The internal structure and composition of a plate-boundary-scale serpentinite shear zone: the Livingstone Fault, New Zealand

Abstract. Deciphering the internal structure and composition of large serpentinite-dominated shear zones will lead to an improved understanding of the rheology of the lithosphere in a range of tectonic settings. The Livingstone Fault in New Zealand is a terrane-bounding structure that separates the basal portions (peridotite; serpentinised peridotite; metagabbros) of the Dun Mountain Ophiolite Belt from the quartzofeldspathic schists of the Caples and Aspiring Terrane. Field and microstructural observations from 11 localities along a strike length of ca. 140 km show that the Livingstone Fault is a steeply dipping, serpentinite-dominated shear zone tens of metres to several hundred metres wide. The bulk shear zone has a pervasive scaly fabric that wraps around fractured and faulted pods of massive serpentinite, rodingite and partially metasomatised quartzofeldspathic schist up to a few tens of metres long. S–C fabrics and lineations in the shear zone consistently indicate a steep east-side-up shear sense, with significant local dispersion in kinematics where the shear zone fabrics wrap around pods. The scaly fabric is dominated (>98 % vol) by fine-grained (≪10 µm) fibrous chrysotile and lizardite–polygonal serpentine, but infrequent (<1 % vol) lenticular relicts of antigorite are also preserved. Dissolution seams and foliation surfaces enriched in magnetite, as well as the widespread growth of fibrous chrysotile in veins and around porphyroclasts, suggest that bulk shear zone deformation involved pressure–solution. Syn-kinematic metasomatic reactions occurred along all boundaries between serpentinite, schist and rodingite, forming multigenerational networks of nephritic tremolite veins that are interpreted to have caused reaction hardening within metasomatised portions of the shear zone. We propose a conceptual model for plate-boundary-scale serpentinite shear zones which involves bulk-distributed deformation by pressure–solution creep, accompanied by a range of physical (e.g. faulting in pods and wall rocks; smearing of magnetite along fault surfaces) or chemical (e.g. metasomatism) processes that result in localised brittle deformation within creeping shear zone segments

Crystallographic orientation mapping of lizardite serpentinite by Raman spectroscopy

The serpentine mineral lizardite displays strong Raman anisotropy in the OH-stretching region, resulting in significant wavenumber shifts (up to ca. 14.5 cm−1) that depend on the orientation of the impinging excitation laser relative to the crystallographic axes. We quantified the relationship between crystallographic orientation and Raman wavenumber using well-characterised samples of Monte Fico lizardite by applying Raman spectroscopy and electron backscatter diffraction (EBSD) mapping on thin sections of polycrystalline samples and grain mounts of selected single crystals, as well as by a spindle stage Raman study of an oriented cylinder drilled from a single crystal. We demonstrate that the main band in the OH-stretching region undergoes a systematic shift that depends on the inclination of the c-axis of the lizardite crystal. The data are used to derive an empirical relationship between the position of this main band and the c-axis inclination of a measured lizardite crystal: y=14.5cos 4 (0.013x+0.02)+(3670±1), where y is the inclination of the c-axis with respect to the normal vector (in degrees), and x is the main band position (wavenumber in cm −1) in the OH-stretching region. This new method provides a simple and cost-effective technique for measuring and quantifying the crystallographic orientation of lizardite-bearing serpentinite fault rocks, which can be difficult to achieve using EBSD alone. In addition to the samples used to determine the above empirical relationship, we demonstrate the applicability of the technique by mapping the orientations of lizardite in a more complex sample of deformed serpentinite from Elba Island, Italy.publishedVersio

ATM Limits Incorrect End Utilization during Non-Homologous End Joining of Multiple Chromosome Breaks

Chromosome rearrangements can form when incorrect ends are matched during end joining (EJ) repair of multiple chromosomal double-strand breaks (DSBs). We tested whether the ATM kinase limits chromosome rearrangements via suppressing incorrect end utilization during EJ repair of multiple DSBs. For this, we developed a system for monitoring EJ of two tandem DSBs that can be repaired using correct ends (Proximal-EJ) or incorrect ends (Distal-EJ, which causes loss of the DNA between the DSBs). In this system, two DSBs are induced in a chromosomal reporter by the meganuclease I-SceI. These DSBs are processed into non-cohesive ends by the exonuclease Trex2, which leads to the formation of I-SceI–resistant EJ products during both Proximal-EJ and Distal-EJ. Using this method, we find that genetic or chemical disruption of ATM causes a substantial increase in Distal-EJ, but not Proximal-EJ. We also find that the increase in Distal-EJ caused by ATM disruption is dependent on classical non-homologous end joining (c-NHEJ) factors, specifically DNA-PKcs, Xrcc4, and XLF. We present evidence that Nbs1-deficiency also causes elevated Distal-EJ, but not Proximal-EJ, to a similar degree as ATM-deficiency. In addition, to evaluate the roles of these factors on end processing, we examined Distal-EJ repair junctions. We found that ATM and Xrcc4 limit the length of deletions, whereas Nbs1 and DNA-PKcs promote short deletions. Thus, the regulation of end processing appears distinct from that of end utilization. In summary, we suggest that ATM is important to limit incorrect end utilization during c-NHEJ

