On the use of Li isotopes as a proxy for water–rock interaction in fractured crystalline rocks: a case study from the Gotthard rail base tunnel

We present Li isotope measurements of groundwater samples collected during drilling of the 57 km long Gotthard rail base tunnel in Switzerland, to explore the use of Li isotope measurements for tracking water–rock interactions in fractured crystalline rocks at temperatures of up to 43 °C. The 17 groundwater samples originate from water-conducting fractures within two specific crystalline rock units, which are characterized by a similar rock mineralogy, but significantly different fluid composition. In particular, the aqueous Li concentrations observed in samples from the two units vary from 1–4 mg/L to 0.01–0.02 mg/L. Whereas δ7Li values from the unit with high Li concentrations are basically constant (δ7Li = 8.5–9.1‰), prominent variations are recorded for the samples from the unit with low Li concentrations (δ7Li = 10–41‰). This observation demonstrates that Li isotope fractionation can be highly sensitive to aqueous Li concentrations. Moreover, δ7Li values from the unit with low Li concentrations correlate well with reaction progress parameters such as pH and [Li]/[Na] ratios, suggesting that δ7Li values are mainly controlled by the residence time of the fracture groundwater. Consequently, 1D reactive transport modeling was performed to simulate mineral reactions and associated Li isotope fractionation along a water-conducting fracture system using the code TOUGHREACT. Modeling results confirm the residence time hypothesis and demonstrate that the absence of δ7Li variation at high Li concentrations can be well explained by limitation of the amount of Li that is incorporated into secondary minerals. Modeling results also suggest that Li uptake by kaolinite forms the key process to cause Li isotope fractionation in the investigated alkaline system (pH >9), and that under slow flow conditions (<10 m/year), this process is associated with a very large Li isotope fractionation factor (ε ≈ −50‰). Moreover, our simulations demonstrate that for simple and well-defined systems with known residence times and low Li concentrations, δ7Li values may help to quantify mineral reaction rates if more thermodynamic data about the temperature-dependent incorporation of Li in secondary minerals as well as corresponding fractionation factors become available in the future. In conclusion, δ7Li values may be a powerful tool to track water–rock interaction in fractured crystalline rocks at temperature higher than those at the Earth’s surface, although their use is restricted to low Li concentrations and well defined flow systems

Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data

BACKGROUND: The Affymetrix technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies. However, changes in gene expression levels are not the only way to link genes and disease. The existence of gene isoforms specifically linked with cancer or apoptosis is increasingly found in literature. Hence it is of great interest to associate the results of a gene expression study with updated evidences on the transcript structure and its possible variants. RESULTS: We present here a web-based software tool, Splicy, whose primary task is to retrieve data on the mapping of Affymetrix probes to single exons of gene transcripts and displaying graphically this information projected on the gene physical structure.Starting from a list of Affymetrix probesets the program produces a series of graphical displays, each relative to a transcript associated with the gene targeted by a given probe. The information on the transcript-by-transcript and exon-by-exon mapping of probe pairs can be retrieved both graphically and in the form of tab-separated files. The mapping of single probes to NCBI RefSeq or EMBL cDNAs is handled by the ISREC mapping tables used in the CleanEx Expression Reference Database Project. We currently maintain these mappings for most popular human and mouse Affymetrix chips, and Splicy can be queried for matches with human and mouse NCBI RefSeq or EMBL cDNAs. CONCLUSION: Splicy generates probeset annotations and images describing the relation between the single probes and intron/exon structure of the target transcript in all its known variants. We think that Splicy will be useful for giving to the researcher a clearer picture of the possible transcript variants linked with a given gene and an additional view on the interpretation of microarray experiment data. Splicy is publicly available and has been realized in the framework of a bioinformatics grant from the Italian Cancer Research Association

