Computing JSJ decompositions of hyperbolic groups

We present an algorithm that computes Bowditch's canonical JSJ decomposition of a given one-ended hyperbolic group over its virtually cyclic subgroups. The algorithm works by identifying topological features in the boundary of the group. As a corollary we also show how to compute the JSJ decomposition of such a group over its virtually cyclic subgroups with infinite centre. We also give a new algorithm that determines whether or not a given one-ended hyperbolic group is virtually fuchsian. Our approach uses only the geometry of large balls in the Cayley graph and avoids Makanin's algorithm

Analysis of gas chromatography/mass spectrometry data for catalytic lignin depolymerization using positive matrix factorization

Various catalytic technologies are being developed to efficiently convert lignin into renewable chemicals. However, due to its complexity, catalytic lignin depolymerization often generates a wide and complex distribution of product compounds. Gas chromatography/mass spectrometry (GC-MS) is a common analytical technique to profile the compounds that comprise lignin depolymerization products. GC-MS is applied not only to determine the product composition, but also to develop an understanding of the catalytic reaction pathways and of the relationships among catalyst structure, reaction conditions, and the resulting compounds generated. Although a very useful tool, the analysis of lignin depolymerization products with GC-MS is limited by the quality and scope of the available mass spectral libraries and the ability to correlate changes in GC-MS chromatograms to changes in lignin structure, catalyst structure, and other reaction conditions. In this study, the GC-MS data of the depolymerization products generated from organosolv hybrid poplar lignin using a copper-doped porous metal oxide catalyst and a methanol/dimethyl carbonate co-solvent was analyzed by applying a factor analysis technique, positive matrix factorization (PMF). Several different solutions for the PMF model were explored. A 13-factor solution sufficiently explains the chemical changes occurring to lignin depolymerization products as a function of lignin, reaction time, catalyst, and solvent. Overall, seven factors were found to represent aromatic compounds, while one factor was defined by aliphatic compounds

Axial and transverse deep‐water sediment supply to syn‐rift fault terraces: insights from the West Xylokastro Fault Block, Gulf of Corinth, Greece

Deep‐water syn‐rift systems develop in partially‐ or transiently‐linked depocentres to form complicated depositional architectures, which are characterised by short transport distances, coarse grain sizes, and a wide range of sedimentary processes. Exhumed systems that can help to constrain the tectono‐stratigraphic evolution of such systems are rare or complicated by inversion tectonics. Here, we document a mid‐Pleistocene deep‐water syn‐rift system fed by Gilbert‐type fan deltas in the hangingwall of a rift margin fault bounding the West Xylokastro Horst block, on the southern margin of the Gulf of Corinth, Greece. Structural and stratigraphic mapping combined with digital outcrop models permit observations along this syn‐rift depositional system from hinterland source to deep‐water sink. The West Xylokastro Fault hangingwall is filled by two distinct sediment systems; an axial system fed by coarse‐grained sediment gravity flows derived from fault‐tip Gilbert‐type fan deltas and a lateral system dominated by mass transport deposits fed from an evolving fault‐scarp apron. Abrupt changes in stratigraphic architecture across the axial system are interpreted to record changes in relative base level, sediment supply and tectonics. Locally, depositional topography and intra‐basinal structures controlled sediment dispersal patterns, from bed‐scale infilling of local rugose topography above mass transport complexes, to basin‐scale confinement from the fault scarp apron. These acted to generate a temporally and spatially variable, heterogeneous stratigraphic architecture throughout the basin‐fill. The transition of the locus of sedimentation from a rift margin to a fault terrace through the syn‐sedimentary growth of a basinward fault produced regressive surfaces updip, which manifest themselves as channels in the deep‐water realm and acted to prograde the system. We present a new conceptual model that recognises coeval axial and transverse systems based on the stratigraphic architecture around the West Xylokastro fault block that emphasises the lateral and vertical heterogeneity of rift basin‐fills with multiple entry points

Quantifying faulting and base level controls on syn-rift sedimentation using stratigraphic architectures of coeval, adjacent Early-Middle Pleistocene fan deltas in Lake Corinth, Greece

Quantification of allogenic controls in rift basin‐fills requires analysis of multiple depositional systems because of marked along‐strike changes in depositional architecture. Here, we compare two coeval Early‐Middle Pleistocene syn‐rift fan deltas that sit 6 km apart in the hangingwall of the Pirgaki‐Mamoussia Fault, along the southern margin of the Gulf of Corinth, Greece. The Selinous fan delta is located near the fault tip and the Kerinitis fan delta towards the fault centre. Selinous and Kerinitis have comparable overall aggradational stacking patterns. Selinous comprises 15 cyclic stratal units (ca. 25 m thick), whereas at Kerinitis 11 (ca. 60 m thick) are present. Eight facies associations are identified. Fluvial and shallow water facies dominate the major stratal units in the topset region, with shelfal fine‐grained facies constituting ca. 2 m thick intervals between major topset units and thick conglomeratic foresets building down‐dip. It is possible to quantify delta build times (Selinous: 615 kyr; Kerinitis: >450 kyr) and average subsidence and equivalent sedimentation rates (Selinous: 0.65 m/kyr; Kerinitis: >1.77 m/kyr). The presence of sequence boundaries at Selinous, but their absence at Kerinitis, enables sensitivity analysis of the most uncertain variables using a numerical model, ‘Syn‐Strat’, supported by an independent unit thickness extrapolation method. Our study has three broad outcomes: (a) the first estimate of lake level change amplitude in Lake Corinth for the Early‐Middle Pleistocene (10–15 m), which can aid regional palaeoclimate studies and inform broader climate‐system models; (b) demonstration of two complementary methods to quantify faulting and base level signals in the stratigraphic record—forward modelling with Syn‐Strat and a unit thickness extrapolation—which can be applied to other rift basin‐fills; and (c) a quantitative approach to the analysis of stacking patterns and key surfaces that could be applied to stratigraphic pinch‐out assessment and cross‐hole correlations in reservoir analysis

