Benchmarking acid and base dopants with respect to enabling the ice V to XIII and ice VI to XV hydrogen-ordering phase transitions

Doping the hydrogen-disordered phases of ice V, VI and XII with hydrochloric acid (HCl) has led to the discovery of their hydrogen-ordered counterparts ices XIII, XV and XIV. Yet, the mechanistic details of the hydrogen-ordering phase transitions are still not fully understood. This includes in particular the role of the acid dopant and the defect dynamics that it creates within the ices. Here we investigate the effects of several acid and base dopants on the hydrogen ordering of ices V and VI with calorimetry and X-ray diffraction. HCl is found to be most effective for both phases which is attributed to a favourable combination of high solubility and strong acid properties which create mobile H3O+ defects that enable the hydrogen-ordering processes. Hydrofluoric acid (HF) is the second most effective dopant highlighting that the acid strengths of HCl and HF are much more similar in ice than they are in liquid water. Surprisingly, hydrobromic acid doping facilitates hydrogen ordering in ice VI whereas only a very small effect is observed for ice V. Conversely, lithium hydroxide (LiOH) doping achieves a performance comparable to HF-doping in ice V but it is ineffective in the case of ice VI. Sodium hydroxide, potassium hydroxide (as previously shown) and perchloric acid doping are ineffective for both phases. These findings highlight the need for future computational studies but also raise the question why LiOH-doping achieves hydrogen-ordering of ice V whereas potassium hydroxide doping is most effective for the 'ordinary' ice Ih.Comment: 18 pages, 7 figures, 1 tabl

Excess electron solvation in ammonia clusters

We performed a combination of quantum chemical calculations and molecular dynamics simulations to assess the stability of various size ("N" "H" _"3" )_n^- ammonia cluster anions up to n = 32 monomers. In the n = 3 – 8 size range, cluster anions are optimized and the vertical detachment energy of the excess electron (VDE) from increasing size clusters are computed using various level methods including density functional theory (DFT), MP2 and CCSD(T) calculations. These clusters bind the electron in non-branched hydrogen bonding chains in dipole bound states. The VDE increases with size from a few meV up to ~200 meV. The electron binding energy is weaker than in water clusters but comparable to small methanol cluster VDEs. We located the first branched hydrogen bonding cluster that binds the excess electron at n = 7. For larger (n = 8 – 32) clusters we generated cold, neutral clusters by semiempirical and ab initio molecular dynamics (AIMD) simulations, and added an extra electron to selected neutral configurations. VDE calculations on the adiabatic and the relaxed anionic structures suggest that the n = 12 - 32 neutral clusters weakly bind the excess electron. Electron binding energies for these clusters (~ 100 meV) appear to be significantly weaker than extrapolated from experimental data. The observed excess electron states are diffuse and localized outside the molecular frame (surface states) with minor (~1%) penetration to the nitrogen frontier orbitals. Stable minima with excess electron states surrounded by solvent molecules (cavity states) were not found in this size regime

Een excursie naar Edinburgh

Het was niet de mooiste dag van het jaar, toen een groepje studenten zich op het de trappen van Leiden C.S. verzamelde. Uit een grijze grauwe hemel daalde het water vrijelijk neer. Het deerde niet, want dit groepje stond op het punt aan een reis te beginnen: de B.I.L. excursie naar Edinburgh en iedereen was er die maandag de dertigste september klaar voor

Recruitment of ethnic minority patients to a cardiac rehabilitation trial: The Birmingham Rehabilitation Uptake Maximisation (BRUM) study [ISRCTN72884263]

Background: Concerns have been raised about low participation rates of people from minority ethnic groups in clinical trials. However, the evidence is unclear as many studies do not report the ethnicity of participants and there is insufficient information about the reasons for ineligibility by ethnic group. Where there are data, there remains the key question as to whether ethnic minorities more likely to be ineligible (e.g. due to language) or decline to participate. We have addressed these questions in relation to the Birmingham Rehabilitation Uptake Maximisation (BRUM) study, a randomized controlled trial (RCT) comparing a home-based with a hospital-based cardiac rehabilitation programme in a multi-ethnic population in the UK. Methods: Analysis of the ethnicity, age and sex of presenting and recruited subjects for a trial of cardiac rehabilitation in the West-Midlands, UK. Participants: 1997 patients presenting post-myocardial infarction, percutaneous transluminal coronary angioplasty or coronary artery bypass graft surgery. Data collected: exclusion rates, reasons for exclusion and reasons for declining to participate in the trial by ethnic group. Results: Significantly more patients of South Asian ethnicity were excluded (52% of 'South Asian' v 36% 'White European' and 36% 'Other', p < 0.001). This difference in eligibility was primarily due to exclusion on the basis of language (i.e. the inability to speak English or Punjabi). Of those eligible, similar proportions were recruited from the different ethnic groups (white, South Asian and other). There was a marked difference in eligibility between people of Indian, Pakistani or Bangladeshi origin

