Maximally-localized generalized Wannier functions for composite energy bands

We discuss a method for determining the optimally-localized set of generalized Wannier functions associated with a set of Bloch bands in a crystalline solid. By ``generalized Wannier functions'' we mean a set of localized orthonormal orbitals spanning the same space as the specified set of Bloch bands. Although we minimize a functional that represents the total spread sum_n [ _n - _n^2 ] of the Wannier functions in real space, our method proceeds directly from the Bloch functions as represented on a mesh of k-points, and carries out the minimization in a space of unitary matrices U_mn^k describing the rotation among the Bloch bands at each k-point. The method is thus suitable for use in connection with conventional electronic-structure codes. The procedure also returns the total electric polarization as well as the location of each Wannier center. Sample results for Si, GaAs, molecular C2H4, and LiCl will be presented.Comment: 22 pages, two-column style with 4 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#nm_wan

Is Canada ready for patient accessible electronic health records? A national scan

<p>Abstract</p> <p>Background</p> <p>Access to personal health information through the electronic health record (EHR) is an innovative means to enable people to be active participants in their own health care. Currently this is not an available option for consumers of health. The absence of a key technology, the EHR, is a significant obstacle to providing patient accessible electronic records. To assess the readiness for the implementation and adoption of EHRs in Canada, a national scan was conducted to determine organizational readiness and willingness for patient accessible electronic records.</p> <p>Methods</p> <p>A survey was conducted of Chief Executive Officers (CEOs) of Canadian public and acute care hospitals.</p> <p>Results</p> <p>Two hundred thirteen emails were sent to CEOs of Canadian general and acute care hospitals, with a 39% response rate. Over half (54.2%) of hospitals had some sort of EHR, but few had a record that was predominately electronic. Financial resources were identified as the most important barrier to providing patients access to their EHR and there was a divergence in perceptions from healthcare providers and what they thought patients would want in terms of access to the EHR, with providers being less willing to provide access and patients desire for greater access to the full record.</p> <p>Conclusion</p> <p>As the use of EHRs becomes more commonplace, organizations should explore the possibility of responding to patient needs for clinical information by providing access to their EHR. The best way to achieve this is still being debated.</p

Lost in translation: Returning germline genetic results in genome-scale cancer research

Background: The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have on clinical care and health outcomes, is sorely lacking. Through the work of the Australian Pancreatic Cancer Genome Initiative (APGI) we: (1) delineate the pathway back to the patient where actionable research data were identified; and (2) report the clinical utilisation of individual results returned. Using this experience, we discuss barriers and opportunities associated with a comprehensive process of RoR in large-scale genomic research that may be useful for others developing their own policies. Methods: We performed whole-genome (n = 184) and exome (n = 208) sequencing of matched tumour-normal DNA pairs from 392 patients with sporadic pancreatic cancer (PC) as part of the APGI. We identified pathogenic germline mutations in candidate genes (n = 130) with established predisposition to PC or medium-high penetrance genes with well-defined cancer associated syndromes or phenotypes. Variants from candidate genes were annotated and classified according to international guidelines. Variants were considered actionable if clinical utility was established, with regard to prevention, diagnosis, prognostication and/or therapy. Results: A total of 48,904 germline variants were identified, with 2356 unique variants undergoing annotation and in silico classification. Twenty cases were deemed actionable and were returned via previously described RoR framework, representing an actionable finding rate of 5.1%. Overall, 1.78% of our cohort experienced clinical benefit from RoR. Conclusion: Returning research results within the context of large-scale genomics research is a labour-intensive, highly variable, complex operation. Results that warrant action are not infrequent, but the prevalence of those who experience a clinical difference as a result of returning individual results is currently low

Homozygosity for the C9orf72 GGGGCC repeat expansion in frontotemporal dementia

An expanded hexanucleotide repeat in the C9orf72 gene is the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis (c9FTD/ALS). We now report the first description of a homozygous patient and compare it to a series of heterozygous cases. The patient developed early-onset frontotemporal dementia without additional features. Neuropathological analysis showed c9FTD/ALS characteristics, with abundant p62-positive inclusions in the frontal and temporal cortices, hippocampus and cerebellum, as well as less abundant TDP-43-positive inclusions. Overall, the clinical and pathological features were severe, but did not fall outside the usual disease spectrum. Quantification of C9orf72 transcript levels in post-mortem brain demonstrated expression of all known C9orf72 transcript variants, but at a reduced level. The pathogenic mechanisms by which the hexanucleotide repeat expansion causes disease are unclear and both gain- and loss-of-function mechanisms may play a role. Our data support a gain-of-function mechanism as pure homozygous loss of function would be expected to lead to a more severe, or completely different clinical phenotype to the one described here, which falls within the usual range. Our findings have implications for genetic counselling, highlighting the need to use genetic tests that distinguish C9orf72 homozygosity

Microbial Symbionts in Insects Influence Down-Regulation of Defense Genes in Maize

