bluuebunny/crossref_metadata_2025 huggingface dataset:
Survey of Clinical and Anatomic Pathology Laboratory Infrastructure in Mozambique
Authors: Ismail Mamudo R , Noormahomed Emília V , Lawicki Shaun , Eichbaum Quentin
Published: February 2021

Objectives

Pathology services are limited in most areas of sub-Saharan Africa. This study’s aim was to survey anatomic and clinical pathology services and laboratory infrastructure in Mozambique.

Methods

A survey was conducted from October-December 2018 across the four central hospitals of Mozambique to determine infrastructure and pathology services available.

Results

Most laboratory/pathology services in Mozambique are limited to the four central hospitals. Only 14 pathologists practice in the country despite a population of 29.5 million for the world’s fifth worst workforce/population ratio. Approximately 35,000 anatomic pathology specimens are evaluated annually. Standard services across chemistry, hematology, microbiology, and blood bank are available at the four central hospitals. Esoteric laboratory testing and immunohistochemistry are generally only available in Maputo.

Conclusions

While most pathology services are available in Mozambique, many are available only at the Maputo laboratory. Expansion of pathology services and infrastructure will improve provision of effective and efficient health care as access to timely and accurate clinical diagnoses increases in Mozambique.
Separating Algorithms From Questions and Causal Inference With Unmeasured Exposures: An Application to Birth Cohort Studies of Early Body Mass Index Rebound
Authors: Aris Izzuddin M , Sarvet Aaron L , Stensrud Mats J , Neugebauer Romain , Li Ling-Jun , Hivert Marie-France , Oken Emily , Young Jessica G
Published: February 2021

Observational studies reporting on adjusted associations between childhood body mass index (BMI; weight (kg)/height (m)2) rebound and subsequent cardiometabolic outcomes have often not paid explicit attention to causal inference, including definition of a target causal effect and assumptions for unbiased estimation of that effect. Using data from 649 children in a Boston, Massachusetts–area cohort recruited in 1999–2002, we considered effects of stochastic interventions on a chosen subset of modifiable yet unmeasured exposures expected to be associated with early (<age 4 years) BMI rebound (a proxy measure) on adolescent cardiometabolic outcomes. We considered assumptions under which these effects might be identified with available data. This leads to an analysis where the proxy, rather than the exposure, acts as the exposure in the algorithm. We applied targeted maximum likelihood estimation, a doubly robust approach that naturally incorporates machine learning for nuisance parameters (e.g., propensity score). We found a protective effect of an intervention that assigns modifiable exposures according to the distribution in the observational study of persons without (vs. with) early BMI rebound for fat mass index (fat mass (kg)/ height (m)2; −1.39 units, 95% confidence interval: −1.63, −0.72) but weaker or no effects for other cardiometabolic outcomes. Our results clarify distinctions between algorithms and causal questions, encouraging explicit thinking in causal inference with complex exposures.
RNA2HLA: HLA-based quality control of RNA-seq datasets
Authors: Chelysheva Irina , Pollard Andrew J , O’Connor Daniel
Published: February 2021

RNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participant is evidently of great importance. Here, we propose taking advantage of typing the highly polymorphic genes from the human leukocyte antigen (HLA) complex in order to verify the correct allocation of RNA-seq samples to individuals. We introduce RNA2HLA, a novel quality control (QC) tool for performing study-wide HLA-typing for RNA-seq data and thereby identifying the samples from the common source. RNA2HLA allows precise allocation and grouping of RNA samples based on their HLA types. Strikingly, RNA2HLA revealed wrongly assigned samples from publicly available datasets and thereby demonstrated the importance of this tool for the quality control of RNA-seq studies. In addition, our tool successfully extracts HLA alleles in four-digital resolution and can be used to perform massive HLA-typing from RNA-seq based studies, which will serve multiple research purposes beyond sample QC.
Rank normalization empowers at-test for microbiome differential abundance analysis while controlling for false discoveries
Authors: Davis Matthew L , Huang Yuan , Wang Kai
Published: February 2021

A major task in the analysis of microbiome data is to identify microbes associated with differing biological conditions. Before conducting analysis, raw data must first be adjusted so that counts from different samples are comparable. A typical approach is to estimate normalization factors by which all counts in a sample are multiplied or divided. However, the inherent variation associated with estimation of normalization factors are often not accounted for in subsequent analysis, leading to a loss of precision. Rank normalization is a nonparametric alternative to the estimation of normalization factors in which each count for a microbial feature is replaced by its intrasample rank. Although rank normalization has been successfully applied to microarray analysis in the past, it has yet to be explored for microbiome data, which is characterized by high frequencies of 0s, strongly correlated features and compositionality. We propose to use rank normalization as an alternative to the estimation of normalization factors and examine its performance when paired with a two-sample t-test. On a rigorous 3rd-party benchmarking simulation, it is shown to offer strong control over the false discovery rate, and at sample sizes greater than 50 per treatment group, to offer an improvement in performance over commonly used normalization factors paired with t-tests, Wilcoxon rank-sum tests and methodologies implemented by R packages. On two real datasets, it yielded valid and reproducible results that were strongly in agreement with the original findings and the existing literature, further demonstrating its robustness and future potential. Availability: The data underlying this article are available online along with R code and supplementary materials at https://github.com/matthewlouisdavisBioStat/Rank-Normalization-Empowers-a-T-Test.
Good alimentation can overcome the negative effects of climate change on growth in reptiles
Authors: Rueda-Zozaya Pilar , Plasman Melissa , Reynoso Víctor Hugo
Published: February 2021

