Testing And Data Recovery Excavations At The Jayroe Site (41HM51), Hamilton County, Texas

In 2003–2004, Prewitt and Associates, Inc., performed National Register of Historic Places testing and subsequent data recovery excavations at the Jayroe site (41HM51) in Hamilton County for the Texas Department of Transportation, Environmental Affairs Division, under Texas Antiquities Permit Nos. 3211 and 3405. The investigations were prompted by the planned replacement of the County Road 294 bridge at the Leon River (CSJ No. 0909-29-030), in compliance with Section 106 of the National Historic Preservation Act and its implementing regulations (36 CFR Part 800) and the Antiquities Code of Texas. Testing consisted of the excavation of 6 backhoe trenches and 19 test units, and the data recovery work consisted mainly of hand excavation of 153 contiguous 1x1-m units within a single block, with 2 backhoe trenches and 2 manual units apart from the block excavation. Combined, the testing and data recovery identified 16 cultural features interpreted as 3 open hearths, 4 shallow earth ovens or surface hearths, 8 scatters of various kinds of debris, and 1 knapping station. The excavations recovered 322 chipped stone tools, 26 cores, 6,589 pieces of unmodified debitage, 21 ground or battered stone tools, 38 potential pigment sources, 43 ceramic sherds, 15 modified bone artifacts, 7,649 animal bones, 1,200 mussel shells, and macrobotanical remains. Four analytical units are defined for the site, only one of which—the Toyah phase component— has much interpretive potential. It is interpreted as a campsite used at least several times, mostly in the a.d. 1470s, at which butchering of mostly bison and deer, late-stage lithic tool manufacture and repair, and other maintenance tasks figured prominently in the site activities. The artifacts recovered and records generated by the project are curated at the Center for Archaeological Studies, Texas State University

Sources and resources: importance of nutrients, resource allocation, and ecology in microalgal cultivation for lipid accumulation

Regardless of current market conditions and availability of conventional petroleum sources, alternatives are needed to circumvent future economic and environmental impacts from continued exploration and harvesting of conventional hydrocarbons. Diatoms and green algae (microalgae) are eukaryotic photoautotrophs that can utilize inorganic carbon (e.g., CO2) as a carbon source and sunlight as an energy source, and many microalgae can store carbon and energy in the form of neutral lipids. In addition to accumulating useful precursors for biofuels and chemical feed stocks, the use of autotrophic microorganisms can further contribute to reduced CO2 emissions through utilization of atmospheric CO2. Because of the inherent connection between carbon, nitrogen, and phosphorus in biological systems, macronutrient deprivation has been proven to significantly enhance lipid accumulation in different diatom and algae species. However, much work is needed to understand the link between carbon, nitrogen, and phosphorus in controlling resource allocation at different levels of biological resolution (cellular versus ecological). An improved understanding of the relationship between the effects of N, P, and micronutrient availability on carbon resource allocation (cell growth versus lipid storage) in microalgae is needed in conjunction with life cycle analysis. This mini-review will briefly discuss the current literature on the use of nutrient deprivation and other conditions to control and optimize microalgal growth in the context of cell and lipid accumulation for scale-up processes

HIV/AIDS, Food Supplementation and Livelihood Programs in Uganda: A Way Forward?

BACKGROUND: Over the last decade, health, nutrition and policy experts have become increasingly aware of the many ways in which food insecurity and HIV infection negatively impact and reinforce one another. In response, many organizations providing HIV care began supplying food aid to clients in need. Food supplementation, however, was quickly recognized as an unsustainable and incomplete intervention. Many HIV care organizations therefore developed integrated HIV and livelihood programs (IHLPs) to target the root causes of food insecurity. METHODS AND FINDINGS: We conducted a qualitative study using in-depth interviews with 21 key informants who worked at seven organizations providing HIV care, food aid, or IHLPs in Kampala, Uganda in 2007-2008 to better understand the impact of IHLPs on the well-being of people living with HIV and AIDS (PLWHAs) and the challenges in transitioning clients from food aid to IHLPs. There was strong consensus among those interviewed that IHLPs are an important intervention in addressing food insecurity and its adverse health consequences among PLWHAs. Key informants identified three main challenges in transitioning PLWHAs from food supplementation programs to IHLPs: (1) lack of resources (2) timing of the transition and (3) logistical considerations including geography and weather. Factors seen as contributing to the success of programs included: (1) close involvement of community leaders (2) close ties with local and national government (3) diversification of IHLP activities and (4) close integration with food supplementation programs, all linked through a central program of HIV care. CONCLUSION: Health, policy and development experts should continue to strengthen IHLPs for participants in need. Further research is needed to determine when and how participants should be transitioned from food supplementation to IHLPs, and to determine how to better correlate measures of food insecurity with objective clinical outcomes so as to better evaluate program results

Elevated Hepcidin Is Part of a Complex Relation That Links Mortality with Iron Homeostasis and Anemia in Men and Women with HIV Infection.

