Lithogeochemistry, petrology, and the acid-generating potential of the Goldenville and Halifax groups and associated granitoid rocks in the metropolitan Halifax Regional Municipality, Nova Scotia, Canada

Detailed geological mapping of the Goldenville and Halifax groups in metropolitan Halifax Regional Municipality, Nova Scotia, resulted in two-fold subdivision of both groups. The Goldenville Group was divided into the metasand-stone (feldspathic wacke)-dominated Taylors Head formation and the overlying, metasiltstone-dominated, Mn-rich Beaverbank formation. The Halifax Group was divided into the Cunard formation, dominated by sulphide-rich slate, and the overlying Bluestone formation, consisting of mainly metasiltstone and metasandstone. Lithogeochemical and petrological studies resulted in the characterization of the Beaverbank, Cunard, and Bluestone formations as potential acid-producing units with pyrrhotite as the main iron-sulphide mineral. The presence of acid rock drainage (ARD) is governed by bulk-rock chemical composition and mineral assemblage. To test the predictability of ARD production, a portable XRF instrument was used to obtain relatively inexpensive whole-rock and sulphur data that were used in conjunction with conventional XRF analyses and acid-base accounting tests. Results from the three methods compare favourably. Use of the portable XRF instrument facilitates a timely and cost-effective approach to predicting ARD but does not replace the legally mandated acid-base accounting procedure. RÉSUMÉ Une cartographie géologique détaillée des groupes de Goldenville et de Halifax dans la municipalité régionale de Halifax, en Nouvelle-Écosse, a donné lieu à deux divisions de ces deux groupes. Pour ce qui est du groupe de Gold-enville, les deux formations suivantes ont été établies: la Formation de Taylors Head, composée principalement de métagrès (wacke feldspathique) et la Formation de Beaverbank sus‑jacente, composée principalement de métasiltite riche en Mn. En ce qui concerne le groupe de Halifax, les deux formations que voici ont été identifiées: la Formation de Cunard, composée principalement d’ardoise riche en sulfures, et la Formation de Bluestone sus‑jacente, composée surtout de métasiltite et de métagrès. Les études lithogéochimiques et pétrologiques ont permis d’établir que les Formations de Beaverbank, de Cunard et de Bluestone étaient susceptibles d’agir comme précurseurs acides, la pyrrhotite étant le principal minéral à sulfure de fer présent. La présence d’un drainage rocheux acide (DRA) est régie par la composition chimique de la roche brute et l’association minérale. Pour vérifier la possibilité d’un DRA, de concert avec des analyses traditionnelles à fluorescence X et de bilan acide-base, un appareil portatif à fluorescence X a été utilisé pour recueillir de manière relativement économique des données sur la roche brute et les sulfures. Les résultats obtenus par les trois méthodes se comparent bien. L’utilisation d’un appareil à fluorescence X portatif permet de prédire de manière économique et rapidement la possibilité du DRA, mais cette technique ne saurait se substituer à l’analyse du bilan acide-base prévue par la réglementation

Trapped-ion quantum error-correcting protocols using only global operations

Quantum error-correcting codes are many-body entangled states that are prepared and measured using complex sequences of entangling operations. Each element of such an entangling sequence introduces noise to delicate quantum information during the encoding or reading out of the code. It is important therefore to find efficient entangling protocols to avoid the loss of information. Here we propose an experiment that uses only global entangling operations to encode an arbitrary logical qubit to either the five-qubit repetition code or the five-qubit code, with a six-ion Coulomb crystal architecture in a Penning trap. We show that the use of global operations enables us to prepare and read out these codes using only six and ten global entangling pulses, respectively. The proposed experiment also allows the acquisition of syndrome information during readout. We provide a noise analysis for the presented protocols, estimating that we can achieve a six-fold improvement in coherence time with noise as high as $\sim 1\%$ on each entangling operation.Comment: 7 pages, 4 figures, published version, comments are welcom

Identifying psychiatric diagnosis from missing mood data through the use of log-signature features

The availability of mobile technologies has enabled the efficient collection of prospective longitudinal, ecologically valid self-reported clinical questionnaires from people with psychiatric diagnoses. These data streams have potential for improving the efficiency and accuracy of psychiatric diagnosis as well predicting future mood states enabling earlier intervention. However, missing responses are common in such datasets and there is little consensus as to how these should be dealt with in practice. In this study, the missing-response-incorporated log-signature method achieves roughly 74.8% correct diagnosis, with f1 scores for three diagnostic groups 66% (bipolar disorder), 83% (healthy control) and 75% (borderline personality disorder) respectively. This was superior to the naive model which excluded missing data and advanced models which implemented different imputation approaches, namely, k-nearest neighbours (KNN), probabilistic principal components analysis (PPCA) and random forest-based multiple imputation by chained equations (rfMICE). The log-signature method provided an effective approach to the analysis of prospectively collected mood data where missing data was common and should be considered as an approach in other similar datasets. Because of treating missing responses as a signal, its superiority also highlights that missing data conveys valuable clinical information

Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.

Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. By characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction

Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M

Association between critical care admission and 6-month functional outcome after spontaneous intracerebral haemorrhage

BACKGROUND: There is uncertainty about the clinical benefit of admission to critical care after spontaneous intracerebral haemorrhage (ICH). PURPOSE: We investigated factors associated with critical care admission after spontaneous ICH and evaluated associations between critical care and 6-month functional outcome. METHODS: We included 825 patients with acute spontaneous non-traumatic ICH, recruited to a prospective multicenter observational study. We evaluated the characteristics associated with critical care admission and poor 6-month functional outcome (modified Rankin Scale, mRS > 3) using univariable (chi-square test and Wilcoxon rank-sum test, as appropriate) and multivariable analysis. RESULTS: 286 patients (38.2%) had poor 6-month functional outcome. Seventy-seven (9.3%) patients were admitted to critical care. Patients admitted to critical care were younger (p < 0.001), had lower GCS score (p < 0.001), larger ICH volume (p < 0.001), more often had intraventricular extension (p = 0.008) and underwent neurosurgery (p < 0.001). Critical care admission was associated with poor functional outcome at 6 months (39/77 [50.7%] vs 286/748 [38.2%]; p = 0.034); adjusted OR 2.43 [95%CI 1.36-4.35], p = 0.003), but not with death (OR 1.29 [95%CI 0.71-2.35; p = 0.4). In ordinal logistic regression, patients admitted to critical care showed an OR 1.47 (95% CI 0.98-2.20; p = 0.07) for a shift in the 6-month modified Rankin Scale. CONCLUSIONS: Admission to critical care is associated with poor 6-month functional outcome after spontaneous ICH but not with death. Patients admitted to critical care were a priori more severely affected. Although adjusted for main known predictors of poor outcome, our findings could still be confounded by unmeasured factors. Establishing the true effectiveness of critical care after ICH requires a randomised trial with clinical outcomes and quality of life assessments

Complete genome sequence of “Enterobacter lignolyticus” SCF1

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated “Enterobacter lignolyticus”SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of “E. lignolyticus” SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster

Complete genome sequence of “Enterobacter lignolyticus” SCF1

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated “Enterobacter lignolyticus”SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of “E. lignolyticus” SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster