bluuebunny/crossref_metadata_2025 huggingface dataset:
Fastest time-series prediction rate achieved on a Boolean network reservoir
Authors: Cockbill Louisa
Published: December 2018

The utility of a network of Boolean nodes, with fading-memory property and real-valued input, has been demonstrated to predict the long-term behavior of a chaotic system.
Controlled, localized crystals grown via evaporation and capillary action using micropillar structures
Authors: DeJarnette Drew
Published: December 2018

Micropillar arrays fabricated using direct, femtosecond laser writing provide a tunable and low-cost way for growing microcrystals.
Dietary analysis reveals the vulnerability of the endangered Maugean skate (Zearaja maugeana) to benthic changes in Macquarie Harbour
Authors: Weltz Kay , Lyle Jeremy M. , Bell Justin D. , Semmens Jayson M.
Published: December 2018

Species occupying high trophic positions with a small population size, limited diet and restricted range are vulnerable to extinction. The endangered Maugean skate (Zearaja maugeana) in Macquarie Harbour is potentially threatened by changing benthic environmental conditions (declining dissolved oxygen concentrations and decreased macrofaunal diversity). To inform investigations on potential indirect impacts of benthic environmental changes on the Maugean skate and its prey, non-lethal techniques were used to identify dietary composition and trophic position of the species. The Maugean skate occupies a high trophic position (3.70) in the food web, with both stable-isotope (median 86% contribution to isotopic signatures, credible interval (CI)=44–100%) and stomach-content analysis showing crustaceans, particularly brachyuran crabs (58.5% index of relative importance), as the dominant prey type. Aquaculture feed from salmonid fish farms operating in the harbour was not found to be important in skate diet. This study showed that the Maugean skate consumes a small number of benthic prey species, highlighting its vulnerability to changing environmental conditions in the harbour.
The influence of the delay-period setting on camera-trap data storage, wildlife detections and occupancy models
Authors: Lepard Clara C. , Moll Remington J. , Cepek Jonathon D. , Lorch Patrick D. , Dennis Patricia M. , Robison Terry , Montgomery Robert A.
Published: December 2018

Context The use of camera traps in ecological research has grown exponentially over the past decade, but questions remain about the effect of camera-trap settings on ecological inference. The delay-period setting controls the amount of time that a camera trap is idle between motion-activated triggers. Longer delay periods may potentially extend battery life, reduce data-storage requirements, and shorten data-analysis time. However, they might result in lost data (i.e. missed wildlife detections), which could bias ecological inference and compromise research objectives. Aims We aimed to examine the effect of the delay period on (1) the number of camera-trap triggers, (2) detection and site-occupancy probabilities for eight mammalian species that varied in size, movement rate and commonness and (3) parameter estimates of habitat-based covariates from the occupancy models for these species. Methods We deployed 104 camera traps for 4 months throughout an extensive urban park system in Cleveland, Ohio, USA, using a spatially random design. Using the resultant data, we simulated delay periods ranging from 10s to 60min. For each of these delay periods and for each of our eight focal species, we calculated the number of camera-trap triggers and the parameter estimates of hierarchical Bayesian occupancy models. Key results A simulated increase in the delay period from 10s to 10min decreased the number of triggers by 79.6%, and decreased detection probability and occupancy probability across all species by 1.6% and 4.4% respectively. Further increases in the delay period (i.e. from 10 to 60min) resulted in modest additional reductions in the number of triggers and detection and occupancy probabilities. Variation in the delay period had negligible effects on the qualitative interpretations of habitat-based occupancy models for all eight species. Conclusions Our results suggest that delay-period settings ranging from 5 to 10min can drastically reduce data-storage needs and analysis time without compromising inference resulting from occupancy modelling for a diversity of mammalian species. Implications Broadly, we provide guidance on designing camera-trap studies that optimally trade-off research effort and potential bias, thereby increasing the utility of camera traps as ecological research tools.
Evidence for genuine hydrogen bonding in gold(I) complexes
Authors: Rigoulet Mathilde , Massou Stéphane , Sosa Carrizo E. Daiann , Mallet-Ladeira Sonia , Amgoune Abderrahmane , Miqueu Karinne , Bourissou Didier
Published: December 2018

The ability of gold to act as proton acceptor and participate in hydrogen bonding remains an open question. Here, we report the synthesis and characterization of cationic gold(I) complexes featuring ditopic phosphine-ammonium (P,NH
+
) ligands. In addition to the presence of short Au∙∙∙H contacts in the solid state, the presence of Au∙∙∙H–N hydrogen bonds was inferred by NMR and IR spectroscopies. The bonding situation was extensively analyzed computationally. All features were consistent with the presence of three-center four-electron attractive interactions combining electrostatic and orbital components. The role of relativistic effects was examined, and the analysis is extended to other recently described gold(I) complexes.
The lysine catabolite saccharopine impairs development by disrupting mitochondrial homeostasis
Authors: Zhou Junxiang , Wang Xin , Wang Min , Chang Yuwei , Zhang Fengxia , Ban Zhaonan , Tang Ruofeng , Gan Qiwen , Wu Shaohuan , Guo Ye , Zhang Qian , Wang Fengyang , Zhao Liyuan , Jing Yudong , Qian Wenfeng , Wang Guodong , Guo Weixiang , Yang Chonglin
Published: December 2018