Climate change may lead to higher nest temperatures, which may increase embryo development rate but reduce hatchling size and growth. Larger body size permits better performance, making growth an important fitness trait. In ectotherms, growth is affected by temperature and food quality. To segregate the effects of incubation temperature vs. alimentation on the growth of the Mexican black spiny-tailed iguana, Ctenosaura pectinata, we incubated eggs at 29 or 32 °C, and hatchlings were kept at 30 °C and fed either high- or low-quality food for 1 year, with body size and mass being recorded every 2 weeks. Iguanas incubated at 29 °C grew faster than those incubated at 32 °C. However, food quality had a larger effect on growth than incubation temperature; iguanas fed with high-quality food reached larger body sizes. Growth models suggested that differences in growth between incubation temperatures and food types remain throughout their lives. We found that incubation temperature had long-lasting effects on an ectotherm, and higher incubation temperatures might lead to reduced growth and maturation at a later age. However, food might transcend the effect of increased incubation temperature; therefore, good alimentation might mitigate effects of climate change on growth.
Exponential distribution of velocities and power distribution of quiescent periods in the spontaneous movement patterns of three hunting spiders
Authors: Baatrup Erik , Rasmussen Anders O , Malte Hans , Toft Søren
Published: February 2021

Here, we investigate the spontaneous locomotor patterns in three spiders with different hunting strategies. The locomotor activity of adult wolf spiders Pardosa amentata, with a sit-and-move hunting strategy, has previously been demonstrated to follow strictly mathematical rules, with most time spent at lower velocities and exponentially decreasing time spent at increasing velocities. Likewise, they have an abundance of short quiescent (resting) periods following a power decay function towards longer quiescent periods. In the present study, we explored whether similar distributions were expressed in juveniles of P. amentata and in two other spider species with different hunting strategies: the sit-and-wait spider Xysticus cristatus and the actively searching sac spider Clubiona phragmitis. We found that all three spider species followed the same two general rules of movement. However, there were differences among the three species. On a logarithmic scale of exponential velocities and a double-logarithmic scale of the rest power decay function, the slopes of the lines for the three species differed. We propose that these differences reflect the behavioural and locomotor differences of the three hunting strategies. Furthermore, we compare our results with similar movement distributions in single cells, fruit flies, mice and even humans.
Dimension reduction for covariates in network data
Authors: Zhao Junlong , Liu Xiumin , Wang Hansheng , Leng Chenlei
Published: February 2021

A problem of major interest in network data analysis is to explain the strength of connections using context information. To achieve this, we introduce a novel approach, called network-supervised dimension reduction, in which covariates are projected onto low-dimensional spaces to reveal the linkage pattern without assuming a model. We propose a new loss function for estimating the parameters in the resulting linear projection, based on the notion that closer proximity in the low-dimension projection corresponds to stronger connections. Interestingly, the convergence rate of our estimator is found to depend on a network effect factor, which is the smallest number that can partition a graph in a manner similar to the graph colouring problem. Our method has interesting connections to principal component analysis and linear discriminant analysis, which we exploit for clustering and community detection. The proposed approach is further illustrated by numerical experiments and analysis of a pulsar candidates dataset from astronomy.
The Importance of Considering Functional Outcome and Self-awareness in the Assessment of Care Needs: Initial Evaluation of the Brain Injury Needs Indicator
Authors: Copstick S , Ramos S D S , Griffiths T , Wallace A
Published: February 2021

The relationship between self-awareness (insight) and outcome following acquired brain injury (ABI) is well recognised, but evidence suggests that information regarding brain injury and its cognitive impact is not adequately conveyed to social workers, or appropriately considered when assessing support needs and a person’s capacity to make decisions about their care. The Brain Injury Needs Indicator (BINI) provides a solution, by enabling the valid assessment of the needs of those with brain injuries living in a community setting. This paper investigated associations between impaired insight, functional outcome of brain injury, and level of risk, and validated the use of the BINI as an indicator of need. A high prevalence of severe disability (73 per cent) and low insight (30 per cent) was found in a sample of thirty individuals with ABI. The composite BINI score was the measure most strongly related with a clinical assessment of risk (rs = 0.72, N = 26). Self-report methods may underestimate support needs, especially in those with low levels of insight into their difficulties. The BINI, which combines outcome post-ABI with a measure of insight, provides a more accurate estimate of risk than either measure individually. It is important to include both areas in individual needs assessments.
An Implementable Conversation Between Foucault and Chinese Virtue Ethics in the Context of Youth Social Work
Authors: He Longtao , van Heugten Kate
Published: February 2021

