Calibration of uncertainty in the active learning of machine learning force fields

FFLUX is a machine learning force field that uses the maximum expected prediction error (MEPE) active learning algorithm to improve the efficiency of model training. MEPE uses the predictive uncertainty of a Gaussian process (GP) to balance exploration and exploitation when selecting the next training sample. However, the predictive uncertainty of a GP is unlikely to be accurate or precise immediately after training. We hypothesize that calibrating the uncertainty quantification within MEPE will improve active learning performance. We develop and test two methods to improve uncertainty estimates: post-hoc calibration of predictive uncertainty using the CRUDE algorithm, and replacing the GP with a student- t process. We investigate the impact of these methods on MEPE for single sample and batch sample active learning. Our findings suggest that post-hoc calibration does not improve the performance of active learning using the MEPE method. However, we do find that the student- t process can outperform active learning strategies and random sampling using a GP if the training set is sufficiently large

Anderson localisation in steady states of microcavity polaritons

We present an experimental signature of the Anderson localisation of microcavity polaritons, and provide a systematic study of the dependence on disorder strength. We reveal a controllable degree of localisation, as characterised by the inverse-participation ratio, by tuning the positional disorder of arrays of interacting mesas. This constitutes the realisation of disorder-induced localisation in a driven-dissipative system. In addition to being an ideal candidate for investigating localisation in this regime, microcavity polaritons hold promise for low-power, ultra-small devices and their localisation could be used as a resource in quantum memory and quantum information processing.Comment: 7 pages, 3 figure

Pancreas preserving distal duodenectomy: a versatile operation for a range of infra-papillary pathologies

AIM To investigate the range of pathologies treated by pancreas preserving distal duodenectomy (PPDD) and present the outcome of follow-up. METHODS Neoplastic lesions of the duodenum are treated conventionally by pancreaticoduodenectomy. Lesions distal to the major papilla may be suitable for a pancreas-preserving distal duodenectomy, potentially reducing morbidity and mortality. We present our experience with this procedure. Selective intraoperative duodenoscopy assessed the relationship of the papilla to the lesion. After duodenal mobilisation and confirmation of the site of the lesion, the duodenum was transected distal to the papilla and beyond the duodenojejunal flexure and a side-to-side duodenojejunal anastomosis was formed. Patients were identified from a prospectively maintained database and outcomes determined from digital health records with a dataset including demographics, co-morbidities, mode of presentation, preoperative imaging and assessment, nutritional support needs, technical operative details, blood transfusion requirements, length of stay, pathology including lymph node yield and lymph node involvement, length of follow-up, complications and outcomes. Related published literature was also reviewed. RESULTS Twenty-four patients had surgery with the intent of performing PPDD from 2003 to 2016. Nineteen underwent PPDD successfully. Two patients planned for PPDD proceeded to formal pancreaticoduodenectomy (PD) while three had unresectable disease. Median post-operative follow-up was 32 mo. Pathologies resected included duodenal adenocarcinoma (n = 6), adenomas (n = 5), gastrointestinal stromal tumours (n = 4) and lipoma, bleeding duodenal diverticulum, locally advanced colonic adenocarcinoma and extrinsic compression (n = 1 each). Median postoperative length of stay (LOS) was 8 d and morbidity was low [pain and nausea/vomiting (n = 2), anastomotic stricture (n = 1), pneumonia (n = 1), and overwhelming postsplenectomy sepsis (n = 1, asplenic patient)]. PPDD was associated with a significantly shorter LOS than a contemporaneous PD series [PPDD 8 (6-14) d vs PD 11 (10-16) d, median (IQR), P = 0.026]. The 30-d mortality was zero and 16 of 19 patients are alive to date. One patient died of recurrent duodenal adenocarcinoma 18 mo postoperatively and two died of unrelated disease (at 2 mo and at 8 years respectively). CONCLUSION PPDD is a versatile operation that can provide definitive treatment for a range of duodenal pathologies including adenocarcinoma

Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Abstract Background Research into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage. Results Here we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily. Conclusions The retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae.http://deepblue.lib.umich.edu/bitstream/2027.42/112762/1/13100_2013_Article_86.pd

Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Background: Research into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage. Results: Here we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily. Conclusions: The retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae. © 2013 McLain et al.; licensee BioMed Central Ltd

DENV-specific IgA contributes protective and non-pathologic function during antibody-dependent enhancement of DENV infection.

Dengue represents a growing public health burden worldwide, accounting for approximately 100 million symptomatic cases and tens of thousands of fatalities yearly. Prior infection with one serotype of dengue virus (DENV) is the greatest known risk factor for severe disease upon secondary infection with a heterologous serotype, a risk which increases as serotypes co-circulate in endemic regions. This disease risk is thought to be mediated by IgG-isotype antibodies raised during a primary infection, which poorly neutralize heterologous DENV serotypes and instead opsonize virions for uptake by FcγR-bearing cells. This antibody-dependent enhancement (ADE) of infection leads to a larger proportion of susceptible cells infected, higher viremia and greater immunopathology. We have previously characterized the induction of a serum IgA response, along with the typical IgM and IgG responses, during dengue infection, and have shown that DENV-reactive IgA can neutralize DENV and competitively antagonize IgG-mediated ADE. Here, we evaluate the potential for IgA itself to cause ADE. We show that IgG, but not IgA, mediated ADE of infection in cells expressing both FcαR and FcγRs. IgG-mediated ADE stimulated significantly higher pro-inflammatory cytokine production by primary human macrophages, while IgA did not affect, or slightly suppressed, this production. Mechanistically, we show that DENV/IgG immune complexes bind susceptible cells significantly more efficiently than DENV/IgA complexes or virus alone. Finally, we show that over the course of primary dengue infection, the expression of FcγRI (CD64) increases during the period of acute viremia, while FcγRIIa (CD32) and FcαR (CD89) expression decreases, thereby further limiting the ability of IgA to facilitate ADE in the presence of DENV. Overall, these data illustrate the distinct protective role of IgA during ADE of dengue infection and highlight the potential therapeutic and prognostic value of DENV-specific IgA