Amino acid catabolism is frequently executed in mitochondria; however, it is largely unknown how aberrant amino acid metabolism affects mitochondria. Here we report the requirement for mitochondrial saccharopine degradation in mitochondrial homeostasis and animal development. In Caenorhbditis elegans, mutations in the saccharopine dehydrogenase (SDH) domain of the bi-functional enzyme α-aminoadipic semialdehyde synthase AASS-1 greatly elevate the lysine catabolic intermediate saccharopine, which causes mitochondrial damage by disrupting mitochondrial dynamics, leading to reduced adult animal growth. In mice, failure of mitochondrial saccharopine oxidation causes lethal mitochondrial damage in the liver, leading to postnatal developmental retardation and death. Importantly, genetic inactivation of genes that raise the mitochondrial saccharopine precursors lysine and α-ketoglutarate strongly suppresses SDH mutation-induced saccharopine accumulation and mitochondrial abnormalities in C. elegans. Thus, adequate saccharopine catabolism is essential for mitochondrial homeostasis. Our study provides mechanistic and therapeutic insights for understanding and treating hyperlysinemia II (saccharopinuria), an aminoacidopathy with severe developmental defects.
(Semi-)global analytic hypoellipticity for a class of “sums of squares” which fail to be locally analytic hypoelliptic
Authors: Chinni Gregorio
Published: December 2018

The global and semi-global analytic hypoellipticity on the torus is proved for two classes of sums of squares operators, introduced by P. Albano, A. Bove, and M. Mughetti, satisfying the Hörmander condition and which fail to be either locally or microlocally analytic hypoelliptic.
Widespread Cognitive Deficits in Alcoholism Persistent Following Prolonged Abstinence: An Updated Meta-analysis of Studies That Used Standardised Neuropsychological Assessment Tools
Authors: Crowe Simon F , Cammisuli Davide M , Stranks Elizabeth K
Published: December 2018

Objective

This study presents an updated meta-analysis replicating the study of (Stavro, K., Pelletier, J., & Potvin, S. (2013). Widespread and sustained cognitive deficits in alcoholism: A meta-analysis. Addiction Biology, 18, 203–213. doi:10.1111/j.1369-1600.2011.00418.x) regarding the cognitive functioning of alcoholics as a function of time abstinent.

Methods

A total of 34 studies (including a total of 2,786 participants) that met pre-determined inclusion and exclusion criteria were included in the analyses. The alcoholics were categorised into recently detoxified alcoholics (0–31 days sober), alcoholics 32–365 days sober and alcoholics >365 days sober consistent with the previous study. The current study employed more stringent control on the tests included in the analysis to include only those tasks described in contemporary neuropsychological test compendia. Forty-seven percent of the papers surveyed were not include in the previous meta-analysis.

Results

The results indicated that there was a diffuse and pervasive pattern of cognitive deficit among recently detoxified alcoholics and that these deficits, particularly with regard to memory functioning, persisted even in longer term abstinent alcoholics. This was inconsistent with the prior meta-analysis which contended that significant cognitive recovery was possible after as little as 1 year.

Conclusion

The persisting cognitive deficits were noted across a wide range of cognitive functions, supporting the notion of a diffuse rather than a specific compromise of cognition in alcoholism following discontinuation, as measured using standardised neuropsychological tests. Limitations on the finding included the fact that it was a cross-sectional rather than a longitudinal analysis, was subject to heterogeneity of method, had low representation of females in the samples, and had fewer studies of long-term sober samples.
Fully unsupervised symmetry-based mitosis detection in time-lapse cell microscopy
Authors: Gilad Topaz , Reyes Jose , Chen Jia-Yun , Lahav Galit , Riklin Raviv Tammy
Published: December 2018

Motivation

Cell microscopy datasets have great diversity due to variability in cell types, imaging techniques and protocols. Existing methods are either tailored to specific datasets or are based on supervised learning, which requires comprehensive manual annotations. Using the latter approach, however, poses a significant difficulty due to the imbalance between the number of mitotic cells with respect to the entire cell population in a time-lapse microscopy sequence.

Results

We present a fully unsupervised framework for both mitosis detection and mother–daughters association in fluorescence microscopy data. The proposed method accommodates the difficulty of the different cell appearances and dynamics. Addressing symmetric cell divisions, a key concept is utilizing daughters’ similarity. Association is accomplished by defining cell neighborhood via a stochastic version of the Delaunay triangulation and optimization by dynamic programing. Our framework presents promising detection results for a variety of fluorescence microscopy datasets of different sources, including 2D and 3D sequences from the Cell Tracking Challenge.

Availability and implementation

Code is available in github (github.com/topazgl/mitodix).

Supplementary information

Supplementary data are available at Bioinformatics online.
PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization
Authors: Yu Jialin , Shi Shaoping , Zhang Fang , Chen Guodong , Cao Man
Published: December 2018

Motivation

Protein glycation is a familiar post-translational modification (PTM) which is a two-step non-enzymatic reaction. Glycation not only impairs the function but also changes the characteristics of the proteins so that it is related to many human diseases. It is still much more difficult to systematically detect glycation sites due to the glycated residues without crucial patterns. Computational approaches, which can filter supposed sites prior to experimental verification, can extremely increase the efficiency of experiment work. However, the previous lysine glycation prediction method uses a small number of training datasets. Hence, the model is not generalized or pervasive.

