bluuebunny/crossref_metadata_2025_split huggingface dataset:
Echo2Pheno: a deep-learning application to uncover echocardiographic phenotypes in conscious mice
Authors: Bukas Christina , Galter Isabella , da Silva-Buttkus Patricia , Fuchs Helmut , Maier Holger , Gailus-Durner Valerie , Müller Christian L. , Hrabě de Angelis Martin , Piraud Marie , Spielmann Nadine 
Published: May 2023

AbstractEchocardiography, a rapid and cost-effective imaging technique, assesses cardiac function and structure. Despite its popularity in cardiovascular medicine and clinical research, image-derived phenotypic measurements are manually performed, requiring expert knowledge and training. Notwithstanding great progress in deep-learning applications in small animal echocardiography, the focus has so far only been on images of anesthetized rodents. We present here a new algorithm specifically designed for echocardiograms acquired in conscious mice called Echo2Pheno, an automatic statistical learning workflow for analyzing and interpreting high-throughput non-anesthetized transthoracic murine echocardiographic images in the presence of genetic knockouts. Echo2Pheno comprises a neural network module for echocardiographic image analysis and phenotypic measurements, including a statistical hypothesis-testing framework for assessing phenotypic differences between populations. Using 2159 images of 16 different knockout mouse strains of the German Mouse Clinic, Echo2Pheno accurately confirms known cardiovascular genotype–phenotype relationships (e.g., Dystrophin) and discovers novel genes (e.g., CCR4-NOT transcription complex subunit 6-like, Cnot6l, and synaptotagmin-like protein 4, Sytl4), which cause altered cardiovascular phenotypes, as verified by H&E-stained histological images. Echo2Pheno provides an important step toward automatic end-to-end learning for linking echocardiographic readouts to cardiovascular phenotypes of interest in conscious mice.
Graphical abstract
Long-term spatial variations in turbidity and temperature provide new insights into coral-algal states on extreme/marginal reefs
Authors: Cartwright Paula J. , Browne Nicola K. , Belton David , Parnum Iain , O’Leary Michael , Valckenaere Jurgen , Fearns Peter , Lowe Ryan 
Published: May 2023

AbstractGlobally, coral reefs are under threat, with many exhibiting degradation or a shift towards algal-dominated regimes following marine heat waves, and other disturbance events. Marginal coral reefs existing under naturally extreme conditions, such as turbid water reefs, may be more resilient than their clear water counterparts as well as offer some insight into how reefs could look in the future under climate change. Here, we surveyed 27 benthic habitats across an environmental stress gradient in the Exmouth Gulf region of north Western Australia immediately following a marine heatwave event. We used multidecadal remotely sensed turbidity (from an in-situ validated dataset) and temperature, to assess how these environmental drivers influence variability in benthic communities and coral morphology. Long-term turbidity and temperature variability were associated with macroalgal colonisation when exceeding a combined threshold. Coral cover was strongly negatively associated with temperature variability, and positively associated with depth, and wave power, while coral morphology diversity was positively associated with turbidity. While moderate turbidity (long-term average ~ 2 mg/L suspended matter) appeared to raise the threshold for coral bleaching and macroalgal dominance, regions with higher temperature variability (> 3.5 °C) appeared to have already reached this threshold. The region with the least turbidity and temperature variability had the highest amount of coral bleaching from a recent heatwave event and moderate levels of both these variables may confer resilience to coral reefs.
Impact of processing-latency induced interaural delay and level discrepancy on sensitivity to interaural level differences in cochlear implant users
Authors: Körtje Monika , Stöver Timo , Baumann Uwe , Weissgerber Tobias 
Published: May 2023

Abstract
Purpose
This study investigated whether an interaural delay, e.g. caused by the processing latency of a hearing device, can affect sensitivity to interaural level differences (ILDs) in normal hearing subjects or cochlear implant (CI) users with contralateral normal hearing (SSD-CI).

Methods
Sensitivity to ILD was measured in 10 SSD-CI subjects and in 24 normal hearing subjects. The stimulus was a noise burst presented via headphones and via a direct cable connection (CI). ILD sensitivity was measured for different interaural delays in the range induced by hearing devices. ILD sensitivity was correlated with results obtained in a sound localization task using seven loudspeakers in the frontal horizontal plane.