BACKGROUND: Early and chronic inflammation is a hallmark of HIV infection, and inflammation is known to increase hepcidin expression. Consequently, hepcidin may be a key determinant of the iron homeostasis and anemia associated with poorer HIV prognoses. OBJECTIVE: The objective of this study was to understand how hepcidin is related to anemia, iron homeostasis, and inflammation at HIV diagnosis and to investigate associations between hepcidin and all-cause mortality in HIV infection. METHODS: In a retrospective cohort, baseline plasma hepcidin was measured by competitive enzyme immunoassay within 3 mo of HIV diagnosis in 196 antiretroviral-naive Gambians. Iron homeostasis [hemoglobin, plasma transferrin, ferritin, iron, soluble transferrin receptor (sTfR)] and inflammation [α1-antichymotrypsin (ACT)] from the same plasma sample were available, as were absolute CD4 cell counts, age, gender, body mass index (BMI), and HIV type. RESULTS: Anemia was common across the spectrum of immunosuppression [CD4 cell counts (prevalence of anemia): >500 cells/μL (68%), 200-500 cells/μL (73%), and <200 cells/μL (89%); P = 0.032] and in men (81%) and women (76%). Increasing hepcidin was associated with iron homeostasis biomarkers (higher ferritin and lower transferrin, hemoglobin, and sTfR), inflammation (higher ACT), and key health indicators (lower CD4 or BMI, advancing age, and male gender; P < 0.001 except for hemoglobin, P = 0.021). Elevated hepcidin was associated with greater all-cause mortality in a dose-dependent manner [intermediate vs. lowest tertile: unadjusted HR (95% CI), 1.95 (1.22, 3.10); upper vs. lowest tertile: 3.02 (1.91, 4.78)]. Principal components analysis identified 2 patterns composed of hepcidin-ferritin-transferrin, with or without ACT, and iron-sTfR-hemoglobin that may distinguish inflammation and erythropoiesis iron functions. CONCLUSIONS: Elevated hepcidin is independently associated with greater mortality in men and women with HIV infection, and hepcidin is also part of a complex relation linking iron homeostasis, anemia, and HIV. Understanding the mechanisms and role of hepcidin modulation may further guide evidence-based interventions needed to counter detrimental iron homeostasis and anemia in HIV infection

Food Insufficiency Is Associated with High-Risk Sexual Behavior among Women in Botswana and Swaziland

In a cross-sectional study, Sheri Weiser and colleagues found that food insufficiency was an important risk factor for increased sexual risk-taking in women in Botswana and Swaziland

Food Insecurity and Sexual Risk in an HIV Endemic Community in Uganda

Food insecurity has been linked to high-risk sexual behavior in sub-Saharan Africa, but there are limited data on these links among people living with HIV/AIDS, and on the mechanisms for how food insecurity predisposes individuals to risky sexual practices. We undertook a series of in-depth open-ended interviews with 41 individuals living with HIV/AIDS to understand the impact of food insecurity on sexual-risk behaviors. Participants were recruited from the Immune Suppression Clinic at the Mbarara University of Science and Technology in Mbarara, Uganda. Interviews were recorded, transcribed verbatim, translated, and coded following the strategy of grounded theory. Four major themes emerged from the interview data: the relationship between food insecurity and transactional sex for women; the impact of a husband’s death from HIV on worsening food insecurity among women and children; the impact of food insecurity on control over condom use, and the relationship between food insecurity and staying in violent/abusive relationships. Food insecurity led to increased sexual vulnerability among women. Women were often compelled to engage in transactional sex or remain in violent or abusive relationships due to their reliance on men in their communities to provide food for themselves and their children. There is an urgent need to prioritize food security programs for women living with HIV/AIDS and address broader gender-based inequities that are propelling women to engage in risky sexual behaviors based on hunger. Such interventions will play an important role in improving the health and well-being of people living with HIV/AIDS, and preventing HIV transmission

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

BACKGROUND: We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. RESULTS: We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. CONCLUSION: Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses

Peri-conception and first trimester diet modifies reproductive development in bulls

Nutritional perturbation during gestation alters male reproductive development in rodents and sheep. In cattle both the developmental trajectory of the feto–placental unit and its response to dietary perturbations is dissimilar to that of these species. This study examined the effects of dietary protein perturbation during the peri-conception and first trimester periods upon reproductive development in bulls. Nulliparous heifers (n = 360) were individually fed a high- or low-protein diet (HPeri and LPeri) from 60 days before conception. From 24 until 98 days post conception, half of each treatment group changed to the alternative post-conception high- or low-protein diet (HPost and LPost) yielding four treatment groups in a 2 × 2 factorial design. A subset of male fetuses (n = 25) was excised at 98 days post conception and fetal testis development was assessed. Reproductive development of singleton male progeny (n = 40) was assessed until slaughter at 598 days of age, when adult testicular cytology was evaluated. Low peri-conception diet delayed reproductive development: sperm quality was lowered during pubertal development with a concomitant delay in reaching puberty. These effects were subsequent to lower FSH concentrations at 330 and 438 days of age. In the fetus, the low peri-conception diet increased the proportion of seminiferous tubules and decreased blood vessel area in the testis, whereas low first trimester diet increased blood vessel number in the adult testis. We conclude that maternal dietary protein perturbation during conception and early gestation may alter male testis development and delay puberty in bulls