Results

By searching from a new database, we collected a large dataset in Homo sapiens. PredGly, a novel software, can predict lysine glycation sites for H.sapiens, which was developed by combining multiple features. In addition, XGboost was adopted to optimize feature vectors and to improve the model performance. Through comparing various classifiers, support vector machine achieved an optimal performance. On the basis of a new independent test set, PredGly outperformed other glycation tools. It suggests that PredGly can provide more instructive guidance for further experimental research of lysine glycation.

Availability and implementation

https://github.com/yujialinncu/PredGly

Supplementary information

Supplementary data are available at Bioinformatics online.
mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation
Authors: Manavalan Balachandran , Basith Shaherin , Shin Tae Hwan , Wei Leyi , Lee Gwang
Published: December 2018

Motivation

Cardiovascular disease is the primary cause of death globally accounting for approximately 17.7 million deaths per year. One of the stakes linked with cardiovascular diseases and other complications is hypertension. Naturally derived bioactive peptides with antihypertensive activities serve as promising alternatives to pharmaceutical drugs. So far, there is no comprehensive analysis, assessment of diverse features and implementation of various machine-learning (ML) algorithms applied for antihypertensive peptide (AHTP) model construction.

Results

In this study, we utilized six different ML algorithms, namely, Adaboost, extremely randomized tree (ERT), gradient boosting (GB), k-nearest neighbor, random forest (RF) and support vector machine (SVM) using 51 feature descriptors derived from eight different feature encodings for the prediction of AHTPs. While ERT-based trained models performed consistently better than other algorithms regardless of various feature descriptors, we treated them as baseline predictors, whose predicted probability of AHTPs was further used as input features separately for four different ML-algorithms (ERT, GB, RF and SVM) and developed their corresponding meta-predictors using a two-step feature selection protocol. Subsequently, the integration of four meta-predictors through an ensemble learning approach improved the balanced prediction performance and model robustness on the independent dataset. Upon comparison with existing methods, mAHTPred showed superior performance with an overall improvement of approximately 6–7% in both benchmarking and independent datasets.

Availability and implementation

The user-friendly online prediction tool, mAHTPred is freely accessible at http://thegleelab.org/mAHTPred.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fast nonconvex deconvolution of calcium imaging data
Authors: Jewell Sean W , Hocking Toby Dylan , Fearnhead Paul , Witten Daniela M
Published: December 2018

Calcium imaging data promises to transform the field of neuroscience by making it possible to record from large populations of neurons simultaneously. However, determining the exact moment in time at which a neuron spikes, from a calcium imaging data set, amounts to a non-trivial deconvolution problem which is of critical importance for downstream analyses. While a number of formulations have been proposed for this task in the recent literature, in this article, we focus on a formulation recently proposed in Jewell and Witten (2018. Exact spike train inference via $\ell_{0} $ optimization. The Annals of Applied Statistics12(4), 2457–2482) that can accurately estimate not just the spike rate, but also the specific times at which the neuron spikes. We develop a much faster algorithm that can be used to deconvolve a fluorescence trace of 100 000 timesteps in less than a second. Furthermore, we present a modification to this algorithm that precludes the possibility of a “negative spike”. We demonstrate the performance of this algorithm for spike deconvolution on calcium imaging datasets that were recently released as part of the $\texttt{spikefinder}$ challenge (http://spikefinder.codeneuro.org/). The algorithm presented in this article was used in the Allen Institute for Brain Science’s “platform paper” to decode neural activity from the Allen Brain Observatory; this is the main scientific paper in which their data resource is presented. Our $\texttt{C++}$ implementation, along with $\texttt{R}$ and $\texttt{python}$ wrappers, is publicly available. $\texttt{R}$ code is available on $\texttt{CRAN}$ and $\texttt{Github}$, and $\texttt{python}$ wrappers are available on $\texttt{Github}$; see https://github.com/jewellsean/FastLZeroSpikeInference.
Prevalence, Predictors, and Successful Treatment Outcomes of Xpert MTB/RIF–identified Rifampicin-resistant Tuberculosis in Post-conflict Eastern Democratic Republic of the Congo, 2012–2017: A Retrospective Province-Wide Cohort Study
Authors: Bulabula André N H , Nelson Jenna A , Musafiri Eric M , Machekano Rhoderick , Sam-Agudu Nadia A , Diacon Andreas H , Shah Maunank , Creswell Jacob , Theron Grant , Warren Robin M , Jacobson Karen R , Chirambiza Jean-Paul , Kalumuna Dieudonné , Bisimwa Bertin C , Katoto Patrick D M C , Kaswa Michel K , Birembano Freddy M , Kitete Liliane , Grobusch Martin P , Kashongwe Zacharie M , Nachega Jean B
Published: December 2018

Background

Multidrug-resistant tuberculosis (MDR-TB) jeopardizes global TB control. The prevalence and predictors of Rifampicin-resistant (RR) TB, a proxy for MDR-TB, and the treatment outcomes with standard and shortened regimens have not been assessed in post-conflict regions, such as the South Kivu province in the eastern Democratic Republic of the Congo (DRC). We aimed to fill this knowledge gap and to inform the DRC National TB Program.

Methods

of adults and children evaluated for pulmonary TB by sputum smear microscopy and Xpert MTB/RIF (Xpert) from February 2012 to June 2017. Multivariable logistic regression, Kaplan–Meier estimates, and multivariable Cox regression were used to assess independent predictors of RR-TB and treatment failure/death.