Design and conduct of Xtreme Everest 2: an observational cohort study of Sherpa and lowlander responses to graduated hypobaric hypoxia

Objective: oxygen availability falls with ascent to altitude and also as a consequence of critical illness. Because cellular sequelae and adaptive processes may be shared in both circumstances, high altitude exposure (‘physiological hypoxia’) assists in the exploration of the response to pathological hypoxia. We therefore studied the response of healthy participants to progressive hypobaric hypoxia at altitude. The primary objective of the study was to identify differences between high altitude inhabitants (Sherpas) and lowland comparators.Methods: we performed an observational cohort study of human responses to progressive hypobaric hypoxia (during ascent) and subsequent normoxia (following descent) comparing Sherpas with lowlanders. Studies were conducted in London (35m), Kathmandu (1300m), Namche Bazaar (3500m) and Everest Base Camp (5300m). Of 180 healthy volunteers departing from Kathmandu, 64 were Sherpas and 116 were lowlanders. Physiological, biochemical, genetic and epigenetic data were collected. Core studies focused on nitric oxide metabolism, microcirculatory blood flow and exercise performance. Additional studies performed in nested subgroups examined mitochondrial and metabolic function, and ventilatory and cardiac variables. Of the 180 healthy participants who left Kathmandu, 178 (99%) completed the planned trek. Overall, more than 90% of planned testing was completed. Forty-four study protocols were successfully completed at altitudes up to and including 5300m. A subgroup of identical twins (all lowlanders) was also studied in detail.Conclusion: this programme of study (Xtreme Everest 2) will provide a rich dataset relating to human adaptation to hypoxia, and the responses seen on re-exposure to normoxia. It is the largest comprehensive high altitude study of Sherpas yet performed. Translational data generated from this study will be of relevance to diseases in which oxygenation is a major facto

Temporal Variability of Human Vaginal Bacteria and Relationship with Bacterial Vaginosis

Little is known about short-term bacterial fluctuations in the human vagina. This study used PCR to assess the variability in concentrations of key vaginal bacteria in healthy women and the immediate response to antibiotic treatment in women with bacterial vaginosis (BV).Twenty-two women assessed for BV using Amsel's criteria were evaluated daily for 7 or 14 days, then at 2, 3 and 4 weeks, using a panel of 11 bacterium-specific quantitative PCR assays. Participants with BV were treated with 5 days of intravaginal metronidazole. Participants without BV had vaginal biotas dominated by lactobacilli, whose levels fluctuated with menses. With onset of menstruation, quantities of Lactobacillus jensenii and Lactobacillus crispatus decreased and were found to be inversely related to Gardnerella vaginalis concentrations (p<0.001). Women with BV had a variety of fastidious bacteria whose concentrations dropped below detection thresholds 1-5 days after starting metronidazole. Recurrent BV was characterized by initial profound decreases of BV-associated bacteria after treatment followed by subsequent increases at relapse.The microbiota of the human vagina can be highly dynamic. Healthy women are colonized with Lactobacillus species, but levels can change dramatically over a month. Marked increases in G. vaginalis were observed during menses. Participants with BV have diverse communities of fastidious bacteria that are depleted by vaginal metronidazole therapy. Women with recurrent BV initially respond to antibiotic treatment with steep declines in bacterial concentrations, but these bacteria later reemerge, suggesting that antibiotic resistance in these bacteria is not an important factor mediating BV recurrence

Clonal hematopoiesis and therapy-related myeloid neoplasms following neuroblastoma treatment.

Therapy-related myeloid neoplasms (TMN) constitute one of the most challengingcomplications of cancer treatment.1 Whilst understanding of TMN pathogenesis remains fragmentary, genomic studies in adults have thus far refuted the notion that TMN simply result from cytotoxin-induced DNA damage.2–4 Analysis of the preclinical evolution of a limited number of adult TMN have retraced the majority of cases to clonal haematopoiesis (CH) that predates cytotoxic treatment and lacks the mutational footprint of genotoxic therapies.2–6 Balanced translocations, generally attributed to treatment with topoisomerase II inhibitors, are implicated in a minority of TMN.1 TMN is a leading cause of premature death in childhood cancer survivors, and affects 7-11% of children treated for high-risk neuroblastoma and sarcoma.7,8 However, the origin of pediatric TMN remains unclear. Targeted sequencing of known cancer genes detects CH in ~4% of children following cytotoxic treatment,6,9 whereas CH is vanishingly rare in young individuals in the general population.10,11 Moreover, to our knowledge, no cases of childhood TMN have been retraced to pretreatment CH. In light of these observations, we asked whether a broader driver landscape had eluded targeted CH screens in pediatric cancer patients and/or whether therapy-induced mutagenesis may be an under-recognised catalyst of CH and TMN in this patient group