Use of an Anaerobic Chamber Environment for the Assay of Endogenous Cellular Protein-Tyrosine Phosphatase Activities

Protein-tyrosine phosphatases (PTPases) have a catalytic cysteine residue whose reduced state is integral to the reaction mechanism. Since exposure to air can artifactually oxidize this highly reactive thiol, PTPase assays have typically used potent reducing agents to reactivate the enzymes present; however, this approach does not allow for the measurement of the endogenous PTPase activity directly isolated from the in vivo cellular environment. Here we provide a method for using an anaerobic chamber to preserve the activity of the total PTPase complement in a tissue lysate or of an immunoprecipitated PTPase homolog to characterize their endogenous activation state. Comparison with a sample treated with biochemical reducing agents allows the determination of the activatable (reducible) fraction of the endogenous PTPase pool

Diurnal differences in human muscle isometric force and rate of force development in vivo are associated with differential phosphorylation of sarcomeric M-band proteins.

The maximum force of skeletal muscle exhibits circadian variation that is associated with time-of-day differences in athletic performance. We investigated whether the diurnal difference in force is associated with the post-translational state of muscle proteins. Twenty physically active men (mean ± SD; age 26.0 ± 4.4 y, height 177.3 ± 6.8 cm, body mass 75.1 ± 8.2.8 kg) completed 5 familiarisation sessions where-in they practiced all maximal efforts. Thereafter they performed experimental sessions, in the morning (08:00 h) and evening (17:00 h), counterbalanced in order of administration and separated by at least 72 h. Rectal, skin, muscle temperatures and ratings of perceived effort measurements where made after the subjects had reclined for 30 min (rest) and after the 5-min cycle ergometry warm-ups and prior to the measurement of knee extensor maximal voluntary isometric contraction (MVIC; including twitch-interpolation) and peak rate of force development (RFD). Data handling: 10 subjects from the cohort of 20 volunteered for muscle biopsy procedures, hence only their data is reported for temperature, MVIC and RFD to align with proteomic analyses. Samples of vastus lateralis were collected immediately after exercise and were analysed by ‘top-down’ and ‘bottom-up’ proteomic methods. Rectal and muscle temperatures were higher at rest in the evening (mean difference of 0.51°C and 0.69°C; p<0.05) than in the morning. MVIC force in the evening was significantly greater than in the morning (mean difference of 67 N, 9.3%; p<0.05), similarly peak RFD (mean difference of 1080 N/s, 15.3%; p<0.05) was improved in the evening. 2D gel analysis encompassed 122 proteoforms and discovered 6 statistically significant (p<0.05; false discovery rate [FDR] = 10%) diurnal differences. Phosphopeptide analysis identified 1,693 phosphopeptides and detected 140 phosphopeptides from 104 proteins that were more phosphorylated (p<0.05, FDR=22%) in the morning vs. evening. Myomesin 2, muscle creatine kinase and the C-terminus of titin, exhibited the most robust (FDR<10%) diurnal differences. In summary, the effects of time of day where seen in measures of rectal and muscle temperature and muscle performance. Exercise in the morning, compared to the evening, coincided with greater phosphorylation of M-band-associated proteins in human muscle. These protein modifications may alter M-band structure and disrupt force transmission, thus potentially explaining the lower force output in the morning

Melarsoprol cyclodextrin inclusion complexes as promising oral candidates for the treatment of human African trypanosomiasis