Recently, virtue ethics has been increasingly considered as one of the most appropriate alternative ethical frameworks for youth social work internationally and in China. Extant literature has the tendency to emphasise cultural difference and neglect the universality of (virtue) ethics; instead, this article aims to inspire a balanced theoretical conversation on similarities between western (Foucauldian) and Chinese virtue ethics (mainly classical Confucianism and Daoism) supported by examples from case studies. Three areas are addressed: (i) similarities in the interior (personal) dimension and the exterior (relational) dimension of the self; (ii) the situational and universal features of virtue ethics, and the need for a reflective approach to balance both; and (iii) ethical cultivation of the reflective approach. These key themes add to a body of knowledge for the development of a virtue ethics framework for Chinese youth social work.
Temporal Trends of Candidemia Incidence Rates and Potential Contributions of Infection Control Initiatives Over 18 Years Within the United States Veterans Health Administration System: A Joinpoint Time-Series Analysis
Authors: Suzuki Hiroyuki , Perencevich Eli N , Diekema Daniel J , Livorsi Daniel J , Nair Rajeshwari , Kralovic Stephen M , Roselle Gary A , Goto Michihiko
Published: February 2021

Background

Candidemia is one of the most common causes of nosocomial bloodstream infections, but the impacts of factors affecting its incidence have not been evaluated.

Methods

We analyzed a retrospective cohort of all candidemia patients at 130 acute care hospitals in the Veterans Health Administration (VHA) system from January 2000 through December 2017. Cases were classified as hospital-onset (HO) and non-hospital-onset (NHO). We used Joinpoint regression analysis to assess temporal associations between significant changes in candidemia incidence rates and guidelines or horizontal infection control (IC) interventions.

Results

Over 18 years, 17 661 candidemia episodes were identified. Incidence rates of HO cases were increasing until the mid-2000s, followed by a sustained decline, while NHO cases showed a steady decline. The first change in HO candidemia incidence rates (August 2004 [95% confidence interval {CI}, February 2003–April 2005]) was preceded by the publication of catheter-related bloodstream infection (CRBSI) prevention guidelines and the CRBSI surveillance initiation. The second (September 2007 [95% CI, September 2006–June 2009]) had close temporal proximity to the expansion of IC resources within the VHA system. Collectively, these trend changes resulted in a 77.1% reduction in HO candidemia incidence rates since its peak in 2004.

Conclusions

A substantial and sustained systemwide reduction in candidemia incidence rates was observed after the publication of guidelines, VHA initiatives about CRBSI reporting and education on CRBSI prevention, and the systemwide expansion of IC resources.
Asymmetric Competition on a New Battleground? Middle Eastern Perspectives on Sino-US Rivalry
Authors: She Gangzheng
Published: February 2021

During the last few years, and especially since the outbreak of the COVID-19 pandemic, growing number of Middle East scholars and analysts have been closely observing an escalation of tensions between China and the United States and their impact beyond bilateral ties. Considering the major differences of focus and approach among these observers, this article aims to review systematically such Middle Eastern perspectives, both globally and regionally, on the emerging Sino-US rivalry. Certain Middle East analysts regard Beijing and Washington as largely “homogeneous” extra-regional powers competing in international politics, economy, and technology. Many others emphasise their “heterogeneity,” arguing that the essence of Sino-US confrontation lies in the clash of two models. Most Middle East scholars note that, in contrast to Washington’s waning influence, Beijing’s growing presence in the region during the past decade has rendered the Middle East a “new battleground” for the two great powers. Although China and the United States still have shared interests in certain regional affairs, most intellectuals focus on and collectively identify five domains across the Middle East wherein Beijing and Washington are locked in asymmetric competition. In light of both the opportunities and challenges that the emerging Sino-US rivalry engenders, Middle Eastern observers raise various policy suggestions, and debate on whether regional players should proactively take advantage of this great power competition, cautiously hedge against strategic uncertainty and risk, or constructively help reduce hostility between the United States and the People’s Republic of China.
Starvation on First or Second Day of Adulthood Reverses Larval-Stage Decision to Migrate in Beet Webworm (Lepidoptera: Pyralidae)
Authors: Cheng Yunxia , Sappington Thomas W , Luo Lizhi , Zhang Lei , Jiang Xingfu
Published: February 2021

