bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-molecule localisation microscopy: accounting for chance co-localisation between foci in bacterial cells
Authors: Åberg Christoffer , Robinson Andrew 
Published: June 2021

AbstractUsing single-molecule fluorescence microscopes, individual biomolecules can be observed within live bacterial cells. Using differently coloured probes, physical associations between two different molecular species can be assessed through co-localisation measurements. However, bacterial cells are finite and small (~ 1 μm) relative to the resolution limit of optical microscopes (~ 0.25 μm). Furthermore, the images produced by optical microscopes are typically two-dimensional projections of three-dimensional objects. These limitations mean that a certain proportion of object pairs (molecules) will inevitably be assigned as being co-localised, even when they are distant at molecular distance scales (nm). What is this proportion? Here, we attack this problem, theoretically and computationally, by creating a model of the co-localisation expected purely due to chance. We thus consider a bacterial cell wherein objects are distributed at random and evaluate the co-localisation in a fashion that emulates an experimental analysis. We consider simplified geometries where we can most transparently investigate the effect of a finite size of the cell and the effect of probing a three-dimensional cell in only two dimensions. Coupling theory to simulations, we also study the co-localisation expected due to chance using parameters relevant to bacterial cells. Overall, we show that the co-localisation expected purely due to chance can be quite substantial and describe the parameters that it depends upon.
Host genetic control of gut microbiome composition
Authors: Bubier Jason A. , Chesler Elissa J. , Weinstock George M. 
Published: June 2021

AbstractThe gut microbiome plays a significant role in health and disease, and there is mounting evidence indicating that the microbial composition is regulated in part by host genetics. Heritability estimates for microbial abundance in mice and humans range from (0.05–0.45), indicating that 5–45% of inter-individual variation can be explained by genetics. Through twin studies, genetic association studies, systems genetics, and genome-wide association studies (GWAS), hundreds of specific host genetic loci have been shown to associate with the abundance of discrete gut microbes. Using genetically engineered knock-out mice, at least 30 specific genes have now been validated as having specific effects on the microbiome. The relationships among of host genetics, microbiome composition, and abundance, and disease is now beginning to be unraveled through experiments designed to test causality. The genetic control of disease and its relationship to the microbiome can manifest in multiple ways. First, a genetic variant may directly cause the disease phenotype, resulting in an altered microbiome as a consequence of the disease phenotype. Second, a genetic variant may alter gene expression in the host, which in turn alters the microbiome, producing the disease phenotype. Finally, the genetic variant may alter the microbiome directly, which can result in the disease phenotype. In order to understand the processes that underlie the onset and progression of certain diseases, future research must take into account the relationship among host genetics, microbiome, and disease phenotype, and the resources needed to study these relationships.
Discrepancy in exchangeable and soluble ammonium-induced effects on aerobic methane oxidation: a microcosm study of a paddy soil
Authors: van Dijk Hester , Kaupper Thomas , Bothe Clemens , Lee Hyo Jung , Bodelier Paul L. E. , Horn Marcus A. , Ho Adrian 
Published: June 2021

AbstractAmmonium-induced stimulatory, inhibitory, and/or neutral effects on soil methane oxidation have been attributable to the ammonium concentration and mineral forms, confounded by other edaphic properties (e.g., pH, salinity), as well as the site-specific composition of the methanotrophic community. We hypothesize that this inconsistency may stem from the discrepancy in the cation adsorption capacity of the soil. We postulate that the effects of ammonium on the methanotrophic activity in soil are more accurately portrayed by relating methane uptake rates to the soluble ammonium (bioavailable), rather than the exchangeable (total) ammonium. To reduce adsorption (exchangeable) sites for ammonium in a paddy soil, two successive pre-incubation steps were introduced resulting in a 1000-fold soil dilution (soil enrichment), to be compared to a soil slurry (tenfold dilution) incubation. Ammonium was supplemented as NH4Cl at 0.5–4.75gL−1 after pre-incubation. While NH4Cl significantly stimulated the methanotrophic activity at all concentrations in the soil slurry incubation, methane uptake showed a dose-dependent effect in the soil enrichment. The trend in methane uptake could be explained by the soluble ammonium concentration, which was proportionate to the supplemented ammonium in the soil enrichment. In the soil slurry incubation, a fraction (36–63%) of the supplemented ammonium was determined to be adsorbed to the soil. Accordingly, Methylosarcina was found to predominate the methanotrophic community after the incubation, suggesting the relevance of this methanotroph at elevated ammonium levels (< 3.25gL−1 NH4Cl). Collectively, our results showed that the soluble, rather than the exchangeable ammonium concentration, is relevant when determining the effects of ammonium on methane oxidation, but this does not exclude other (a)biotic factors concurrently influencing methanotrophic activity.
Post-haemorrhagic hydrocephalus is associated with poorer surgical and neurodevelopmental sequelae than other causes of infant hydrocephalus
Authors: Mohamed Malak , Mediratta Saniya , Chari Aswin , da Costa Cristine Sortica , James Greg , Dawes William , Aquilina Kristian 
Published: June 2021