Results

Of 1535 patients Xpert-positive for TB, 11% had RR-TB. Independent predictors of RR-TB were a positive sputum smear (adjusted odds ratio [aOR] 2.42, 95% confidence interval [CI] 1.63–3.59), retreatment of TB (aOR 4.92, 95% CI 2.31–10.45), and one or more prior TB episodes (aOR 1.77 per episode, 95% CI 1.01–3.10). Over 45% of RR-TB patients had no prior TB history or treatment. The median time from Xpert diagnosis to RR-TB treatment initiation was 12 days (interquartile range 3–60.2). Cures were achieved in 30/36 (83%) and 84/114 (74%) of patients on 9- vs 20/24-month MDR-TB regimens, respectively (P = .06). Predictors of treatment failure/death were the absence of directly observed therapy (DOT; adjusted hazard ratio [aHR] 2.77, 95% CI 1.2–6.66) and any serious adverse drug event (aHR 4.28, 95% CI 1.88–9.71).

Conclusions

Favorable RR-TB cure rates are achievable in this post-conflict setting with a high RR-TB prevalence. An expanded Xpert scale-up; the prompt initiation of shorter, safer, highly effective MDR-TB regimens; and treatment adherence support are critically needed to optimize outcomes.
Tetralogy of Fallot: morphological variations and implications for surgical repair
Authors: Khan Saad M , Drury Nigel E , Stickley John , Barron David J , Brawn William J , Jones Timothy J , Anderson Robert H , Crucean Adrian
Published: December 2018

OBJECTIVES

Tetralogy of Fallot is characterized by anterocephalad deviation of the outlet septum, along with abnormal septoparietal trabeculations, which lead to subpulmonary infundibular stenosis. Archives of retained hearts are an important resource for improving our understanding of congenital heart defects and their morphological variability. This study aims to define variations in aortic override, coronary arterial patterns and ventricular septal defects in tetralogy of Fallot as observed in a morphological archive, highlighting implications for surgical management.

METHODS

The Birmingham Children’s Hospital archive contains 211 hearts with tetralogy of Fallot, of which 164 were analysed [69 (42.1%) unrepaired and 95 (57.9%) operated specimens]. A detailed morphological and geometric analysis was performed using a rigorous 5-layer review process.

RESULTS

Anomalies were observed in the orifices, origins and course of the coronary arteries: 20 hearts (13.0%) had more than 2 orifices and 3 hearts (1.9%) had a single orifice. In 7 hearts (4.3%), a coronary artery crossed the right ventricular outflow tract. The extent of aortic override ranged from 31.0% to 100% (median of 59.5%). The ventricular septal defect was most often perimembranous (139, 84.8%), but we also found muscular (14, 8.5%), atrioventricular (7, 4.3%) and doubly committed juxta-arterial (2, 1.2%) variants.

CONCLUSIONS

Anatomical variations are common and can impact surgical management. Anomalous coronary arteries may require a conduit rather than a transannular patch. Variability in aortic override determines the size of patch used to baffle blood to the aorta. The type of ventricular septal defect affects patch closure and the risk of postoperative conduction defects.
Glycated haemoglobin (HbA1c) as a reliable option for detecting diabetes among the urban poor population in Bangladesh
Authors: Chiang Chifa , Aoyama Atsuko , Khalequzzaman Md , Choudhury Sohel R. , Paul Debatosh , Rayna Shahrin E. , Khan Fahmida A. , Hirakawa Yoshihisa , Iso Hiroyasu , Yatsuya Hiroshi
Published: December 2018

Our previous epidemiological survey targeting urban slum dwellers in Bangladesh showed that the prevalence of diabetes defined by glycated haemoglobin (HbA1c) was higher than the national estimation, and higher in women than men. Subsequently, we conducted the oral glucose tolerance test (OGTT) and found that HbA1c values were consistent with the OGTT findings for detecting diabetes. Our findings indicated that HbA1c ≥6.5% was a rational cut-off, but the optimal HbA1c cut-off for this population might be lower than the internationally recommended threshold. Measuring HbA1c would be a reliable and feasible option for detecting diabetes among underprivileged population in developing countries.
Barriers to GPs identifying patients at the end-of-life and discussions about their care: a qualitative study
Authors: Pocock Lucy V , Wye Lesley , French Lydia R M , Purdy Sarah
Published: December 2018

Background

Identification of patients at the end-of-life is the first step in care planning and many general practices have Palliative Care Registers. There is evidence that these largely comprise patients with cancer diagnoses, but little is known about the identification process.

Objective

To explore the barriers that hinder GPs from identifying and registering patients on Palliative Care Registers.

Methods

An exploratory qualitative approach was undertaken using semi-structured interviews with GPs in South West England. GPs were asked about their experiences of identifying, registering and discussing end-of-life care with patients. Interviews were audio recorded, transcribed and analysed thematically.

Results

Most practices had a Palliative Care Register, which were mainly composed of patients with cancer. They reported identifying non-malignant patients at the end-of-life as challenging and were reluctant to include frail or elderly patients due to resource implications. GPs described rarely using prognostication tools to identify patients and conveyed that poor communication between secondary and primary care made prognostication difficult. GPs also detailed challenges around talking to patients about end-of-life care.