A facultative commitment to adult migration in the larval stage can be modified again after adult emergence in some Lepidoptera when influenced by an appropriate environmental cue during a sensitive stage. This phenomenon is termed secondary regulation of migration. The sensitive stage in adult beet webworm, Loxostege sticticalis L. (Lepidoptera: Pyralidae), was determined experimentally by starvation of presumed migrant females reared from gregarious-phase larvae (induced by crowding at 10 larvae per 650-ml jar). When presumed migrant adults were starved for 24 h on either of the first 2 d after emergence, the preoviposition period was shortened. In contrast, preoviposition periods were not significantly shortened for migrants starved on day 3 or when starvation lasted for more than 1 d after emergence. Because the preoviposition period corresponds to the migratory period in beet webworm, the results suggest that the first 2 d of adult life in the beet webworm is the sensitive stage during which presumed migrants can be switched to residents by an appropriate environmental cue. During the sensitive stage or not, starvation did not influence lifetime fecundity, oviposition period, longevity, or hatching rate of eggs laid by the starvation-stressed moths. Starvation on the first day also increased tethered flight performance and accelerated both flight muscle and ovarian development. The results suggest that a pulse of starvation in the sensitive period may inhibit the expected migration by accelerating and compressing the cycle of migratory flight muscle development and degeneration, while accelerating ovarian development, which is normally suppressed until after migration.
Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems
Authors: Cerecetto Victoria , Smalla Kornelia , Nesme Joseph , Garaycochea Silvia , Fresia Pablo , Sørensen Søren Johannes , Babin Doreen , Leoni Carolina
Published: February 2021

Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.
Soil Carbon and CO2 Efflux as Influenced by the Thinning of Loblolly Pine (Pinus taeda L.) Plantations on the Piedmont of Virginia
Authors: Selig Marcus F. , Seiler John R. , Tyree Michael C.
Published: February 2021

The thinning of loblolly pine plantations has a great potential to influence the fluxes and storage of carbon within managed stands. In this study we investigated the effects of thinning on mineral soil carbon distribution and storage 14 years after the thinning of an 8-year-old loblolly pine plantation on the Piedmont of Virginia. Additionally, we examined patterns of soil CO2 efflux (Es) for 1 year after the second thinning of the same stands at age 22. The study was conducted using three replicate 0.22-ha stands planted using 3.05 × 3.05 m spacing in 1980. Soil carbon in the fine soil fraction (<2 mm) was evenly dispersed throughout thinned plots, and random sampling techniques were adequate for capturing spatial variability. Soil carbon decreased with depth, was higher at all depths in thinned stands, and was significantly higher (P = 0.06) at the 10- to 20-cm depth in the thinned stands (1.04%) compared with unthinned stands (0.76%). Soil temperature was approximately 1–2°C warmer in the growing season and 1°C cooler in the dormant season in thinned stands. Soil moisture was consistently higher in thinned stands by approximately 5%. Temperature was positively and significantly correlated with Es in thinned and unthinned stands. When modeled using regression, thinning was a significant variable for predicting Es (P < 0.0009) but explained less than 1% of the variation. Whereas thinning decreased Es when standardized to a constant temperature, actual Es was elevated in thinned stands because of higher soil temperature.
Leveraging the cell lineage to predict cell-type specificity of regulatory variation from bulk genomics
Authors: Yankovitz Gal , Cohn Ofir , Bacharach Eran , Peshes-Yaloz Naama , Steuerman Yael , Iraqi Fuad A , Gat-Viks Irit
Published: February 2021

Recent computational methods have enabled the inference of the cell-type-specificity of eQTLs based on bulk transcriptomes from highly heterogeneous tissues. However, these methods are limited in their scalability to highly heterogeneous tissues and limited in their broad applicability to any cell-type specificity of eQTLs. Here we present and demonstrate Cell Lineage Genetics (CeL-Gen), a novel computational approach that allows inference of eQTLs together with the subsets of cell types in which they have an effect, from bulk transcriptome data. To obtain improved scalability and broader applicability, CeL-Gen takes as input the known cell lineage tree and relies on the observation that dynamic changes in genetic effects occur relatively infrequently during cell differentiation. CeL-Gen can therefore be used not only to tease apart genetic effects derived from different cell types but also to infer the particular differentiation steps in which genetic effects are altered.
N- and C-terminal Gln3–Tor1 interaction sites: one acting negatively and the other positively to regulate nuclear Gln3 localization
Authors: Tate Jennifer J , Rai Rajendra , De Virgilio Claudio , Cooper Terrance G
Published: February 2021

Gln3 activates Nitrogen Catabolite Repression, NCR-sensitive expression of the genes required for Saccharomyces cerevisiae to scavenge poor nitrogen sources from its environment. The global TorC1 kinase complex negatively regulates nuclear Gln3 localization, interacting with an α-helix in the C-terminal region of Gln3, Gln3656–666. In nitrogen replete conditions, Gln3 is sequestered in the cytoplasm, whereas when TorC1 is down-regulated, in nitrogen restrictive conditions, Gln3 migrates into the nucleus. In this work, we show that the C-terminal Gln3–Tor1 interaction site is required for wild type, rapamycin-elicited, Sit4-dependent nuclear Gln3 localization, but not for its dephosphorylation. In fact, truncated Gln31-384 can enter the nucleus in the absence of Sit4 in both repressive and derepressive growth conditions. However, Gln31-384 can only enter the nucleus if a newly discovered second positively-acting Gln3–Tor1 interaction site remains intact. Importantly, the N- and C-terminal Gln3–Tor1 interaction sites function both autonomously and collaboratively. The N-terminal Gln3–Tor1 interaction site, previously designated Gln3URS contains a predicted α-helix situated within an unstructured coiled-coil region. Eight of the thirteen serine/threonine residues in the Gln3URS are dephosphorylated 3–15-fold with three of them by 10–15-fold. Substituting phosphomimetic aspartate for serine/threonine residues in the Gln3 URS abolishes the N-terminal Gln3–Tor1 interaction, rapamycin-elicited nuclear Gln3 localization, and ½ of the derepressed levels of nuclear Gln3 localization. Cytoplasmic Gln3 sequestration in repressive conditions, however, remains intact. These findings further deconvolve the mechanisms that achieve nitrogen-responsive transcription factor regulation downstream of TorC1.
A Systematic Review of Interventions to Increase Physical Activity Among American Indian and Alaska Native Older Adults
Authors: Pedersen Maja , Harris Kari Jo , Brown Blakely , Anderson Keith , Lewis Jordan P
Published: February 2021

Background and Objectives

Physical activity (PA) is a powerful protective factor known to reduce risk for chronic conditions across the life span. PA levels are lower among American Indians and Alaska Natives (AIANs) when compared with other racial/ethnic groups and decrease with age. This evidence justifies a synthesis of current intervention research to increase PA levels among AIANs. This systematic review examines completed interventions to increase PA among AIAN older adults and considers recommended practices for research with Indigenous communities.

Research Design and Methods

The systematic review was designed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement for systematic review protocols and reporting guidelines. Three electronic databases, PubMed, Web of Science, and PsycINFO, were searched for academic literature. Trials investigating interventions to increase PA among AIAN adults older than 50 years were eligible. The Quality Assessment Tool for Quantitative Studies was used to evaluate the quality of evidence.

Results

Three published trials were identified, including one group-level, clinic-based and two individual-level, home-based interventions. All were 6 weeks in duration, took place in urban areas, and used self-report PA measures. Findings indicated an overall increase in PA levels, improved PA-related outcomes, and improved psychosocial health among participants. None described community-engaged or culture-centered research strategies.

Discussion and Implications

The narrow yet promising evidence represents a need for expanded research and a call to action for using culture-centered strategies. An advanced understanding of cultural and contextual aspects of PA may produce more impactful interventions, supporting health and mobility across the life span.
Controls on the present-day dynamic topography predicted from mantle flow models since 410 Ma
Authors: Yang An , Yang Ting
Published: February 2021

Mantle convection induces dynamic topography, the lithosphere's surface deflections driven by the vertical stresses from sublithospheric mantle convection. Dynamic topography has important influences on a range of geophysical and geological observations. Here, we studied controls on the Earth's dynamic topography through 3-D spherical models of mantle convection, which use reconstructed past 410 Myr global plate motion history as time-dependent surface mechanical boundary condition. The numerical model assumes the extended-Boussinesq approximation and includes strongly depth- and temperature-dependent viscosity and phase changes in the mantle. Our results show that removing the chemical layer above the core–mantle boundary (CMB) and including depth-dependent thermal expansivity have both a limited influence on the predicted present-day dynamic topography. Considering phase transitions in our models increases the predicted amplitude of dynamic topography, which is mainly influenced by the 410 km exothermic phase transition. The predicted dynamic topography is very sensitive to shallow temperature-induced lateral viscosity variations (LVVs) and Rayleigh number. The preservation of LVVs significantly increases the negative dynamic topography at subduction zones. A decrease (or increase) of Rayleigh number increases (or decreases) the predicted present-day dynamic topography considerably. The dynamic topography predicted from the model considering LVVs and with a Rayleigh number of 6 × 108 is most compatible with residual topography models. This Rayleigh number is consistent with the convective vigor of the Earth as supported by generating more realistic lower mantle structure, slab sinking rate and surface and CMB heat fluxes. The evolution of the surface heat flux pattern is similar to the long-term eustatic sea level change. Before the formation of Pangea, large negative dynamic topography formed between the plate convergence region of Gondwana and Laurussia. The predicted dynamic topography similar to that of present-day has already emerged by about 262 Ma. Powers for degrees 1–3 dynamic topography at 337 and 104 Ma which correspond to times of higher plate velocities and higher surface heat fluxes are larger.
Tissue Proteomic Approaches to Understand the Pathogenesis of Inflammatory Bowel Disease
Authors: Baldan-Martin Montserrat , Chaparro María , Gisbert Javier P
Published: February 2021