Nuclear Magnetic Resonance and Hyperfine Structure

Contains reports on four research projects

Bottom sediments of Lake Rotoma

Lake Rotoma is a deep (70-80 m), oligotrophic, warm monomictic lake of volcanic origin with insignificant stream inflow and no clearly defined outflow. For at least 60 years up to 1972 the lake level fluctuated markedly about an overall rising trend of some 6-10 m. Nearshore profiles are related to the prevailing wave climate superimposed upon the overall rising lake level, shelves being wider, less steep, and deeper about the more exposed eastern and southern shorelines. The outer portions of shelves extending well below modern storm wave base into waters as deep as 15-25 m are relict features from lower lake level stands. Sediments fine from sand-gravel mixtures nearshore to silts in basinal areas. Their composition reflects a composite provenance involving the lavas and tephras about the lake, as well as intralake diatom frustules and organic matter. The distribution pattern of surficial bottom sediments is an interplay between grains of both biological and terrigenous origin, supplied presently and in the past by a variety of processes, that have been dispersed either by the modern hydrodynamic regime or by former ones associated with lower lake levels. These interrelationships are structured by erecting 5 process-age sediment classes in the lake, namely neoteric, amphoteric, proteric, palimpsest, and relict sediments, analogous to categories postulated for sediments on oceanic continental shelves. Short-core stratigraphy includes the Kaharoa (A.D. -1020) and Tarawera (A.D. 1886) tephras. The rates of sedimentation of diatomaceous silts in basinal areas have more than doubled since the Tarawera eruption, indicating an overall increase in the fertility level of lake waters associated, perhaps, with recent farm development in the catchment

Incorporation of dUTP does not mediate mutation of A:T base pairs in Ig genes in vivo

Activation-induced cytidine deaminase (AID) protein initiates Ig gene mutation by deaminating cytosines, converting them into uracils. Excision of AID-induced uracils by uracil-N-glycosylase is responsible for most transversion mutations at G:C base pairs. On the other hand, processing of AID-induced G:U mismatches by mismatch repair factors is responsible for most mutation at Ig A:T base pairs. Why mismatch processing should be error prone is unknown. One theory proposes that long patch excision in G1-phase leads to dUTP-incorporation opposite adenines as a result of the higher G1-phase ratio of nuclear dUTP to dTTP. Subsequent base excision at the A:U base pairs produced could then create non-instructional templates leading to permanent mutations at A:T base pairs (1). This compelling theory has remained untested. We have developed a method to rapidly modify DNA repair pathways in mutating mouse B cells in vivo by transducing Ig knock-in splenic mouse B cells with GFP-tagged retroviruses, then adoptively transferring GFP+ cells, along with appropriate antigen, into primed congenic hosts. We have used this method to show that dUTP-incorporation is unlikely to be the cause of AID-induced mutation of A:T base pairs, and instead propose that A:T mutations might arise as an indirect consequence of nucleotide paucity during AID-induced DNA repair

Sedimentation in an artificial lake -Lake Matahina, Bay of Plenty

Lake Matahina, an 8 km long hydroelectric storage reservoir, is a small (2.5 km2), 50 m deep, warm monomictic, gorge-type lake whose internal circulation is controlled by the inflowing Rangitaiki River which drains a greywacke and acid volcanic catchment. Three major proximal to distal subenvironments are defined for the lake on the basis of surficial sediment character and dominant depositional process: (a) fluvial-glassy, quartzofeld-spathic, and lithic gravel-sand mixtures deposited from contact and saltation loads in less than 3 m depth; (b) (pro-)deltaic-quartzofeldspathic and glassy sand-silt mixtures deposited from graded and uniform suspension loads in 3-20 m depth; and (c) basinal-diatomaceous, argillaceous, and glassy silt-clay mixtures deposited from uniform and pelagic suspension loads in 20-50 m depth. The delta face has been prograding into the lake at a rate of 35-40 m/year and vertical accretion rates in pro-delta areas are 15-20 cm/year. Basinal deposits are fed mainly from river plume dispersion involving overflows, interflows, and underflows, and by pelagic settling, and sedimentation rates behind the dam have averaged about 2 cm/year. Occasional fine sand layers in muds of basinal cores attest to density currents or underflows generated during river flooding flowing the length of the lake along a sublacustrine channel marking the position of the now submerged channel of the Rangitaiki River

The Deep Poincare Map: A Novel Approach for Left Ventricle Segmentation

Precise segmentation of the left ventricle (LV) within cardiac MRI images is a prerequisite for the quantitative measurement of heart function. However, this task is challenging due to the limited availability of labeled data and motion artifacts from cardiac imaging. In this work, we present an iterative segmentation algorithm for LV delineation. By coupling deep learning with a novel dynamic-based labeling scheme, we present a new methodology where a policy model is learned to guide an agent to travel over the image, tracing out a boundary of the ROI – using the magnitude difference of the Poincaré map as a stopping criterion. Our method is evaluated on two datasets, namely the Sunnybrook Cardiac Dataset (SCD) and data from the STACOM 2011 LV segmentation challenge. Our method outperforms the previous research over many metrics. In order to demonstrate the transferability of our method we present encouraging results over the STACOM 2011 data, when using a model trained on the SCD dataset