Conclusions

Palliative Care Registers are widely used by GPs for patients with malignant diagnoses, but seldom for other patients. The findings from our study suggest that this arises because GPs find prognosticating for patients with non-malignant disease more challenging. GPs would value better communication from secondary care, tools for prognostication and training in speaking with patients at the end-of-life enabling them to better identify non-malignant patients at the end-of-life.
Determining the extent and drivers of attrition losses from wind using long-term datasets and machine learning techniques
Authors: Moore John , Lin Yue
Published: December 2018

In addition to causing large-scale catastrophic damage to forests, wind can also cause damage to individual trees or small groups of trees. Over time, the cumulative effect of this wind-induced attrition can result in a significant reduction in yield in managed forests. Better understanding of the extent of these losses and the factors associated with them can aid better forest management. Information on wind damage attrition is often captured in long-term growth monitoring plots but analysing these large datasets to identify factors associated with the damage can be problematic. Machine learning techniques offer the potential to overcome some of the challenges with analysing these datasets. In this study, we applied two commonly-available machine learning algorithms (Random Forests and Gradient Boosting Trees) to a large, long-term dataset of tree growth for radiata pine (Pinus radiata D. Don) in New Zealand containing more than 157 000 observations. Both algorithms identified stand density and height-to-diameter ratio as being the two most important variables associated with the proportion of basal area lost to wind. The algorithms differed in their ease of parameterization and processing time as well as their overall ability to predict wind damage loss. The Random Forest model was able to predict ~43 per cent of the variation in the proportion of basal area lost to wind damage in the training dataset (a random sample of 80 per cent of the original data) and 45 per cent of the validation dataset (the remaining 20 per cent of the data). Conversely, the Gradient Boosting Tree model was able to predict more than 99 per cent of the variation in wind damage loss in the training dataset, but only ~49 per cent of the variation in the validation dataset, which highlights the potential for overfitting models to specific datasets. When applying these techniques to long-term datasets, it is also important to be aware of potential issues with the underlying data such as missing observations resulting from plots being abandoned without measurement when damage levels have been very high.
Impact of Sarcopenia on Adverse Outcomes After Allogeneic Hematopoietic Cell Transplantation
Authors: Armenian Saro H , Xiao Meisi , Berano Teh Jennifer , Lee Brandyn , Chang Howard A , Mascarenhas Kristen , Lee Sean , Iukuridze Alex , Xie Jack J , Scott Jessica M , Jones Lee W , Lennie Wong F , Forman Stephen J , Nakamura Ryotaro
Published: December 2018

Background

High intensity treatments such as hematopoietic cell transplantation (HCT) can be curative for patients with hematologic malignancies, but this needs to be balanced by the high risk of nonrelapse mortality (NRM) during the first 2 years after HCT. Sarcopenia (low muscle mass) is associated with physical disability and premature mortality in individuals with nonmalignant diseases and may be a predictor of NRM and poor overall survival in patients undergoing HCT.

Methods

This was a retrospective cohort study of 859 patients with acute leukemia or myelodysplastic syndrome who underwent a first HCT as adults (≥18 years) between 2007 and 2014. Sarcopenia was assessed from pre-HCT abdominal computed tomography scans. Two-year cumulative incidence of NRM was calculated, with relapse/progression considered as a competing risk event. Fine-Gray subdistribution hazard ratio estimates and 95% confidence intervals (CI) were obtained and adjusted for relevant covariates. Kaplan-Meier method was used to examine overall survival. All statistical tests were two-sided.

Results

Median age at HCT was 51 years (range = 18–74 years); 52.5% had a high [≥3] HCT-comorbidity index; 33.7% had sarcopenia pre-HCT. Sarcopenia was an independent predictor of higher NRM risk (hazard ratio = 1.58, 95% CI = 1.16 to 2.16) compared with patients who were not. The 2-year incidence of NRM approached 30% in patients with sarcopenia and high (≥3) HCT-comorbidity index. Patients with sarcopenia had on average a longer hospitalization (37.2 days vs 31.5 days, P < .001) and inferior overall survival at 2 years (55.2%, 95% CI = 49.5% to 61.0% vs 66.9%, 95% CI = 63.0% to 70.8%, P < .001).

Conclusions

Sarcopenia is an important and independent predictor of survival after HCT, with potential additional downstream impacts on health-economic outcomes. This information can be used to facilitate treatment decisions prior to HCT and guide interventions to decrease the risk of treatment-related complications after HCT.
Molecular types of Cryptococcus neoformans and Cryptococcus gattii in Western Australia and correlation with antifungal susceptibility
Authors: Lee Gar-hing Andrew , Arthur Ian , Merritt Adam , Leung Michael
Published: December 2018