Results
In the normal hearing subjects the sensitivity to interaural level differences deteriorated significantly with increasing interaural delays. In the CI group, no significant effect of interaural delays on ILD sensitivity was found. The NH subjects were significantly more sensitive to ILDs. The mean localization error in the CI group was 10.8° higher than in the normal hearing group. No correlation between sound localization ability and ILD sensitivity was found.

Conclusion
Interaural delays influence the perception of ILDs. For normal hearing subjects a significant decrement in sensitivity to ILD was measured. The effect could not be confirmed in the tested SSD-CI group, probably due to a small subject group with large variations. The temporal matching of the two sides may be beneficial for ILD processing and thus sound localization for CI patients. However, further studies are needed for verification.
Normative data for certain vocal fold biomarkers among young normophonic adults using ultrasonography
Authors: Rai Santosh , Ramdas Divya , Jacob Nidhi Lalu , Bajaj Gagan , Balasubramanium Radish Kumar , Bhat Jayashree S. 
Published: May 2023

Abstract
Purpose
The current study aimed to profile vocal fold morphology, vocal fold symmetry, gender and task-specific data for vocal fold length (VFL) and vocal fold displacement velocity (VFDV) in young normophonic adults in the age range of 18–30 years using ultrasonography (USG).

Methods
Participants underwent USG across quiet breathing, /a/ phonation and /i/ phonation tasks, and acoustic analysis was conducted to explore the relationship between USG and acoustic measures.

Results
The study found that males have longer vocal folds than females, and overall greater velocities were observed in /a/ phonation, followed by /i/ phonation, with the lowest velocity observed in the quiet breathing task.

Conclusions
The obtained norms can be used as a quantitative benchmark for analyzing the vocal fold behavior in young adults.
Escaping the enemy’s bullets: an update on how malaria parasites evade host immune response
Authors: Ezema Chinonso Anthony , Okagu Innocent Uzochukwu , Ezeorba Timothy Prince Chidike 
Published: May 2023

AbstractMalaria continues to cause untold hardship to inhabitants of malaria-endemic regions, causing significant morbidity and mortality that severely impact global health and the economy. Considering the complex life cycle of malaria parasites (MPs) and malaria biology, continued research efforts are ongoing to improve our understanding of the pathogenesis of the diseases. Female Anopheles mosquito injects MPs into its hosts during a blood meal, and MPs invade the host skin and the hepatocytes without causing any serious symptoms. Symptomatic infections occur only during the erythrocytic stage. In most cases, the host’s innate immunity (for malaria-naïve individuals) and adaptive immunity (for pre-exposed individuals) mount severe attacks and destroy most MPs. It is increasingly understood that MPs have developed several mechanisms to escape from the host’s immune destruction. This review presents recent knowledge on how the host’s immune system destroys invading MPs as well as MPs survival or host immune evasion mechanisms. On the invasion of host cells, MPs release molecules that bind to cell surface receptors to reprogram the host in a way to lose the capacity to destroy them. MPs also hide from the host immune cells by inducing the clustering of both infected and uninfected erythrocytes (rosettes), as well as inducing endothelial activation. We hope this review will inspire more research to provide a complete understanding of malaria biology and promote interventions to eradicate the notorious disease.
Amniotic fluid content in children with kidney and urinary tract anomalies determines pre- and postnatal development
Authors: Schulz Anne Mareike , Lauten Angela , Lehmann Thomas , Proquitté Hans , Eckoldt Felicitas , Weigel Friederike , Mentzel Hans-Joachim , Schneider Uwe , John-Kroegel Ulrike 
Published: May 2023

Abstract

Background
Renal oligohydramnios (ROH) describes an abnormally low volume of amniotic fluid (AF) during pregnancy. ROH is mostly caused by congenital fetal kidney anomalies. The ROH diagnosis frequently implies an increased risk of peri- and postnatal fetal mortality and morbidity. The present study aimed to evaluate the impact of ROH on pre-and postnatal development in children with congenital kidney anomalies.

Methods
This retrospective study included 168 fetuses with anomalies in the kidney and urinary tract. Based on the amount of AF measured by ultrasound, patients were divided into three groups: normal amniotic fluid (NAF), amniotic fluid in the lower normal range (LAF), and ROH. These groups were compared with respect to prenatal sonographic parameters, perinatal outcomes, and postnatal outcomes.