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.National Institute of Allergy and Infectious Diseases (U.S.)National Institutes of Health. Department of Health and Human Services (contract HHSN266200400001C)National Institutes of Health. Department of Health and Human Services(contract HHSN2722009000018C)Brazil. National Council for Scientific and Technological Developmen

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Distinguishing the Raman spectrum of polygonal serpentine

Positively identifying serpentine mineral types is important for a wide range of disciplines in the Earth sciences and health sciences. Although Raman spectroscopy has been widely applied as a tool to distinguish four of the main serpentine minerals (i.e., antigorite, lizardite, chrysotile, and polygonal serpentine), some uncertainty remains as to whether all four varieties have unique Raman spectra. In this paper, submicron Raman spectroscopy mapping was performed directly on electron-transparent regions of serpentine samples that were unambiguously identified by transmission electron microscopy (TEM). The increased spatial resolution of the Raman mapping technique (~370 nm), combined with the detailed characterization provided by TEM, indicates that polygonal serpentine has the same Raman spectrum as lizardite and therefore cannot be spectrally distinguished from lizardite. Furthermore, the Raman spectral profile that has previously been reported as unique to polygonal serpentine is likely to represent a mixture of chrysotile and polygonal serpentine/lizardite. To positively discriminate between lizardite and polygonal serpentine requires TEM investigation

Structural disorder of graphite and implications for graphite thermometry

Graphitization, or the progressive maturation of carbonaceous material, is considered an irreversible process. Thus, the degree of graphite crystallinity, or its structural order, has been calibrated as an indicator of the peak metamorphic temperatures experienced by the host rocks. However, discrepancies between temperatures indicated by graphite crystallinity versus other thermometers have been documented in deformed rocks. To examine the possibility of mechanical modifications of graphite structure and the potential impacts on graphite thermometry, we performed laboratory deformation experiments. We sheared highly crystalline graphite powder at normal stresses of 5 and 25  megapascal (MPa) and aseismic velocities of 1, 10 and 100 µm s−1. The degree of structural order both in the starting and resulting materials was analyzed by Raman microspectroscopy. Our results demonstrate structural disorder of graphite, manifested as changes in the Raman spectra. Microstructural observations show that brittle processes caused the documented mechanical modifications of the aggregate graphite crystallinity. We conclude that the calibrated graphite thermometer is ambiguous in active tectonic settings

Crystallographic orientation mapping of lizardite serpentinite by Raman spectroscopy

The serpentine mineral lizardite displays strong Raman anisotropy in the OH-stretching region, resulting in significant wavenumber shifts (up to ca. 14.5 cm−1) that depend on the orientation of the impinging excitation laser relative to the crystallographic axes. We quantified the relationship between crystallographic orientation and Raman wavenumber using well-characterised samples of Monte Fico lizardite by applying Raman spectroscopy and electron backscatter diffraction (EBSD) mapping on thin sections of polycrystalline samples and grain mounts of selected single crystals, as well as by a spindle stage Raman study of an oriented cylinder drilled from a single crystal. We demonstrate that the main band in the OH-stretching region undergoes a systematic shift that depends on the inclination of the c-axis of the lizardite crystal. The data are used to derive an empirical relationship between the position of this main band and the c-axis inclination of a measured lizardite crystal: y=14.5cos 4 (0.013x+0.02)+(3670±1), where y is the inclination of the c-axis with respect to the normal vector (in degrees), and x is the main band position (wavenumber in cm −1) in the OH-stretching region. This new method provides a simple and cost-effective technique for measuring and quantifying the crystallographic orientation of lizardite-bearing serpentinite fault rocks, which can be difficult to achieve using EBSD alone. In addition to the samples used to determine the above empirical relationship, we demonstrate the applicability of the technique by mapping the orientations of lizardite in a more complex sample of deformed serpentinite from Elba Island, Italy

Higher religiosity and spirituality are associated with ethnic group membership among middle-aged and older adults living with HIV.

Background: HIV is a chronic illness that impacts the lives of more than 1 million people in the United States. As persons living with HIV (PWH) are living longer, it is important to understand the influence that religiosity/spirituality has among middle-aged and older PWH.Objective: Compare the degree of religiosity/spirituality among middle-aged and older PWH and HIV-negative individuals, and to identify demographic, clinical, and psychosocial factors associated with religiosity/spirituality among PWH.Method: Baseline data on 122 PWH and 92 HIV-negative individuals (ages 36-65 years; 61.1% Non-Hispanic White) from a longitudinal study were analyzed for the current study. Recruitment occurred through HIV treatment clinics and community organizations in San Diego. Participants completed questionnaires on religiosity, spirituality, and psychosocial functioning. Independent samples t-tests, Pearson correlations, and multiple linear regression analyses were conducted to test the study objective.Results: No significant differences in religiosity/spirituality were found between PWH and HIV-negative individuals. Demographic and psychosocial variables were unrelated to religiously/spirituality among HIV-negative individuals. Among PWH, multiple linear regression models indicated higher daily spirituality was significantly associated with racial/ethnic minority membership (Hispanic/Latino, African American/Black, or Other), fewer years of estimated duration of HIV, greater social support, and higher grit. Greater engagement in private religious practices was significantly associated with racial/ethnic minority membership and higher social support.Conclusions: For PWH, being a racial/ethnic minority and having higher social support was associated with greater engagement in religious/spiritual practices. Future longitudinal studies should examine whether religion/spirituality impacts well-being across the lifespan among racial/ethnic minority groups of PWH