Cryptococcus neoformans and Cryptococcus gattii species complexes have a worldwide distribution; however, there is geographical variation in the prevalence of different molecular types. Additionally, antifungal susceptibility differences between molecular types have been demonstrated. This study investigates the distribution of cryptococcal molecular types among human clinical isolates over a 10-year period from a Western Australian population. Molecular type was determined based on polymorphisms in the phospholipase gene locus identified through amplification and sequencing. Minimum inhibitory concentrations (MICs) were identified for fluconazole, 5-fluorocytosine, posaconazole, itraconazole, voriconazole, and amphotericin B. Most isolates were C. neoformans complex (42) of which over half were molecular type VNI (22) followed by VNII (20). Among the remaining C. gattii complex (13) the majority were VGI (11) with VGII (2) uncommonly found. All isolates demonstrated low MICs to antifungal agents including fluconazole. Geometric mean MIC values against 5-fluorocytosine for VNI (1.741 mg/l) were significantly higher than those for VGI (0.47 mg/l, P = .002). Similarly fluconazole geometric mean MICs against fluconazole for VNI (2.3 mg/l) were significantly higher than VNII (0.87 mg/l, P = .036). These data reveal the presence of four molecular types (VNI, VNII, VGI and VGII) within clinical Western Australian cryptococcal isolates and, while elevated antifungal MICs were not encountered, significant molecular type dependent differences in susceptibility were found.
Effect of denosumab on trabecular bone score in de novo kidney transplant recipients
Authors: Bonani Marco , Frey Diana , Graf Nicole , Wüthrich Rudolf P
Published: December 2018

Background

Kidney transplant recipients (KTR) are at risk to lose bone mass. The trabecular bone score (TBS) represents a recently developed parameter of lumbar spine trabecular bone texture that correlates with the occurrence of fractures.

Methods

We analysed the 1-year changes in TBS in 44 de novo KTR that were randomized 1:1 to denosumab or no treatment. TBS was derived from dual energy X-ray absorptiometry and was correlated with 1-year areal bone mineral density (aBMD) changes at the lumbar spine and total hip. Correlations were also performed with parameters of peripheral bone microarchitecture and bone strength at the distal tibia and distal radius, as assessed by high-resolution peripheral quantitative computed tomography (HRpQCT) and micro-finite element analysis.

Results

The baseline TBS in KTR amounted to 1.312 ± 0.101, which is lower than the TBS of an age-matched normal control population (range 1.364–1.471). The TBS correlated positively with aBMD at the lumbar spine (Spearman’s ρ = 0.56; P < 0.001) and total hip (ρ = 0.33; P < 0.05). The baseline TBS also correlated with HRpQCT-derived total (ρ = 0.49; P < 0.05) and trabecular volumetric BMD (ρ = 0.57; P < 0.01) and trabecular separation (ρ = −0.46; P < 0.05) at the tibia. Denosumab treatment led to an increase in TBS, paralleling the BMD changes at the lumbar spine.

Conclusions

The TBS is a useful additional score of bone health, which may help to better define fracture risk. Treatment with denosumab led to improved trabecular bone texture in de novo KTR in addition to its beneficial effect on BMD.
Pilot randomized, controlled trial of a dyadic yoga program for glioma patients undergoing radiotherapy and their family caregivers
Authors: Milbury Kathrin , Li Jing , Weathers Shiao-Pei , Mallaiah Smitha , Armstrong Terri , Li Yisheng , Bruera Eduardo , Cohen Lorenzo
Published: December 2018

Background

While the use of behavioral medicine in managing glioma patients’ symptoms is not well studied, the high symptom burden in patients and their family caregivers is well established. We conducted a pilot randomized, controlled trial to examine the feasibility and preliminary efficacy of a dyadic yoga (DY) intervention as a supportive care strategy.

Methods

Glioma patients undergoing radiotherapy and their caregivers were randomized to a 12-session DY or waitlist control (WLC) group. Prior to radiotherapy and randomization, both groups completed measures of cancer-related symptoms (MD Anderson Symptom Inventory-Brain Tumor module), depressive symptoms (Center for Epidemiological Studies-Depression measure), fatigue (Brief Fatigue Inventory), and overall quality of life (QOL; Medical Outcomes Study 36-item short-form survey). Dyads were reassessed at the last day of radiotherapy.

Results

Twenty patients (mean age: 46 years, 50% female, 80% WHO grade IV and caregivers (mean age: 50 years, 70% female, 50% spouses) participated in the trial. A priori feasibility criteria were met regarding consent (70%), adherence (88%), and retention (95%) rates. Controlling for relevant covariates, change score analyses revealed clinically significant improvements for patients in the DY compared with the WLC group for overall cancer symptom severity (d = 0.96) and symptom interference (d = 0.74), depressive symptoms (d = 0.71), and mental QOL (d = 0.69). Caregivers in the DY group reported clinically significant improvements in depressive symptoms (d = 1.12), fatigue (d = 0.89), and mental QOL (d = 0.49) relative to those in the WLC group.

Conclusion

A DY intervention appears to be a feasible and beneficial symptom and QOL management strategy for glioma patients undergoing radiotherapy and their caregivers. An efficacy trial with a more stringent control group is warranted.

Clinical Trial Number

NCT02481349
Glioma surgery under awake condition can lead to good independence and functional outcome excluding deep sensation and visuospatial cognition
Authors: Nakajima Riho , Kinoshita Masashi , Okita Hirokazu , Yahata Tetsutaro , Nakada Mitsutoshi
Published: December 2018

Background

Awake surgery for the eloquent cortex is a common strategy for glioma surgery. Although a recent emphasis has been placed on awake surgery both for dominant and nondominant cerebral hemispheres to preserve neurological/neuropsychological functions, those functional outcomes are not well investigated because few studies have focused on the longitudinal recovery process. This study explored the outcome of neurological/neuropsychological functions following awake surgery until the chronic phase.