Results
Among the 168 patients with congenital kidney anomalies, 26 (15%) had ROH, 132 (79%) had NAF, and 10 (6%) had LAF. Of the 26 families affected by ROH, 14 (54%) decided to terminate pregnancy. Of 10 live-born children in the ROH group, 6 (60%) survived the observation time; of these, 5/6 presented with chronic kidney disease, stages I–III, at their last examination. The main differences in postnatal development between the ROH group and the NAF and LAF groups were: restricted height and weight gain, respiratory issues, complicated feeding, and the presence of extrarenal malformations.

Conclusions
ROH is not a mandatory indicator of severe postnatal kidney function impairment. However, children with ROH have complicated peri-and postnatal periods, due to the presence of concomitant malformations, which must be considered in prenatal care.

Graphical abstract
A novel model associated with tumor microenvironment on predicting prognosis and immunotherapy in triple negative breast cancer
Authors: Zhang Juan , Zhang Mi , Tian Qi , Yang Jin 
Published: May 2023

AbstractTriple negative breast cancer (TNBC) is the most aggressive and malignant subtype in breast cancer. Immunotherapy is a currently promising and effective treatment for TNBC, while not all patients are responsive. Therefore, it is necessary to explore novel biomarkers to screen sensitive populations for immunotherapy. All mRNA expression profiles of TNBC from The Cancer Genome Atlas (TCGA) database were clustered into two subgroups by analyzing tumor immune microenvironment (TIME) with single sample gene set enrichment analysis (ssGSEA). A risk score model was constructed based on differently expressed genes (DEGs) identified from two subgroups using Cox and Least Absolute Shrinkage and Selector Operation (LASSO) regression model. And it was validated by Kaplan–Meier analysis and Receiver Operating Characteristic (ROC) analysis in Gene Expression Omnibus (GEO) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases. Multiplex immunofluorescence (mIF) and Immunohistochemical (IHC) staining were performed on clinical TNBC tissue samples. The relationship between risk score and immune checkpoint blockades (ICB) related signatures was further investigated, as well as the biological processes were performed by gene set enrichment analysis (GSEA). We obtained three DEGs positively related to prognosis and infiltrating immune cells in TNBC. Our risk score model could be an independent prognostic factor and the low risk group exhibited a prolonged overall survival (OS). Patients in low risk group were more likely to present a higher immune infiltration and stronger response to immunotherapy. GSEA revealed the model was associated with immune-related pathways. We constructed and validated a novel model based on three prognostic genes related to TIME in TNBC. The model contributed a robust signature that could predict the prognosis in TNBC, especially for the efficacy of immunotherapy.
Root aphid (Aploneura lentisci) population size on perennial ryegrass is determined by drought and endophyte strain
Authors: Hewitt Katrin G. , Hofmann Rainer W. , Ball Oliver J. , Cox Neil , Bryant Racheal H. , Finch Sarah C. , Popay Alison J. 
Published: May 2023

AbstractClimate change is anticipated to lead to an increase in the occurrence and intensity of drought and fluctuations in insect cycles that will challenge modern pasture systems. Feeding by root aphids such as Aploneura lentisci Pass. can be a significant challenge to pastures. These below-ground living aphids are commonly found in New Zealand and Australia, feeding year-round on the roots of graminaceous plants such as perennial ryegrass (Lolium perenne L.). Some strains of the fungal endophyte Epichloë festucae var. lolii in perennial ryegrass can provide protection against root aphids and greater resilience under drought, contributing to higher persistency and growth than endophyte-free plants. However, the interaction between insect pressure and drought is not understood. This study examined the effect of drought on root aphid populations and plant performance in perennial ryegrass plants relative to endophyte status (±) and endophyte strain (AR37, NZCT) in a glasshouse experiment. Plants were cloned across the drought and well-watered treatments, and half of the plants were inoculated with root aphids, whilst half of the plants were treated with insecticide. Endophyte infection with strain NZCT and AR37 reduced root aphid numbers. Aphid populations were significantly higher in drought-stressed than in well-watered plants in both endophyte-infected and endophyte-free treatments. Under drought conditions, root aphid populations were increased 4-fold in NZCT and 8-fold in AR37 and endophyte-free plants in comparison with their well-watered counterparts. Root aphids reduced shoot dry weight by 16% in drought-exposed and 26% in well-watered plants in comparison with their insecticide-treated counterparts whilst reducing root biomass by 49%. Our results suggest that root aphids are likely able to exploit the higher availability of amino acids in the plant sap of drought-exposed plants. This study provides evidence that climate change-mediated impacts of root aphids could reduce production in perennial ryegrass-dominant pastures. However, field trials would be necessary to determine whether this effect is seen in situ, where numerous additional factors will be operating at the same time.
The Conley–Zehnder indices of the spatial Hill three-body problem
Authors: Aydin Cengiz 
Published: May 2023

AbstractWe explore the interaction between the Conley–Zehnder index and bifurcation points of symmetric planar as well as spatial periodic orbits in the spatial Hill three-body problem. We start with the fundamental families of planar periodic orbits which are those of direct (familyg) and retrograde periodic orbits (familyf). Since the spatial system is invariant under a symplectic involution, whose fixed point set corresponds to the planar problem, planar orbits have planar and spatial Floquet multipliers, and planar and spatial Conley–Zehnder indices. When the Floquet multipliers move through a root of unity, new families of periodic orbits bifurcate and the index jumps. For very low energies, the familiesgand farise dynamically from the rotating Kepler problem, and in a recent work (Aydin From Babylonian lunar observations to Floquet multipliers and Conley-Zehnder Indices) we determined analytically their indices. By their numerical continuations for higher energies, we determine the index of various families of planar and spatial periodic orbits bifurcating fromgandf. Since these families can bifurcate again and meet each other, this procedure can get complicated. This index leads to a grading on local Floer homology. Since the local Floer homology and its Euler characteristic stay invariant under bifurcation, the index provides important information about the interconnectedness of such families, which we illustrate in form of bifurcation graphs. Since the solutions of Hill’s system may serve as orbits for space mission design or astronomical observations, our results promote the interaction between Symplectic Geometry and practical problems.
Clinical characteristics, treatment, and long-term outcome of patients with brain metastases from thyroid cancer
Authors: Wolff Ladislaia , Steindl Ariane , Popov Petar , Dieckmann Karin , Gatterbauer Brigitte , Widhalm Georg , Berghoff Anna Sophie , Preusser Matthias , Raderer Markus , Kiesewetter Barbara 
Published: May 2023

AbstractBrain metastases (BM) in patients with thyroid cancer (TC) are rare with an incidence of 1% for papillary and follicular, 3% for medullary and up to 10% for anaplastic TC (PTC, FTC, MTC and ATC). Little is known about the characteristics and management of BM from TC. Thus, we retrospectively analyzed patients with histologically verified TC and radiologically verified BM identified from the Vienna Brain Metastasis Registry. A total of 20/6074 patients included in the database since 1986 had BM from TC and 13/20 were female. Ten patients had FTC, 8 PTC, one MTC and one ATC. The median age at diagnosis of BM was 68 years. All but one had symptomatic BM and 13/20 patients had a singular BM. Synchronous BM at primary diagnosis were found in 6 patients, while the median time to BM diagnosis was 13 years for PTC (range 1.9–24), 4 years for FTC (range 2.1–41) and 22 years for the MTC patient. The overall survival from diagnosis of BM was 13 months for PTC (range 1.8–57), 26 months for FTC (range 3.9–188), 12 years for the MTC and 3 months for the ATC patient. In conclusion, development of BM from TC is exceedingly rare and the most common presentation is a symptomatic single lesion. While BM generally constitute a poor prognostic factor, individual patients experience long-term survival following local therapy.
Performance models of data parallel DAG workflows for large scale data analytics
Authors: Shi Juwei , Lu Jiaheng 
Published: May 2023

AbstractDirected Acyclic Graph (DAG) workflows are widely used for large-scale data analytics in cluster-based distributed computing systems. The performance model for a DAG on data-parallel frameworks (e.g., MapReduce) is a research challenge because the allocation of preemptable system resources among parallel jobs may dynamically vary during execution. This resource allocation variation during execution makes it difficult to accurately estimate the execution time. In this paper, we tackle this challenge by proposing a new cost model, called Bottleneck Oriented Estimation (BOE), to estimate the allocation of preemptable resources by identifying the bottleneck to accurately predict task execution time. For a DAG workflow, we propose a state-based approach to iteratively use the resource allocation property among stages to estimate the overall execution plan. Furthermore, to handle the skewness of various jobs, we refine the model with the order statistics theory to improve estimation accuracy. Extensive experiments were performed to validate these cost models with HiBench and TPC-H workloads. The BOE model outperforms the state-of-the-art models by a factor of five for task execution time estimation. For the refined skew-aware model, the average prediction error is under $$3\%$$

3
%

when estimating the execution time of 51 hybrid analytics (HiBench) and query (TPC-H) DAG workflows.
The circular economy of electric vehicle batteries: a Finnish case study
Authors: Rönkkö Pasi , Majava Jukka , Hyvärinen Tatu , Oksanen Ilari , Tervonen Pekka , Lassi Ulla 
Published: May 2023

AbstractThe automotive industry faces challenges because of the electrification of vehicles and the rapidly increasing need for electric vehicle batteries (EVBs). Raw materials availability is limited; however, there will also be a significant number of end-of-life (EOL) batteries. This creates various circular economy (CE) business opportunities for EVB manufacturers, third-party providers, and other stakeholders. However, not all CE solutions are sustainable or economically feasible. In this study, through the use of case studies, expert interviews, and a survey, we determined the current state of the EVB CE in Finland, the possible options for utilizing EOL vehicle batteries, and the greatest barriers for the EVB CE. We found that some EVB-related CE applications are not supported by the government and legislation, for example environmental regulations and building standards. CE opportunities include a shorter lead time for some components, which makes them attractive for EOL applications.
Threshold and power of pulsed red-emitting diode lasers with a bulk active layer near p-cladding under high-temperature operation
Authors: Ryvkin Boris S. , Avrutin Eugene A. 
Published: May 2023

AbstractThreshold properties and pulsed output of AlGaInP visible-emitting lasers with an asymmetric waveguide structure and a bulk active layer are analysed. The effects of the current leakage, increased by the heating of the laser due to the proximity of the electrical pulse source and the Joule heating in and around this source are analysed. When optimising the laser design, waveguiding properties of the bulk active layer are shown to be important, leading to threshold currents decreasing, and injection efficiency increasing, with active layer thickness in lasers with moderately thick (< 0.1 μm) active layers.
Cystine rather than cysteine is the preferred substrate for β-elimination by cystathionine γ-lyase: implications for dietary methionine restriction
Authors: Jeitner Thomas M. , Azcona Juan A. , Ables Gene P. , Cooke Diana , Horowitz Mark C. , Singh Pradeep , Kelly James M. , Cooper Arthur J. L. 
Published: May 2023

AbstractDietary methionine restriction (MR) increases longevity by improving health. In experimental models, MR is accompanied by decreased cystathionine β-synthase activity and increased cystathionine γ-lyase activity. These enzymes are parts of the transsulfuration pathway which produces cysteine and 2-oxobutanoate. Thus, the decrease in cystathionine β-synthase activity is likely to account for the loss of tissue cysteine observed in MR animals. Despite this decrease in cysteine levels, these tissues exhibit increased H2S production which is thought to be generated by β-elimination of the thiol moiety of cysteine, as catalyzed by cystathionine β-synthase or cystathionine γ-lyase. Another possibility for this H2S production is the cystathionine γ-lyase-catalyzed β-elimination of cysteine persulfide from cystine, which upon reduction yields H2S and cysteine. Here, we demonstrate that MR increases cystathionine γ-lyase production and activities in the liver and kidneys, and that cystine is a superior substrate for cystathionine γ-lyase catalyzed β-elimination as compared to cysteine. Moreover, cystine and cystathionine exhibit comparable Kcat/Km values (6000 M−1 s−1) as substrates for cystathionine γ-lyase-catalyzed β-elimination. By contrast, cysteine inhibits cystathionine γ-lyase in a non-competitive manner (Ki ~ 0.5 mM), which limits its ability to function as a substrate for β-elimination by this enzyme. Cysteine inhibits the enzyme by reacting with its pyridoxal 5′-phosphate cofactor to form a thiazolidine and in so doing prevents further catalysis. These enzymological observations are consistent with the notion that during MR cystathionine γ-lyase is repurposed to catabolize cystine and thereby form cysteine persulfide, which upon reduction produces cysteine.