AbstractPurposeThis retrospective cohort study aimed to investigate the surgical and neurodevelopmental outcomes (NDO) of infant hydrocephalus. We also sought to determine whether these outcomes are disproportionately poorer in post-haemorrhagic hydrocephalus (PHH) compared to other causes of infant hydrocephalus.MethodsA review of all infants with hydrocephalus who had ventriculoperitoneal (VP) shunts inserted at Great Ormond Street Hospital (GOSH) from 2008 to 2018 was performed. Demographic, surgical, neurodevelopmental, and other clinical data extracted from electronic patient notes were analysed by aetiology. Shunt survival, NDO, cerebral palsy (CP), epilepsy, speech delay, education, behavioural disorders, endocrine dysfunction, and mortality were evaluated.ResultsA total of 323 infants with median gestational age of 37.0 (23.29–42.14) weeks and birthweight of 2640 g (525–4684 g) were evaluated. PHH was the most common aetiology (31.9%) and was associated with significantly higher 5-year shunt revision rates, revisions beyond a year, and median number of revisions than congenital or “other” hydrocephalus (allp < 0.02). Cox regression demonstrated poorest shunt survival in PHH, related to gestational age at birth and corrected age at shunt insertion. PHH also had the highest rate of severe disabilities, increasing with age to 65.0% at 10 years, as well as the highest CP rate; only genetic hydrocephalus had significantly higher endocrine dysfunction (p = 0.01) and mortality rates (p = 0.04).ConclusionsInfants with PHH have poorer surgical and NDO compared to all other aetiologies, except genetic hydrocephalus. Research into measures of reducing neurodisability following PHH is urgently required. Long-term follow-up is essential to optimise support and outcomes.
Evaluation of non-exudative microcystoid macular abnormalities secondary to retinal vein occlusion
Authors: Francone Anibal , Govetto Andrea , Yun Lisa , Essilfie Juliet , Nouri-Mahdavi Kouros , Sarraf David , Hubschman Jean-Pierre 
Published: June 2021

Abstract
Purpose
We aimed to investigate non-exudative microcystoid macular abnormalities for visual and anatomical outcome in patients with retinal vein occlusion (RVO) with and without glaucomatous optic neuropathy (GON).

Methods
Medical records of 124 eyes (105 patients) with RVO were reviewed and analyzed. Eyes demonstrating microcystoid macular abnormalities were divided into 2 groups, those with evidence of glaucoma (group A) and those without glaucoma (group B). Best-corrected visual acuity (BCVA), the prevalence and number of microcystoid macular abnormalities, and number of intravitreal anti-vascular endothelial growth factor (anti-VEGF) injections were compared at baseline and follow-up.

Results
Seventy-one out of 105 eyes (67.6%) with RVO displayed microcystoid macular abnormalities. Thirty-eight out of 71 eyes (53.5%) presented with concomitant glaucoma (group A), while the remaining 33 eyes (42.6%) had no history of glaucoma (group B). At the end of the follow-up period, mean BCVA was worse in group A versus group B (20/80 versus 20/40, respectively; p = .003). The mean number of anti-VEGF injections was 10.1 ± 9.2 in group A versus 5.9 ± 6.9 in group B (p = .03).