Methods

A total of 87 patients with glioma who underwent awake surgery were included, and of these 66 patients matched our inclusion criteria. Each patient was assessed for neurological/neuropsychological functions before surgery, as well as acute and chronic phase. Additionally, scores for the KPS were collected.

Results

Almost all functions recovered within 3 months postoperatively, even when transient deficits were observed in the acute phase; however, deep sensory perception deficits and visuospatial cognitive disorders persisted into the chronic phase (15.4% of patients with parietal lesions, 14.3% of patients with right cerebral hemispheric lesion, respectively). KPS score ≥90 was achieved in 86.0% of patients with lower-grade glioma, whereas only 52.2% of glioblastoma patients scored ≥90. Primary causes of declined KPS were disorder of visuospatial cognition, sensorimotor function including deep sensation, aphasia, and emotional function.

Conclusions

Awake surgery leads to good functional outcome at the chronic phase of neurological/neuropsychological functions, except for deep sensory and visuospatial cognition. Because sensation and visuospatial cognitive disorder have major impacts on patients’ independence level, further importance should be placed on preserving these functions during surgery.
Multidimensional Consequentialism and Population Ethics
Authors: Peterson Martin
Published: December 2018

The main claim of this chapter is that multidimensional consequentialists have reason to reject some of the key premises of Parfit’s Mere Addition Paradox as well as Arrhenius’s sixth impossibility theorem. The latter is the most general and far-reaching impossibility theorem in the literature on population ethics. The chapter shows that multidimensional consequentialists can reasonably maintain that the mere addition of people who have lives worth living is not always entirely right. To add what Parfit calls “extra people” is right with respect to one moral aspect (the size of the population) but wrong with respect to another (the average quality of life).
Sonidos Negros
Authors: Goldberg K. Meira
Published: December 2018

How is the politics of Blackness figured in the flamenco dancing body? What does flamenco dance tell us about the construction of race in the Atlantic world? Sonidos Negros traces how, between 1492—when Christian reconquest of the Iberian Peninsula coincided with Christopher Columbus’s landing on Hispaniola—and 1933—when Andalusian poet Federico García Lorca published his “Theory and Play of the Duende”—the vanquished Moor became Black; and how the imagined Gitano (“Gypsy,” or Roma) embodies the warring images and sounds of this process. By the nineteenth-century nadir of its colonial reach, Spanish identity was paradoxically enacted in terms of a minstrelized Gitano, a hybrid of Spanish and American representations of Blackness. Flamenco’s imagined Gypsy, teetering between ostentatious ignorance and the humility of epiphany, references an earlier trope: the pastor bobo (foolish shepherd), who, seeing an angelic apparition, must decide whether to accept the light of Christ—or remain in darkness. Spain’s symbolic linkage of this religious peril with the Blackness of abjection scripts the evangelical narrative which defeated the Moors and enslaved the Americas. The bobo’s confusion, appealingly comic but holding the pathos of the ultimate stakes of his decision—heaven or hell, safety or extermination—bares a teeming view of the embodied politics of colonial exploitation and creole identity formation. Flamenco’s Sonidos Negros live in this precarious balance, amid the purposeful ruckus cloaking danced resistance, the lament for what has been lost, and the values and aspirations of those rendered imperceptible by slavery and colonization.
Concentric Circles of Theatricality
Authors: Goldberg K. Meira
Published: December 2018

In early modern Spain, raza (race) signified the stain of Blackness, while casta (chaste, caste) signified purity of blood—Whiteness. But with its empire in decline, eighteenth-century Spain enacted its dreams of sovereignty and autonomy by impersonating a dark Other, whose Semitic and south-Saharan African antecedents were now wrapped within an imaginary Gitano. Majismo, emulating the fashions of the urban underclass, adopted the fandango, an American dance of slaves and outlaws, as an emblem of pure-blooded Spanishness. Adopting fandango dances such as the profane Mexican panaderos, an Africanist belly-to-belly dance incorporated into the bolero school repertoire, majismo figured the deeply political dissonance between the determinism of Christian blood purity and the possibility of redemption implicit in the bobo’s equivocal confusion. Ironically, the fandango was adopted throughout the Western world as a symbol of freedom and class mobility, a metaphor that soon inflected every aspect of the world’s perception of Spain.
Parody and Sorrow
Authors: Goldberg K. Meira
Published: December 2018

Faced with the loss of global hegemony, Spain claimed the outlaw Other as self. As in the United States, this dark vessel for the nation’s “soul” was fulsome in its ironic self-awareness and disillusioned sense of its own diminution. Mariano Soriano Fuertes’s El Tío Caniyitas (1849) records Spain’s response to U.S. blackface minstrelsy in terms of indigenous southern (Andalusian) representational tropes. Spain saw itself in the minstrelized figure of a dispossessed and fractured Black body, yet in this parody of power as powerlessness we sense flamenco’s tragic essence—its tormenting spirit—its duende. There is something of the sacred, of the sublime, in Spain’s exalted antiheroes, enduring public torture, degrading death, or the bondage from which they would not emerge alive. In absorbing American blackface’s heated rhetoric, perhaps because it was already inherent in such equivocal Spanish figures, developing flamenco seems to resonate with these deep and deeply violent contradictions.
Tilting across the Racial Divide
Authors: Goldberg K. Meira
Published: December 2018

Andalusian Gitanophilia, like its forebear majismo, paradoxically asserted wealth, culture, and liberal democratic values. Flamenco’s mid-nineteenth century emergence can therefore be read as responding to U.S. blackface minstrelsy, enacting affiliation with the structures of colonial power. The Spanish bobo’s narrative of transcendence thus weaves through the very flamenco story of Jacinto Padilla, “El Negro Meri,” a black man, and the first recorded male flamenco artist, filmed in 1900 Paris. Long forgotten, Padilla had a colorful career as an equestrian acrobat, bullfighter, and singer-dancer. He bequeaths important gifts to flamenco song, in the Tangos del Piyayo, and to dance, in the virtuosic jumps of the Farruco dynasty. El Negro Meri claimed mastery, body power, and transcendence—the freedom to become. An acrobat on a tightrope between European and American ghettoes of fictitious Blackness, he defied the blackface trope of the broken body and propelled European culture toward a complicated Modernism.
Afterword
Authors: Goldberg K. Meira
Published: December 2018

The projects of “fugitive planning and black study” are mostly about reaching out to find connection; they are about making common cause with the brokenness of being, a brokenness, I would venture to say, that is also blackness.

—Jack Halberstam, The Undercommons

Katherine Lee Bates’s 1899 article in ...
Gabriel Fauré and Théodore Reinach
Authors: Dorf Samuel N.
Published: December 2018

This chapter focuses on archaeologist and music scholar Théodore Reinach’s collaboration with composer Gabriel Fauré. In 1894 Reinach asked the composer to create an instrumental accompaniment to a recently discovered second-century BCE hymn dedicated to Apollo in Delphi. Reinach, along with other scholars from the French school of Athens, deciphered the Greek notation from the marble tablets, and Fauré wrote a modern accompaniment to the original melody. For Reinach, the need to re-enact antiquity transcended scholarly interest in his personal life. Reinach not only reconstructed ancient Greek music, but also built a replica ancient Greek villa in the south of France (with a modern piano hidden behind an ancient cabinet) in order to live out his ancient Greek fantasies. This chapter uses the metaphor of the modern piano hidden behind the ancient veneer of the cabinet to explore the ways modern aesthetics lurk underneath the scientific reconstructions of ancient music carried out by Reinach in the 1890s and 1910s.
Speculation
Authors: Achinstein Peter
Published: December 2018

Newton urged scientists never to speculate, only to prove by establishing experimental facts. Einstein urged scientists to speculate freely, since only daring speculations, not experimental facts, can advance science. Who, if either, is right? Is speculating a legitimate part of science, even in the absence of testing? If so, can speculations be evaluated without testing? How? To answer these questions, the book begins with an attempt to define the concept of speculation, a task not usually investigated by those who express strong views about speculation. The basic idea developed in the book is that speculating involves introducing assumptions, under certain “theorizing” conditions, without knowing that there is evidence for those assumptions. This idea is made precise using a concept of “evidence” that Achinstein has introduced in previous writings and also explains here. With this concept, Achinstein defends a view according to which, by contrast with Newton, speculations are crucial in science and, by contrast with Einstein, they are subject to constraints. The latter include pragmatic ones, reflecting the particular aims of the scientist in speculating, and epistemic ones that are subject to a different standard from that of “evidence sufficient for belief.” This viewpoint is illustrated and evaluated by critically examining historical and contemporary speculations in fundamental physics, as well as more general speculations within or about science, including that: nature is simple, and simplicity is a sign of truth (Newton, Einstein); a theory can only be tested “holistically” (Duhem, Quine); and there is and must be a “Theory of Everything” (string theorists, reductionists).
The Tortuous Road from St. Thomas to River Garden
Authors: Vale Lawrence J.
Published: December 2018

Chapter 4 follows the tortuous course that led St. Thomas to its redevelopment, revealing the machinations of a governance constellation centered on the prerogatives of the Big Developer. Starting in the late 1980s, the struggling housing project had multiple suitors eager to launch a transformation. The redevelopment effort faced a long series of false starts and endured multiple lawsuits and setbacks. Eventually, championed by maverick developer Pres Kabacoff, this yielded the mixed-income community of River Garden, completed in phases between 2001 and 2009. Although the initial HOPE VI application had proposed a majority of low-income housing on the site, subsequent proposals shifted to plans emphasizing market-rate and tax-credit housing plus a Walmart supercenter, with additional scattered-site public housing for large families promised but never constructed. Eventually, however, market conditions soured and the actual development that got built has far less market-rate housing than this midcourse correction had sought to deliver.
Inhabiting and Inhibiting River Garden
Authors: Vale Lawrence J.
Published: December 2018

Chapter 5 reveals the challenges of inhabiting and managing River Garden. Phase 1 opened in November 2004. The devastation wrought by the Katrina disaster in August 2005—coupled with ensuing challenges to the housing market—caused subsequent phases to be delayed, altered, or cancelled. Rather than an investment that would create a “win-win” combination of a revitalized neighborhood and genuine opportunity for the former neighborhood’s least-advantaged residents, the redevelopment process, slowly but surely, shunted public housing tenants to the margins—both literally and figuratively—and also failed to construct the market-dominated community that the developer wanted. Framed by policymakers as a deconcentration of poverty, this strand of HOPE VI instead purged the poorest and yielded many ongoing tensions in community governance. Still, St. Thomas became a precedent for the post-Katrina transformation of many of the remaining large public housing developments in New Orleans.