EVORA: Deep Evidential Traversability Learning for Risk-Aware Off-Road Autonomy

Traversing terrain with good traction is crucial for achieving fast off-road navigation. Instead of manually designing costs based on terrain features, existing methods learn terrain properties directly from data via self-supervision, but challenges remain to properly quantify and mitigate risks due to uncertainties in learned models. This work efficiently quantifies both aleatoric and epistemic uncertainties by learning discrete traction distributions and probability densities of the traction predictor's latent features. Leveraging evidential deep learning, we parameterize Dirichlet distributions with the network outputs and propose a novel uncertainty-aware squared Earth Mover's distance loss with a closed-form expression that improves learning accuracy and navigation performance. The proposed risk-aware planner simulates state trajectories with the worst-case expected traction to handle aleatoric uncertainty, and penalizes trajectories moving through terrain with high epistemic uncertainty. Our approach is extensively validated in simulation and on wheeled and quadruped robots, showing improved navigation performance compared to methods that assume no slip, assume the expected traction, or optimize for the worst-case expected cost.Comment: Under review. Journal extension for arXiv:2210.00153. Project website: https://xiaoyi-cai.github.io/evora

Unsafe Sex and Increased Incidence of Hepatitis C Virus Infection among HIV-Infected Men Who Have Sex with Men: The Swiss HIV Cohort Study

Background. Data on the incidence of hepatitis C virus (HCV) infection among human immunodeficiency virus (HIV)-infected persons are sparse. It is controversial whether and how frequently HCV is transmitted by unprotected sexual intercourse. Methods. We assessed the HCV seroprevalence and incidence of HCV infection in the Swiss HIV Cohort Study between 1988 and 2004. We investigated the association of HCV seroconversion with mode of HIV acquisition, sex, injection drug use (IDU), and constancy of condom use. Data on condom use or unsafe sexual behavior were prospectively collected between 2000 and 2004. Results. The overall seroprevalence of HCV infection was 33% among a total of 7899 eligible participants and 90% among persons reporting IDU. We observed 104 HCV seroconversions among 3327 participants during a total follow-up time of 16,305 person-years, corresponding to an incidence of 0.64 cases per 100 person-years. The incidence among participants with a history of IDU was 7.4 cases per 100 person-years, compared with 0.23 cases per 100 person-years in patients without such a history (P < .001). In men who had sex with men (MSM) without a history of IDU who reported unsafe sex, the incidence was 0.7 cases per 100 person-years, compared with 0.2 cases per 100 person-years in those not reporting unsafe sex (P = .02), corresponding to an incidence rate ratio of 3.5 (95% confidence interval, 1.2-10.0). The hazard of acquiring HCV infection was elevated among younger participants who were MSM. Conclusions. HCV infection incidence in the Swiss HIV Cohort Study was mainly associated with IDU. In HIV-infected MSM, HCV infection was associated with unsafe se

Latent Tuberculosis and Active Tuberculosis Disease Rates among the Homeless, New York, New York, USA, 1992–2006

We conducted a retrospective study to examine trends in latent tuberculosis infection (LTBI) and TB disease rates among homeless persons in shelters in New York, NY, 1992–2006. Although TB case rates fell from 1,502/100,000 population to 0, a 31% LTBI rate in 2006 shows the value of identifying and treating TB in the homeless

Comparing multiple competing interventions in the absence of randomized trials using clinical risk-benefit analysis

<p>Abstract</p> <p>Background</p> <p>To demonstrate the use of risk-benefit analysis for comparing multiple competing interventions in the absence of randomized trials, we applied this approach to the evaluation of five anticoagulants to prevent thrombosis in patients undergoing orthopedic surgery.</p> <p>Methods</p> <p>Using a cost-effectiveness approach from a clinical perspective (i.e. risk benefit analysis) we compared thromboprophylaxis with warfarin, low molecular weight heparin, unfractionated heparin, fondaparinux or ximelagatran in patients undergoing major orthopedic surgery, with sub-analyses according to surgery type. Proportions and variances of events defining risk (major bleeding) and benefit (thrombosis averted) were obtained through a meta-analysis and used to define beta distributions. Monte Carlo simulations were conducted and used to calculate incremental risks, benefits, and risk-benefit ratios. Finally, net clinical benefit was calculated for all replications across a range of risk-benefit acceptability thresholds, with a reference range obtained by estimating the case fatality rate - ratio of thrombosis to bleeding.</p> <p>Results</p> <p>The analysis showed that compared to placebo ximelagatran was superior to other options but final results were influenced by type of surgery, since ximelagatran was superior in total knee replacement but not in total hip replacement.</p> <p>Conclusions</p> <p>Using simulation and economic techniques we demonstrate a method that allows comparing multiple competing interventions in the absence of randomized trials with multiple arms by determining the option with the best risk-benefit profile. It can be helpful in clinical decision making since it incorporates risk, benefit, and personal risk acceptance.</p