Conclusion
Eyes with RVO and concomitant glaucoma exhibited a significantly higher number of microcystoid macular abnormalities and worse BCVA versus eyes with RVO without glaucoma.
Anocutaneous advancement flap provides a quicker cure than fissurectomy in surgical treatment for chronic anal fissure—a retrospective, observational study
Authors: Hancke Edgar , Suchan Katrin , Voelke Knut 
Published: June 2021

Abstract
Purpose
Anocutaneous advancement flap is a surgical procedure for the treatment of chronic anal fissures. This study aimed to assess the results of anocutaneous advancement flap in a consecutive cohort of patients.

Methods
This is a retrospective, observational study. From 2000 to 2011, 481 patients had been operated for a single chronic anal fissure at the Maingau Clinic of the German Red Cross in Frankfurt am Main. The intention was to excise the fissure by fissurectomy (FIS) and then to cover the wound primarily with an anocutaneous advancement flap (AAF). The primary outcomes were resolution of symptoms and healing rates 1 month postoperatively. Secondary outcomes included incidences of early and late complications, postoperative incontinence, and recurrent fissure.

Results
Anocutaneous advancement flap was performed in 455 (94.6%). In 26 (5.4%) patients, AAF failed due to lacking skin and the wound left open after FIS. One month postoperatively, half of the patients with AAF were free of symptoms (53.2%) with complete wound healing (47.9%). The incidence of early complications within 1 month postoperatively was 0.9% after AAF. From 1 month to 5 years after operation anal abscesses and fistula occurred in 2.9%. Mild symptoms of anal incontinence were recorded in 0.2% and recurrent chronic anal fissure in 3.3% of patients. Subgroup analysis revealed improved wound healing 1 month postoperatively in patients with AAF compared to FIS.

Conclusion
Anocutaneous advancement flap is a very safe sphincter-sparing surgical option for CAF, provides a quicker cure than fissurectomy, and may be considered a good first-line surgical treatment option for chronic anal fissures if medical treatment failed.
EBV-positive large B-cell lymphoma with an unusual intravascular presentation and associated haemophagocytic syndrome in an HIV-positive patient: report of a case expanding the spectrum of EBV-positive immunodeficiency-associated lymphoproliferative disorders
Authors: Veloza Luis , Tsai Chun-Yi , Bisig Bettina , Pantet Olivier , Alberio Lorenzo , Sempoux Christine , Cavassini Matthias , de Leval Laurence 
Published: June 2021

AbstractIntravascular large B-cell lymphoma is a rare and aggressive EBV-negative large B-cell lymphoma with a dismal outcome. Here, we describe the case of a 76-year-old HIV-positive patient with an acute presentation of systemic symptoms and rapidly fatal outcome. Autopsy revealed a disseminated large B-cell lymphoma with an intravascular distribution involving the liver, lymph nodes, spleen, and bone marrow and associated to fibrin thrombi in hepatic capillary haemangiomas. The neoplastic B cells (CD79a + / − , CD20 + / − , CD30 + , MUM1 + , PD-L1 +) showed a Hodgkin and Reed-Sternberg-like morphology and were EBV-positive with a latency type II (LMP1 + , EBNA2-). Haemophagocytosis was documented in the bone marrow and lymph nodes. This case illustrates the diagnostic challenges of large B-cell lymphoma with intravascular presentation. We found only five other cases of EBV-positive large B-cell lymphoma with an intravascular presentation in the literature, three of which had an underlying immunodeficiency adding to the broad spectrum of EBV-associated lymphoma in the setting of immunosuppression.
Genome sequencing in families with congenital limb malformations
Authors: Elsner Jonas , Mensah Martin A. , Holtgrewe Manuel , Hertzberg Jakob , Bigoni Stefania , Busche Andreas , Coutelier Marie , de Silva Deepthi C. , Elçioglu Nursel , Filges Isabel , Gerkes Erica , Girisha Katta M. , Graul-Neumann Luitgard , Jamsheer Aleksander , Krawitz Peter , Kurth Ingo , Markus Susanne , Megarbane Andre , Reis André , Reuter Miriam S. , Svoboda Daniel , Teller Christopher , Tuysuz Beyhan , Türkmen Seval , Wilson Meredith , Woitschach Rixa , Vater Inga , Caliebe Almuth , Hülsemann Wiebke , Horn Denise , Mundlos Stefan , Spielmann Malte 
Published: June 2021

AbstractThe extensive clinical and genetic heterogeneity of congenital limb malformation calls for comprehensive genome-wide analysis of genetic variation. Genome sequencing (GS) has the potential to identify all genetic variants. Here we aim to determine the diagnostic potential of GS as a comprehensive one-test-for-all strategy in a cohort of undiagnosed patients with congenital limb malformations. We collected 69 cases (64 trios, 1 duo, 5 singletons) with congenital limb malformations with no molecular diagnosis after standard clinical genetic testing and performed genome sequencing. We also developed a framework to identify potential noncoding pathogenic variants. We identified likely pathogenic/disease-associated variants in 12 cases (17.4%) including four in known disease genes, and one repeat expansion in HOXD13. In three unrelated cases with ectrodactyly, we identified likely pathogenic variants in UBA2, establishing it as a novel disease gene. In addition, we found two complex structural variants (3%). We also identified likely causative variants in three novel high confidence candidate genes. We were not able to identify any noncoding variants. GS is a powerful strategy to identify all types of genomic variants associated with congenital limb malformation, including repeat expansions and complex structural variants missed by standard diagnostic approaches. In this cohort, no causative noncoding SNVs could be identified.
The role of habitat configuration in shaping animal population processes: a framework to generate quantitative predictions
Authors: He Peng , Montiglio Pierre-Olivier , Somveille Marius , Cantor Mauricio , Farine Damien R. 
Published: June 2021

AbstractBy shaping where individuals move, habitat configuration can fundamentally structure animal populations. Yet, we currently lack a framework for generating quantitative predictions about the role of habitat configuration in modulating population outcomes. To address this gap, we propose a modelling framework inspired by studies using networks to characterize habitat connectivity. We first define animal habitat networks, explain how they can integrate information about the different configurational features of animal habitats, and highlight the need for a bottom–up generative model that can depict realistic variations in habitat potential connectivity. Second, we describe a model for simulating animal habitat networks (available in the R packageAnimalHabitatNetwork), and demonstrate its ability to generate alternative habitat configurations based on empirical data, which forms the basis for exploring the consequences of alternative habitat structures. Finally, we lay out three key research questions and demonstrate how our framework can address them. By simulating the spread of a pathogen within a population, we show how transmission properties can be impacted by both local potential connectivity and landscape-level characteristics of habitats. Our study highlights the importance of considering the underlying habitat configuration in studies linking social structure with population-level outcomes.
A review of computer vision-based approaches for physical rehabilitation and assessment
Authors: Debnath Bappaditya , O’Brien Mary , Yamaguchi Motonori , Behera Ardhendu 
Published: June 2021

AbstractThe computer vision community has extensively researched the area of human motion analysis, which primarily focuses on pose estimation, activity recognition, pose or gesture recognition and so on. However for many applications, like monitoring of functional rehabilitation of patients with musculo skeletal or physical impairments, the requirement is to comparatively evaluate human motion. In this survey, we capture important literature on vision-based monitoring and physical rehabilitation that focuses on comparative evaluation of human motion during the past two decades and discuss the state of current research in this area. Unlike other reviews in this area, which are written from a clinical objective, this article presents research in this area from a computer vision application perspective. We propose our own taxonomy of computer vision-based rehabilitation and assessment research which are further divided into sub-categories to capture novelties of each research. The review discusses the challenges of this domain due to the wide ranging human motion abnormalities and difficulty in automatically assessing those abnormalities. Finally, suggestions on the future direction of research are offered.
Toward the development of a weather index insurance for rice farmers in the coastal region of Myanmar
Authors: Furuya Jun , Omori Keisuke , Aizaki Hideo 
Published: June 2021