Inflammatory bowel disease (IBD) has become a global disease encompassing a group of progressive disorders characterized by recurrent chronic inflammation of the gut with variable disease courses and complications. Despite recent advances in the knowledge of IBD pathophysiology, the elucidation of its etiopathology and progression is far from fully understood, requiring complex and multiple approaches. Therefore, limited clinical progress in diagnosis, assessment of disease activity, and optimal therapeutic regimens have been made over the past few decades. This review explores recent advances and challenges in tissue proteomics with an emphasis on biomarker discovery and better understanding of the molecular mechanisms underlying IBD pathogenesis. Future multi-omic studies are required for the comprehensive molecular characterization of disease biology in real time with a future impact on early detection, disease monitoring, and prediction of the clinical outcome.
Improved creatinine-based early detection of acute kidney injury after cardiac surgery
Authors: Vogt Ferdinand , Zibert Janez , Bahovec Alenka , Pollari Francesco , Sirch Joachim , Fittkau Matthias , Bertsch Thomas , Czerny Martin , Santarpino Giuseppe , Fischlein Theodor , Kalisnik Jurij M
Published: February 2021

OBJECTIVES

This study aims to improve early detection of cardiac surgery-associated acute kidney injury (CSA-AKI) compared to classical clinical scores.

METHODS

Data from 7633 patients who underwent cardiac surgery between 2008 and 2018 in our institution were analysed. CSA-AKI was defined according to the Kidney Disease Improving Global Outcomes (KDIGO) criteria. Cleveland Clinical Score served as the reference with an area under the curve (AUC) 0.65 in our cohort. Based on that, stepwise logistic regression modelling was performed on the training data set including creatinine (Cr), estimated glomerular filtration rate (eGFR) levels and deltas (ΔCr, ΔeGFR) at different time points and clinical parameters as preoperative haemoglobin, intraoperative packed red blood cells (units) and cardiopulmonary bypass time (min) to predict CSA-AKI in the early postoperative course. The AUC was determined on the validation data set for each model respectively.

RESULTS

Incidence of CSA-AKI in the early postoperative course was 22.4% (n = 1712). The 30-day mortality was 12.5% in the CSA-AKI group (n = 214) and in the no-CSA-AKI group 0.9% (n = 53) (P < 0.001). Logistic regression models based on Cr and its delta gained an AUC of 0.69; ‘Model eGFRCKD-EPI’ an AUC of 0.73. Finally, ‘Model DynaLab’ including dynamic laboratory parameters and clinical parameters as haemoglobin, packed red blood cells and cardiopulmonary bypass time improved AUC to 0.84.

CONCLUSIONS

Model DynaLab’ improves early detection of CSA-AKI within 12 h after surgery. This simple Cr-based framework poses a fundament for further endeavours towards reduction of CSA-AKI incidence and severity.
Reconstruction of an impenetrable obstacle in anisotropic inhomogeneous background
Authors: Kow Pu-Zhao , Wang Jenn-Nan
Published: February 2021

In this paper, we are interested in the problem of determining the shape of sound-soft or impedance obstacles in the acoustic wave scattering with an anisotropic inhomogeneous medium. The main theme is to extend the factorization method to this setting. Precisely, we can reconstruct the obstacle by the eigenvalues and eigenfunctions of the far-field operator. We also provide some numerical simulations in the paper.
A spectral-in-time Newton–Krylov method for nonlinear PDE-constrained optimization
Authors: Güttel Stefan , Pearson John W
Published: February 2021

We devise a method for nonlinear time-dependent partial-differential-equation-constrained optimization problems that uses a spectral-in-time representation of the residual, combined with a Newton–Krylov method to drive the residual to zero. We also propose a preconditioner to accelerate this scheme. Numerical results indicate that this method can achieve fast and accurate solution of nonlinear problems for a range of mesh sizes and problem parameters. The numbers of outer Newton and inner Krylov iterations required to reach the attainable accuracy of a spatial discretization are robust with respect to the number of collocation points in time and also do not change substantially when other problem parameters are varied.
Estimating TB diagnostic costs incurred under the National Tuberculosis Elimination Programme: a costing study from Tamil Nadu, South India
Authors: Muniyandi Malaisamy , Lavanya Jayabal , Karikalan Nagarajan , Saravanan Balakrishnan , Senthil Sellappan , Selvaraju Sriram , Mondal Rajesh
Published: February 2021

Background

The National Tuberculosis Elimination Programme (NTEP) of India is aiming to eliminate TB by 2025. The programme has increased its services and resources to strengthen the accurate and early detection of TB. It is important to estimate the cost of TB diagnosis in India considering the advancement and implementation of new diagnostic tools under the NTEP. The objective of this study was to estimate the unit costs of providing TB diagnostic services at different levels of public health facilities with different algorithms implemented under the NTEP in Chennai, Tamil Nadu, South India.

Methods

This costing study was conducted from the perspective of the health system. This study used only secondary data and information that were available in the public domain. Data were collected with the approval of health authorities. The patient's diagnostic path from the point of registration until the final diagnosis was considered in the costing exercise. The unit costs of different diagnostic tools used in the NTEP implemented by Chennai Corporation were calculated.