Diabrotica virgifera virgifera larvae are root-feeding insects and significant pests to maize in North America and Europe. Little is known regarding how plants respond to insect attack of roots, thus complicating the selection for plant defense targets. Diabrotica virgifera virgifera is the most successful species in its genus and is the only Diabrotica beetle harboring an almost species-wide Wolbachia infection. Diabrotica virgifera virgifera are infected with Wolbachia and the typical gut flora found in soil-living, phytophagous insects. Diabrotica virgifera virgifera larvae cannot be reared aseptically and thus, it is not possible to observe the response of maize to effects of insect gut flora or other transient microbes. Because Wolbachia are heritable, it is possible to investigate whether Wolbachia infection affects the regulation of maize defenses. To answer if the success of Diabrotica virgifera virgifera is the result of microbial infection, Diabrotica virgifera virgifera were treated with antibiotics to eliminate Wolbachia and a microarray experiment was performed. Direct comparisons made between the response of maize root tissue to the feeding of antibiotic treated and untreated Diabrotica virgifera virgifera show down-regulation of plant defenses in the untreated insects compared to the antibiotic treated and control treatments. Results were confirmed via QRT-PCR. Biological and behavioral assays indicate that microbes have integrated into Diabrotica virgifera virgifera physiology without inducing negative effects and that antibiotic treatment did not affect the behavior or biology of the insect. The expression data and suggest that the pressure of microbes, which are most likely Wolbachia, mediate the down-regulation of many maize defenses via their insect hosts. This is the first report of a potential link between a microbial symbiont of an insect and a silencing effect in the insect host plant. This is also the first expression profile for a plant attacked by a root-feeding insect

Dirty and 40 days in the wilderness: Eliciting childbirth and postnatal cultural practices and beliefs in Nepal.

Background: Pregnancy and childbirth are socio-cultural events that carry varying meanings across different societies and cultures. These are often translated into social expectations of what a particular society expects women to do (or not to do) during pregnancy, birth and/or the postnatal period. This paper reports a study exploring beliefs around childbirth in Nepal, a low-income country with a largely Hindu population. The paper then sets these findings in the context of the wider global literature around issues such as periods where women are viewed as polluted (or dirty even) after childbirth. Methods: A qualitative study comprising five in-depth face-to-face interviews and 14 focus group discussions with mainly women, but also men and health service providers. The qualitative findings in Nepal were compared and contrasted with the literature on practices and cultural beliefs related to the pregnancy and childbirth period across the globe and at different times in history. Results: The themes that emerged from the analysis included: (a) cord cutting & placenta rituals; (b) rest & seclusion; (c) purification, naming & weaning ceremonies and (d) nutrition and breastfeeding. Physiological changes in mother and baby may underpin the various beliefs, ritual and practices in the postnatal period. These practices often mean women do not access postnatal health services. Conclusions: The cultural practices, taboos and beliefs during pregnancy and around childbirth found in Nepal largely resonate with those reported across the globe. This paper stresses that local people’s beliefs and practices offer both opportunities and barriers to health service providers. Maternity care providers need to be aware of local values, beliefs and traditions to anticipate and meet the needs of women, gain their trust and work with them

Searches for Neutrinos from Gamma-Ray Bursts Using the IceCube Neutrino Observatory

Gamma-ray bursts (GRBs) are considered as promising sources of ultra-high-energy cosmic rays (UHECRs) due to their large power output. Observing a neutrino flux from GRBs would offer evidence that GRBs are hadronic accelerators of UHECRs. Previous IceCube analyses, which primarily focused on neutrinos arriving in temporal coincidence with the prompt gamma-rays, found no significant neutrino excess. The four analyses presented in this paper extend the region of interest to 14 days before and after the prompt phase, including generic extended time windows and targeted precursor searches. GRBs were selected between 2011 May and 2018 October to align with the data set of candidate muon-neutrino events observed by IceCube. No evidence of correlation between neutrino events and GRBs was found in these analyses. Limits are set to constrain the contribution of the cosmic GRB population to the diffuse astrophysical neutrino flux observed by IceCube. Prompt neutrino emission from GRBs is limited to ≲1% of the observed diffuse neutrino flux, and emission on timescales up to 104 s is constrained to 24% of the total diffuse flux.Peer Reviewe

Book reviews

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45707/1/11336_2005_Article_BF02288937.pd

Testing Hadronic Interaction Models with Cosmic Ray Measurements at the IceCube Neutrino Observatory

The IceCube Neutrino Observatory provides the opportunity to perform unique measurements of cosmic-ray air showers with its combination of a surface array and a deep detector. Electromagnetic particles and low-energy muons (∼GeV) are detected by IceTop, while a bundle of high-energy muons (>~400 GeV) can be measured in coincidence in IceCube. Predictions of air-shower observables based on simulations show a strong dependence on the choice of the high-energy hadronic interaction model. By reconstructing different composition-dependent observables, one can provide strong tests of hadronic interaction models, as these measurements should be consistent with one another. In this work, we present an analysis of air-shower data between 2.5 and 80 PeV, comparing the composition interpretation of measurements of the surface muon density, the slope of the IceTop lateral distribution function, and the energy loss of the muon bundle, using the models Sibyll 2.1, QGSJet-II.04 and EPOS-LHC. We observe inconsistencies in all models under consideration, suggesting they do not give an adequate description of experimental data. The results furthermore imply a significant uncertainty in the determination of the cosmic-ray mass composition through indirect measurements

Performance of the D-Egg Optical Sensor for the IceCube Upgrade

New optical sensors called the "D-Egg" have been developed for cost-effective instrumentation for the IceCube Upgrade. With two 8-inch high QE photomultipliers, they offer increased effective photocathode area while retaining as much of the successful IceCube Digital Optical Module (DOM) design as possible. Mass production of D-Eggs has started in 2020. By the end of 2021, there will be 310 D-Eggs produced with 288 deployed in the IceCube Upgrade. The D-Egg readout system uses advanced technologies in electronics and computing power. Each of the two PMT signals is digitized using ultra-low-power 14-bit ADCs with a sampling frequency of 250-MSPS, enabling seamless and lossless event recording from single-photon signals to signals exceeding 200pe within 10ns, as well as flexible event triggering. In this paper, we report the single photon detection performance as well as the multiple photon recording capability of D-Eggs from the mass production line which have been evaluated with the built-in DAQ system