse at PSB over the past three decades.

Ancient Plasmodium genomes shed light on the history of human malaria.

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P.

Toll-like receptor 3 neuroimmune signaling and behavior change: A strain comparison between Lewis and Wistar rats.

There are many unanswered questions about the interaction between the immune system and behavior change, including the contributions of individual differences. The present study modeled individual differences in the immune system by comparing inbred Lewis rats, which have dysregulated stress and immune systems, to their genetically diverse parent strain, Wistar rats. The objective was to examine the consequences of an immune challenge on behavior and neuroimmune signaling in both strains.

The Toll-like receptor 7 agonist imiquimod increases ethanol self-administration and induces expression of Toll-like receptor related genes.

There is growing evidence that immune signalling may be involved in both the causes and consequences of alcohol abuse. Toll-like receptor (TLR) expression is increased by alcohol consumption and is implicated in AUD, and specifically TLR7 may play an important role in ethanol consumption. We administered the TLR7-specific agonist imiquimod in male and female Long-Evans rats to determine (1) gene expression changes in brain regions involved in alcohol reinforcement, the nucleus accumbens core and anterior insular cortex, in rats with and without an alcohol history, and (2) whether TLR7 activation could modulate operant alcohol self-administration.

Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations.

Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources- a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America.

Human Intrigue: Meta-analysis approaches for big questions with big data while shaking up the peer review process.

Scientific innovation has long been heralded the collaborative effort of many people, groups, and studies to drive forward research. However, the traditional peer review process relies on reviewers acting in a silo to critically judge research. As research becomes more cross-disciplinary, finding reviewers with appropriate expertise to provide feedback on an entire paper is increasingly difficult.

Ten millennia of hepatitis B virus evolution.

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene.

Raising the stakeholders: Improving patient outcomes through interprofessional collaborations in AI for healthcare.

Research into AI implementations for healthcare continues to boom. However, successfully launching these implementations into healthcare clinics requires the co-operation and collaboration of multiple stakeholders in healthcare including healthcare professionals, administrators, insurers, legislators, advocacy groups, as well as the patients themselves. The co-operation and collaboration of these interprofessional groups is necessary not just in the final stages of launching AI based solutions in healthcare, but along each stage of the research design and analysis.

A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15 century Europe.

Developments in techniques for identification of pathogen DNA in archaeological samples can expand our resolution of disease detection. Our application of a non-targeted molecular screening tool for the parallel detection of pathogens in historical plague victims from post-medieval Lithuania revealed the presence of more than one active disease in one individual. In addition to Yersinia pestis, we detected and genomically characterized a septic infection of Treponema pallidum pertenue, a subtype of the treponemal disease family recognised as the cause of the tropical disease yaws.

Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.

The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods.

Skeletal Lead Burden of the British Royal Navy in Colonial Antigua.

Lead (Pb) has been known to be a cause of human poisoning since ancient times, but despite this, it was a widely used metal in the European colonial period. In this study, the relationship between Pb exposure and the demographic variables ancestry and age was explored by comparing the bone Pb levels of individuals that were of either African or European ancestry, excavated from a British Royal Navy hospital cemetery (1793-1822 CE) at English Harbour in Antigua, West Indies. More direct comparisons of Pb levels between the two ancestral groups were possible in this study because of the unsegregated nature of this cemetery.

Generation of Hydrofluoronickelacycles from Trifluoroethylene and Ni(0): Ligand Effects on Regio-/Stereoselectivity and Reactivity.

Treatment of Ni(0) complexes 1a-e with sub-atmospheric pressures of trifluoroethylene (TrFE) affords hydrofluoronickelacyclopentanes LNi(CFH) 2a-e (L = PPh, P(O-o-tol), PPhMe, PPhMe, PMe). Fluorine NMR analysis of 2a-e demonstrates predominant formation of three (of the possible six) isomers upon oxidative cycloaddition of TrFE: the cis and trans head-tail isomers and the trans head-head isomer, where the CHF group is defined as the TrFE "head". The respective ratios of LNi(CFH) isomers are influenced by the nature of L, with smaller phosphines favoring the thermodynamically preferred (from DFT calculations) trans head-head isomer (cf.

Brønsted acid-promoted C-F bond activation in [P,S]-ligated neutral and anionic perfluoronickelacyclopentanes.

Treatment of L2Ni(CF2)44a-c (L = PPh3, PPh2Me, pyridine) with an external Lewis acid (trimethylsilyl triflate) gives new L-functionalized fluoronickelacyclopentanes 5a-c. Complexes L2Ni(CF2)44a,b react with the thiol form of the bidentate ligand 1,2,4-(HS)(Ph2P)Me(C6H3) [P,SH] through a unique Brønsted acid-promoted Cα-F bond activation mechanism, affording phosphine-functionalized nickelacycles bearing a phosphinothiolate ligand 6a-b. Furthermore, substituting monodentate ligands in L2Ni(CF2)44a-c with the deprotonated form of the bidentate ligand [P,S(-)] leads to the first anionic perfluoronickelacycle 7.