Results

We estimated the unit cost of the eight laboratory tests (Ziehl–Neelsen [ZN], fluorescence microscopy [FM], x-ray, digital x-ray, gene Xpert MTB/RIF (cartridge-based nucleic acid amplification test [NAAT] that identifies rifampicin resistant Mycobacterium Tuberculosis) Mycobacterium Tuberculosis/Rifampicin [MTB/RIF], mycobacteria growth indicator tube [MGIT], line probe assay [LPA] and Lowenstein Jensen [LJ] culture) for diagnosis of drug-sensitive and drug-resistant TB. The unit costs included fixed and variable costs for smear examination by ZN microscopy (₹ [Indian Rupee] 326 [US${\$}$4.72], FM (₹104 [US${\$}$1.5]), x-ray (₹218 [US${\$}$3.15]), digital X-ray (₹281 [US${\$}$4.07]), gene Xpert MTB/RIF (₹1137 [US${\$}$16.47]), MGIT (₹7038 [US${\$}$102]), LPA (₹6448 [US${\$}$93.44]) and LJ culture (₹4850 [US${\$}$70.28]). Out of 10 diagnostic algorithms used for TB diagnosis, algorithms using only smear microscopy had the lowest cost, followed by smear microscopy with x-ray for drug-sensitive TB (₹104 [US${\$}$1.5] to ₹544 [US${\$}$7.88]). Diagnostic algorithms for drug-resistant TB involving LPA and gene Xpert MTB/RIF were the most expensive.

Conclusions

Understanding the various costs contributing to TB diagnosis in India provides crucial evidence for policymakers, programme managers and researchers to optimise programme spending and efficiently use resources.
Keeping Your Enemies Close? The Variety of Social Movements’ Reactions to International Organizations’ Opening Up
Authors: Anderl Felix , Daphi Priska , Deitelhoff Nicole
Published: February 2021

Starting in the 1990s, international organizations (IOs) have created various opportunities of access for civil society to voice criticism. While international relations (IR) scholarship has increasingly addressed the resulting interaction between IOs and civil society with a focus on NGOs, we know little about the particular reactions to IOs’ opening up by social movements. This paper analyzes reactions to opening up by a transnational social movement centrally addressing IOs: the Global Justice Movement (GJM). Examining reactions by different groups of the GJM in Europe and Southeast Asia to IOs’ opening up, we demonstrate that reactions differ considerably depending on activists’ assessments of the nature of opening up. In particular, we identify four pathways of reactions on a continuum from (1) strong cooperation with IOs as a reaction to opening up, (2) temporally limited cooperation with different IOs, (3) a hybrid reaction that combines cooperation with specific IOs with a strong opposition to other IOs in reaction to their opening up, to (4) a continuous rejection of all cooperation with IOs. We show how these different reactions are shaped by activists’ perceptions of the quality of the international opening up in conjunction with national and local context factors. Furthermore, our analysis demonstrates that such perceptions can significantly change over time depending on experiences of interactions. Reactions to opening up are therefore not predictable on the basis of a movement's shape and resources only, but rather depend on a variety of factors such as the movement's perception of the IO's sincerity in a strategic and consequential interaction, as well as the movement's ideological framework and its history of interaction with institutions at other levels, especially in the domestic realm.
Dual-Mode Gradient HPLC and TLC Densitometry Methods for the Simultaneous Determination of Paracetamol and Methionine in the Presence of Paracetamol Impurities
Authors: Ibrahim Hany , Hamdy Abdallah M , Merey Hanan A , Saad Ahmed S
Published: February 2021

Background

Paracetamol (PC) is one of the most widely used analgesic and antipyretic drugs and has recently been integrated into the supportive therapy of COVID-19. Pharmaceuticals containing methionine (MT) with PC may contribute to avoid hepatotoxicity and eventual PC overdose-dependent death.

Objective

The current work purposes to develop and validate two chromatographic methods for the simultaneous determination of MT and PC in the presence of two PC impurities (4-nitrophenol [NP] and 4-aminophenol [AP]).

Method

Two chromatographic methods were established and validated according to the International Conference on Harmonization guidelines. The first one was an RP-HPLC/UV method based on applying a “dual-mode” gradient elution. The separation was realized via varying both the composition of the ternary mobile phase (acetonitrile–methanol–water) and its flow rate. This strategy enabled a relatively rapid analysis with a satisfactory resolution, although the investigated compounds exhibit a significant difference in lipophilicity. The second one relied on TLC-densitometry, where the optimum separation was realized using a quaternary mobile phase system composed of butanol–dioxane–toluene–methanol (8:2.5:3.5:0.3, by volume). Both methods were monitored at 220 nm.

Results

The developed methods were proven to be robust, accurate, specific, and appropriate for the routine analysis of PC in its pure form or in pharmaceutical formulations with MT in quality control laboratories.

Conclusions

The corresponding methods are suitable to determine MT and PC in the presence of PC impurities.