AbstractClimate change is expected to exacerbate damage to agricultural production from natural disasters. Examination of measures to adapt to the damage represents an urgent matter for agriculture. A multidisciplinary research project aimed at providing effective information related to development a weather index insurance (WII) system was conducted for rice farmers in a coastal region of Myanmar to achieve sustainable rice farm management in the country, which is among the world’s poorest and most disaster prone. For lower income countries, WII is one adaptation measure to mitigate damage by climate change. Using remote sensing and statistical data, changes in tracks of cyclones in the Bay of Bengal, the duration of damage by cyclone disasters, and areas affected by saltwater intrusion were analyzed to ascertain risk levels for disasters in the target area: Labutta township in the Ayeyarwady region. Furthermore, demand analysis of WII using discrete choice experiments, a question-based statistical survey method, revealed that farmers’ demand of WIIs for cyclone landfall, flood, and drought is relatively greater than that for saltwater intrusion. This finding indicates that saltwater intrusion might not be a crucially important matter for farmers who cultivate rainfed rice, whereas inland water floods caused by cyclone landfall and drought caused for changing the weather patterns represent a threat for these farmers. Results of econometric model analysis for designing a WII indicate that if a regular farmer in the township were to pay 41.5 US dollars per year to purchase WII for flood damage, their expected income will be stable.
Hot Deformation Behaviour and Processing Map of Cast Alloy 825
Authors: Al-Saadi Munir , Hulme-Smith Christopher , Sandberg Fredrik , Jönsson Pär G. 
Published: June 2021

AbstractAlloy 825 is a nickel-based alloy that is commonly used in applications where both high strength and corrosion resistance are required, such as tanks in the chemical, food and petrochemical industries and oil and gas pipelines. Components made from Alloy 825 are often manufactured using hot deformation. However, there is no systematic study to optimise the processing conditions reported in literature. In this study, a processing map for as-cast Alloy 825 is established to maximise the power dissipation efficiency of hot deformation in the temperature range of 950 to 1250 °C at an interval of 50 °C and strain rate range of$$0.01\, {\text{s}}^{ - 1}$$0.01s-1to$$10.0\, {\text{s}}^{ - 1}$$10.0s-1to a true strain of$$0.7$$0.7using a Gleeble-3500 thermomechanical simulator. The processing conditions are also correlated to the Vickers hardness of the final material, which is also characterised using optical microscopy and scanning electron microscopy, including electron backscattered diffraction. The true stress-true strain curves exhibit peak stresses followed by softening due to occurrence of dynamic recrystallization. The activation energy for plastic flow in the temperature range tested is approximately$$450\,{\text{ kJ mol}}^{ - 1}$$450kJ mol-1, and the value of the stress exponent in the (hyperbolic sine-based) constitutive equation,$$n = 5.0$$n=5.0, suggests that the rate-limiting mechanism of deformation is dislocation climb. Increasing deformation temperature led to a lower Vickers hardness in the deformed material, due to increased dynamic recrystallization. Raising the strain rate led to an increase in Vickers hardness in the deformed material due to increased work hardening. The maximum power dissipation efficiency is over$$35\%$$35%, obtained for deformation in the temperature range 1100-1250 °C and a strain rate of$$0.01\, {\text{s}}^{ - 1}$$0.01s-1-$$0.1\, {\text{s}}^{ - 1}$$0.1s-1. These are the optimum conditions for hot working.
Do Local Sex Ratios Approximate Subjective Partner Markets?
Authors: Filser Andreas , Preetz Richard 
Published: June 2021

AbstractSex ratios have widely been recognized as an important link between demographic contexts and behavior because changes in the ratio shift sex-specific bargaining power in the partner market. Implicitly, the literature considers individual partner market experiences to be a function of local sex ratios. However, empirical evidence on the correspondence between subjective partner availability and local sex ratios is lacking so far. In this paper, we analyzed how closely a set of different local sex ratio measures correlates with subjective partner market experiences. Linking a longitudinal German survey to population data for different entities (states, counties, municipalities), we used multilevel logistic regression models to explore associations between singles’ subjective partner market experiences and various operationalizations of local sex ratios. Results suggest that local sex ratios correlated only weakly with subjective partner market experiences. Adult sex ratios based on broad age brackets, including those for lower-level entities, did not significantly predict whether individuals predominantly met individuals of their own sex. More fine-grained, age-specific sex ratios prove to be better predictors of subjective partner market experiences, in particular when age hypergamy patterns were incorporated. Nevertheless, the respective associations were only significant for selected measures. In a complementary analysis, we illustrate the validity of the subjective indicator as a predictor of relationship formation. In sum, our results suggest that subjective partner availability is not adequately represented by the broad adult sex ratio measures that are frequently used in the literature. Future research should be careful not to equate local sex ratios and conscious partner market experiences.