Human African trypanosomiasis (HAT), or sleeping sickness, results from infection with the protozoan parasites &lt;i&gt;Trypanosoma brucei&lt;/i&gt; (&lt;i&gt;T.b.&lt;/i&gt;) &lt;i&gt;gambiense&lt;/i&gt; or &lt;i&gt;T.b.rhodesiense&lt;/i&gt; and is invariably fatal if untreated. There are 60 million people at risk from the disease throughout sub-Saharan Africa. The infection progresses from the haemolymphatic stage where parasites invade the blood, lymphatics and peripheral organs, to the late encephalitic stage where they enter the central nervous system (CNS) to cause serious neurological disease. The trivalent arsenical drug melarsoprol (Arsobal) is the only currently available treatment for CNS-stage &lt;i&gt;T.b.rhodesiense&lt;/i&gt; infection. However, it must be administered intravenously due to the presence of propylene glycol solvent and is associated with numerous adverse reactions. A severe post-treatment reactive encephalopathy occurs in about 10% of treated patients, half of whom die. Thus melarsoprol kills 5% of all patients receiving it. Cyclodextrins have been used to improve the solubility and reduce the toxicity of a wide variety of drugs. We therefore investigated two melarsoprol cyclodextrin inclusion complexes; melarsoprol hydroxypropyl-&#846;-cyclodextrin and melarsoprol randomly-methylated-&#946;-cyclodextrin. We found that these compounds retain trypanocidal properties &lt;i&gt;in vitro&lt;/i&gt; and cure CNS-stage murine infections when delivered orally, once per day for 7-days, at a dosage of 0.05 mmol/kg. No overt signs of toxicity were detected. Parasite load within the brain was rapidly reduced following treatment onset and magnetic resonance imaging showed restoration of normal blood-brain barrier integrity on completion of chemotherapy. These findings strongly suggest that complexed melarsoprol could be employed as an oral treatment for CNS-stage HAT, delivering considerable improvements over current parenteral chemotherapy

Spatial variability in depositional reservoir quality of deep-water channel-fill and lobe deposits

Initial porosity and permeability in deep-water systems are controlled by primary sedimentary texture and mineralogy. Therefore, understanding the sedimentary processes that control changes in primary texture is critical for improved reservoir quality predictions. A well-constrained, exhumed submarine lobe in the Jaca Basin, and a submarine channel-fill element in the Aínsa Basin, northern Spain, were studied to characterize the depositional reservoir quality in axial to marginal/fringe positions. Construction of architectural panels and strategic sampling enabled analysis of the spatial changes in textural properties, and their relationship to reservoir quality distribution. Samples were analyzed in thin-section to establish how depositional processes inferred from outcrop observations affect textural properties. Results show that high-density turbidites are concentrated in lobe- and channel-axis positions and exhibit good depositional reservoir quality. Lobe off-axis deposits contain high- and low-density turbidites and have moderate depositional reservoir quality. Conversely, low-density turbidites dominate lobe fringe and channel-margin positions and have relatively poor depositional reservoir quality. There is a sharp decrease in depositional reservoir quality between the lobe off-axis and lobe fringe due to: 1) an abrupt increase in matrix content; 2) an abrupt decrease in sandstone amalgamation; and 3) a decrease in grain-size. There is an abrupt increase in depositional reservoir quality from channel margin to channel axis corresponding to: 1) an increase in total sandstone thickness and amalgamation; 2) an increase in grain-size, 3) a decrease in matrix content. Rates of change of key properties are up to two orders of magnitude greater between channel-fill sub-environments compared to lobe sub-environments. Spatial variability in properties of discrete architectural elements, and rates of changes, provides input to reservoir models during exploration, appraisal, and development phases of hydrocarbon fields

Intra- and interreader reproducibility of PI-RADSv2: A multireader study

Background: The Prostate Imaging Reporting and Data System version 2 (PI-RADSv2) has been in use since 2015; while interreader reproducibility has been studied, there has been a paucity of studies investigating the intrareader reproducibility of PI-RADSv2. Purpose: To evaluate both intra- and interreader reproducibility of PI-RADSv2 in the assessment of intraprostatic lesions using multiparametric magnetic resonance imaging (mpMRI). Study Type: Retrospective. Population/Subjects: In all, 102 consecutive biopsy-naïve patients who underwent prostate MRI and subsequent MR/transrectal ultrasonography (MR/TRUS)-guided biopsy. Field Strength/Sequences: Prostate mpMRI at 3T using endorectal with phased array surface coils (TW MRI, DW MRI with ADC maps and b2000 DW MRI, DCE MRI). Assessment: Previously detected and biopsied lesions were scored by four readers from four different institutions using PI-RADSv2. Readers scored lesions during two readout rounds with a 4-week washout period. Statistical Tests: Kappa (κ) statistics and specific agreement (Po) were calculated to quantify intra- and interreader reproducibility of PI-RADSv2 scoring. Lesion measurement agreement was calculated using the intraclass correlation coefficient (ICC). Results: Overall intrareader reproducibility was moderate to substantial (κ = 0.43–0.67, Po = 0.60–0.77), while overall interreader reproducibility was poor to moderate (κ = 0.24, Po = 46). Readers with more experience showed greater interreader reproducibility than readers with intermediate experience in the whole prostate (P = 0.026) and peripheral zone (P = 0.002). Sequence-specific interreader agreement for all readers was similar to the overall PI-RADSv2 score, with κ = 0.24, 0.24, and 0.23 and Po = 0.47, 0.44, and 0.54 in T2-weighted, diffusion-weighted imaging (DWI), and dynamic contrast-enhanced (DCE), respectively. Overall intrareader and interreader ICC for lesion measurement was 0.82 and 0.71, respectively. Data Conclusion: PI-RADSv2 provides moderate intrareader reproducibility, poor interreader reproducibility, and moderate interreader lesion measurement reproducibility. These findings suggest a need for more standardized reader training in prostate MRI. Level of Evidence: 2. Technical Efficacy: Stage 2