Highlights

The study achieves the analysis of MT and PC in the presence of PC impurities via the application of HPLC and TLC-densitometry methods.
Gill morphology and formulae of crayfishes (Decapoda: Astacidea: Parastacidae) from New Guinea and New Zealand and a comparison with other selected species of crayfishes
Authors: Kawai Tadashi , Patoka Jiří
Published: February 2021

The Infraorder Astacidea comprises four superfamilies of decapod crustaceans: the freshwater Astacoidea and Parastacoidea and the marine Enoplometopoidea and Nephropoidea. The gill morphology of four species of crayfishes belonging to Astacoidea and Parastacoidea, two coral reef species of Enoplometopoidea, and 2 deep-water species of Nephropoidea are described and illustrated for comparisons and to determine characters characteristic to members of the family Parastacidae (Parastacoidea) from New Guinea. Morphology of the arthrobranchs and pleurobranchs were similar among all species, having a single stem with filament, but podobranchs of the parastacoideans differed from those of Astacoidea, being corrugated and tubular and having filaments. The astacoidean P. virginalis had a plate-like lamella with filament. The two nephropoid and two enoplometopoid species were similar to each other; their podobranch had a flat blade-like lamella without a filament and a shaft with a filament. The gill formulae of the New Guinea species of Cherax were the same as those of the Australian congeners, but the formula of the New Zealand Paranephrops planifronsWhite, 1842 was the same as those of the South American parastacids.
Beauty Contests and the Term Structure
Authors: Ellison Martin , Tischbirek Andreas
Published: February 2021

A novel decomposition highlights the scope for information to influence the term structure of interest rates. Based on the law of total covariance, we show that real term premia in macroeconomic models contain a component that depends on covariances of realised stochastic discount factors and a component that depends on covariances of expectations of those stochastic discount factors. The covariance of expectations is typically low in macrofinance models, which contributes to the real term premia implied by the models being at least an order of magnitude too small, a result that is unchanged even if we introduce aggregate demand externalities combined with shocks to higher-order beliefs. We argue that generating realistic term premia requires there to be strategic complementarities in the formation of expectations. A quantitative model, in which beliefs are formed in a beauty contest, can explain a significant proportion of observed term premia, when estimated using data on expectations of productivity growth from the Survey of Professional Forecasters.
The Comeback of the IUD in Twenty-First Century USA
Authors: Watkins Elizabeth Siegel
Published: February 2021

From 1995 to 2014, intrauterine devices (IUDs) rose from ranking 10th (out of 11) among contraceptive methods to being the fourth most popular, outnumbered only by the pill, sterilization, and condoms. In 1995, the IUD had been largely abandoned by American doctors; two decades later, major medical associations promoted it as a “first line” method for prospective users of all ages. This paper explains the rapid and dramatic increase in intrauterine contraception by exploring three influential factors from the 1970s-1980s – the Dalkon Shield disaster, the lack of innovation in contraceptive research and development, and the moral panic over teen pregnancy in America – that created circumstances by the early 2000s in which health care providers became more receptive to long-acting reversible contraception. Key thought leaders in obstetrics and gynecology took it upon themselves to rehabilitate the IUD in the court of medical opinion and succeeded in securing professional approval of the device as the initial step in its resurrection.
Current Distribution and Population Persistence of Five Lepidopteran Pests in U.S. Soybean
Authors: Huseth Anders S , Koch Robert L , Reisig Dominic , Davis Jeffrey A , Paula-Moraes Silvana V , Hodgson Erin W
Published: February 2021

The distribution of lepidopteran pests in soybean (Glycine max (L.) Merr.) is a current knowledge gap limiting accurate prioritization of Integrated Pest Management (IPM) research. Regional characterizations of lepidopteran distribution in soybean are now more than 25 yr old. The goal of this study was to generate a contemporary assessment of the distribution and population persistence of lepidopteran soybean pests. To understand which species are currently infesting soybean and their persistence, we conducted a survey of soybean entomologists with responsibility for approximately 33.6 million hectares of production in 31 U.S. states. Soybean entomologists were asked questions about presence of lepidopteran pests and their persistence in their state. We focused this survey on five lepidopteran pests: corn earworm (Helicoverpa zea Boddie) (Lepidoptera: Noctuidae), green cloverworm (Hypena scabra Fabricius) (Lepidoptera: Erebidae), painted lady (Vanessa cardui L.) (Lepidoptera: Nymphalidae), soybean looper (Chrysodeixis includens Walker) (Lepidoptera: Noctuidae), and velvetbean caterpillar (Anticarsia gemmatalis Hübner) (Lepidoptera: Erebidae). Soybean entomologists also provided insight into regionally relevant or sporadic lepidopteran soybean pests. Participants were also questioned about common scouting practices in each state. Results of this survey highlight dissimilar geographic distribution and relative persistence of lepidopteran pests in soybean. Clear differences in occurrence and abundance among species provide important contemporary distributions and persistence estimates. Assessments of scouting practices demonstrate a need to improve IPM adoption in some states. Results of this study and its complementary pest profile (concurrently published in JIPM) provide a contemporary foundation for studies of lepidopteran soybean pests.