Substituting abacavir for hyperlipidemia-associated protease inhibitors in HAART regimens improves fasting lipid profiles, maintains virologic suppression, and simplifies treatment

BACKGROUND: Hyperlipidemia secondary to protease inhibitors (PI) may abate by switching to anti-HIV medications without lipid effects. METHOD: An open-label, randomized pilot study compared changes in fasting lipids and HIV-1 RNA in 104 HIV-infected adults with PI-associated hyperlipidemia (fasting serum total cholesterol >200 mg/dL) who were randomized either to a regimen in which their PI was replaced by abacavir 300 mg twice daily (n = 52) or a regimen in which their PI was continued (n = 52) for 28 weeks. All patients had undetectable viral loads (HIV-1 RNA <50 copies/mL) at baseline and were naïve to abacavir and non-nucleoside reverse transcriptase inhibitors. RESULTS: At baseline, the mean total cholesterol was 243 mg/dL, low density lipoprotein (LDL)-cholesterol 149 mg/dL, high density lipoprotein (HDL)-cholesterol 41 mg/dL, and triglycerides 310 mg/dL. Mean CD4+ cell counts were 551 and 531 cells/mm(3 )in the abacavir-switch and PI-continuation arms, respectively. At week 28, the abacavir-switch arm had significantly greater least square mean reduction from baseline in total cholesterol (-42 vs -10 mg/dL, P < 0.001), LDL-cholesterol (-14 vs +5 mg/dL, P = 0.016), and triglycerides (-134 vs -36 mg/dL, P = 0.019) than the PI-continuation arm, with no differences in HDL-cholesterol (+0.2 vs +1.3 mg/dL, P = 0.583). A higher proportion of patients in the abacavir-switch arm had decreases in protocol-defined total cholesterol and triglyceride toxicity grades, whereas a smaller proportion had increases in these toxicity grades. At week 28, an intent-to treat: missing = failure analysis showed that the abacavir-switch and PI-continuation arms did not differ significantly with respect to proportion of patients maintaining HIV-1 RNA <400 or <50 copies/mL or adjusted mean change from baseline in CD4+ cell count. Two possible abacavir-related hypersensitivity reactions were reported. No significant changes in glucose, insulin, insulin resistance, C-peptide, or waist-to-hip ratios were observed in either treatment arm, nor were differences in these parameters noted between treatments. CONCLUSION: In hyperlipidemic, antiretroviral-experienced patients with HIV-1 RNA levels <50 copies/mL and CD4+ cell counts >500 cells/mm(3), substituting abacavir for hyperlipidemia-associated PIs in combination antiretroviral regimens improves lipid profiles and maintains virologic suppression over a 28-week period, and it simplifies treatment

Origin of Minority Drug-Resistant HIV-1 Variants in Primary HIV-1 Infection

Background. Drug-resistant human immunodeficiency virus type 1 (HIV-1) minority variants (MVs) are present in some antiretroviral therapy (ART)-naive patients. They may result from de novo mutagenesis or transmission. To date, the latter has not been proven. Methods. MVs were quantified by allele-specific polymerase chain reaction in 204 acute or recent seroconverters from the Zurich Primary HIV Infection study and 382 ART-naive, chronically infected patients. Phylogenetic analyses identified transmission clusters. Results. Three lines of evidence were observed in support of transmission of MVs. First, potential transmitters were identified for 12 of 16 acute or recent seroconverters harboring M184V MVs. These variants were also detected in plasma and/or peripheral blood mononuclear cells at the estimated time of transmission in 3 of 4 potential transmitters who experienced virological failure accompanied by the selection of the M184V mutation before transmission. Second, prevalence between MVs harboring the frequent mutation M184V and the particularly uncommon integrase mutation N155H differed highly significantly in acute or recent seroconverters (8.2% vs 0.5%; P < .001). Third, the prevalence of less-fit M184V MVs is significantly higher in acutely or recently than in chronically HIV-1-infected patients (8.2% vs 2.5%; P = .004). Conclusions. Drug-resistant HIV-1 MVs can be transmitted. To what extent the origin—transmission vs sporadic appearance—of these variants determines their impact on ART needs to be further explore