Adapting bioinformatics curricula for big data.

Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data.

[Women's representations and experiences with vaginal and cesarean delivery in public and private maternity hospitals].

This study analyzes the different representations and experiences of women from different social classes, including issues related to their relations with hospital staff in different institutional settings. This qualitative study focused on women who had experienced both types of delivery, in three maternity hospitals in Rio de Janeiro, Brazil (one public, one fully private, and another private under an outsourcing agreement with the public health system). The study showed that variations in public and private service models result in different types of delivery care and different relations with staff, and are reflected in different birthing experiences for the women.

[Marketizing of the State, erosion of democracy and impoverishment of citizenship: global tendencies?].

This article analyses the advance of the neo-liberal regime, in order to contextualise the international formulation of policies focussed on poverty reduction. In recent debates, terms such as 'citizenship' and 'democracy' have been subject to critical scrutiny, revealing changes in the relations between citizens and the State which accompany the hegemony of economic criteria that put financial considerations at the centre of national states. We argue that analyses of such global processes require an ample political economy perspective, capable of illuminating how the substance of democracy and the legitimacy of state authority have been conditioned by the advance of new global entities that represent the interests of capital, favouring the concentration of wealth and the increase of poverty, inequality and exclusion, and installing a state of vital insecurity that affects the majority of the world's population.

Factors associated with cesarean sections in a public hospital in Rio de Janeiro, Brazil.

Brazil has one of the world's highest cesarean section rates. Contributing factors include the organization of obstetric practice, physicians' attitudes, and women's preferences and decisions. This study aimed to identify factors associated with cesarean sections in a public maternity hospital in Rio de Janeiro.

[Quality of birth care in maternity hospitals of Rio de Janeiro, Brazil].

Objective: To evaluate the quality of birth care based on the World Health Organization guidelines.

Methods: A case-control study was carried out in a public and a private maternity hospitals contracted by the Brazilian Health System in the city of Rio de Janeiro, Brazil, from October 1998 to March 1999. The sample comprised 461 women in the public maternity hospital (230 vaginal deliveries and 231 Cesarean sections) and 448 women in the private one (224 vaginal deliveries and 224 Cesarean sections).

[Violence in conjugal relations: concealing and taking sexual violence for granted].

This article presents the results of a qualitative study of women who had filed complaints of domestic violence, situating gender relations in a broader context. The authors focus on the meaning ascribed to sexual coercion in violent relations, suggesting that conjugal sexual violence is related to the perverse effects of changes in the sexual division of labor and the aggravated double demands on women from housework and the workplace, in relation to the dismantling of the male's role as provider in situations of poverty. In this context, women's refusal to engage in sex (a form of resistance which expresses their desire to be sexual protagonists and communicates disappointment with their partners) can be seen as contributing to the exacerbation of conjugal violence.

Mandibular adaptive reposturing: the etiology of a common and multifaceted autodestructive syndrome.

Maximum dental intercuspation (MI) is directed through sensory feedback from periodontal proprioceptors and is a neuromuscularly favored and protective mandibular position for the dentition. MI literally drives the stomatognathic system. When MI and centric relation (CR) are not in harmony, the mandible assumes adaptive reposturing in an effort to achieve as much MI as mechanically possible.

[Cesarean sections: who wants them and under what circumstances?].

Brazil has extremely high cesarean rates. Among related factors, it has been suggested that a "culture of cesarean childbirth" (or a preference for this type of delivery) exists among Brazilian women. Our study investigates this notion.

[Cooperation and conflict in childbirth care: representations and practices of nurses and obstetricians].

In Brazil, where birthing generally occurs in hospitals and under the care of obstetricians, the incorporation of nurses is a strategy that has been used recently in an attempt to improve obstetric care. This study, conducted in two maternity hospitals in Rio de Janeiro, focuses on representations of obstetricians and nurses regarding teamwork and analyzes how the dimensions of power, cooperation/conflict, and technical autonomy are permeated by dualistic conceptions which influence the quality of health care for women during childbirth. On the one hand, the results show a consensus regarding the advantages of professional cooperation in the improvement of health care, assuming the existence of a clear definition of professional roles.

[Poverty, inequality, and equity in health: considerations based on a transversal gender perspective].

This article discusses the modernization of gender inequalities which has occurred in Brazil in the last 20 years under the hegemony of neo-liberal macro-economic policies. A concept of gender as transversal is applied to questions of reproductive health (contraception and abortion, prenatal care and birthing, adolescent pregnancy, maternal and reproductive mortality, STIs/AIDS, and violence, among others), permitting analysis by both gender and social class. The history of the PAISM (Program for Integral Health Care for Women), on the other hand, reveals the complex articulation of this national public health program which, although strongly influenced by the Brazilian women's movement, has been infiltrated by heterogeneous interests in the international context.