bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale investigation of deep learning approaches for ventilated lung segmentation using multi-nuclear hyperpolarized gas MRI
Authors: Astley Joshua R. , Biancardi Alberto M. , Hughes Paul J. C. , Marshall Helen , Smith Laurie J. , Collier Guilhem J. , Eaden James A. , Weatherley Nicholas D. , Hatton Matthew Q. , Wild Jim M. , Tahir Bilal A. 
Published: June 2022

AbstractRespiratory diseases are leading causes of mortality and morbidity worldwide. Pulmonary imaging is an essential component of the diagnosis, treatment planning, monitoring, and treatment assessment of respiratory diseases. Insights into numerous pulmonary pathologies can be gleaned from functional lung MRI techniques. These include hyperpolarized gas ventilation MRI, which enables visualization and quantification of regional lung ventilation with high spatial resolution. Segmentation of the ventilated lung is required to calculate clinically relevant biomarkers. Recent research in deep learning (DL) has shown promising results for numerous segmentation problems. Here, we evaluate several 3D convolutional neural networks to segment ventilated lung regions on hyperpolarized gas MRI scans. The dataset consists of 759 helium-3 (3He) or xenon-129 (129Xe) volumetric scans and corresponding expert segmentations from 341 healthy subjects and patients with a wide range of pathologies. We evaluated segmentation performance for several DL experimental methods via overlap, distance and error metrics and compared them to conventional segmentation methods, namely, spatial fuzzy c-means (SFCM) and K-means clustering. We observed that training on combined 3He and 129Xe MRI scans using a 3D nn-UNet outperformed other DL methods, achieving a mean ± SD Dice coefficient of 0.963 ± 0.018, average boundary Hausdorff distance of 1.505 ± 0.969 mm, Hausdorff 95th percentile of 5.754 ± 6.621 mm and relative error of 0.075 ± 0.039. Moreover, limited differences in performance were observed between 129Xe and 3He scans in the testing set. Combined training on 129Xe and 3He yielded statistically significant improvements over the conventional methods (p < 0.0001). In addition, we observed very strong correlation and agreement between DL and expert segmentations, with Pearson correlation of 0.99 (p < 0.0001) and Bland–Altman bias of − 0.8%. The DL approach evaluated provides accurate, robust and rapid segmentations of ventilated lung regions and successfully excludes non-lung regions such as the airways and artefacts. This approach is expected to eliminate the need for, or significantly reduce, subsequent time-consuming manual editing.
The speed acuity test as a diagnostic aid in cerebral visual impairment
Authors: Tanke Nouk , Barsingerhorn Annemiek D. , Goossens Jeroen , Boonstra F. Nienke 
Published: June 2022

AbstractOne of the characteristics of children with cerebral visual impairments (CVI) is that they need more time to process visual information. However, currently, few tests are available that can reliably measure visual processing speed. The speed acuity test, a discrimination reaction-time test in which participants indicate the orientation of Landolt-C symbols as quickly and accurately as possible, was specifically developed to determine the time a child needs to discern visual details. The test measures both the accuracy and the latency of the responses for nine different optotype sizes in order to control for decreased visual acuity. The results show that children with CVI need significantly more time to respond to the largest optotype sizes than age-matched normally sighted children and children with visual impairments due to an ocular disorder (VIo). This effect is independent of the time it takes to make a motor response. However, the reaction-time difference between the children with CVI and VIo is not seen for optotype sizes at the acuity threshold. Together with reaction times on visual and auditory detection tasks as controls, reaction times measured in the speed-acuity test allow for acceptable discrimination (AUC in ROC analysis: 0.81) between CVI and VIo.
A set of gene knockouts as a resource for global lipidomic changes
Authors: Spiegel Aleksandra , Lauber Chris , Bachmann Mandy , Heninger Anne-Kristin , Klose Christian , Simons Kai , Sarov Mihail , Gerl Mathias J. 
Published: June 2022

AbstractEnzyme specificity in lipid metabolic pathways often remains unresolved at the lipid species level, which is needed to link lipidomic molecular phenotypes with their protein counterparts to construct functional pathway maps. We created lipidomic profiles of 23 gene knockouts in a proof-of-concept study based on a CRISPR/Cas9 knockout screen in mammalian cells. This results in a lipidomic resource across 24 lipid classes. We highlight lipid species phenotypes of multiple knockout cell lines compared to a control, created by targeting the human safe-harbor locus AAVS1 using up to 1228 lipid species and subspecies, charting lipid metabolism at the molecular level. Lipid species changes are found in all knockout cell lines, however, some are most apparent on the lipid class level (e.g., SGMS1 and CEPT1), while others are most apparent on the fatty acid level (e.g., DECR2 and ACOT7). We find lipidomic phenotypes to be reproducible across different clones of the same knockout and we observed similar phenotypes when two enzymes that catalyze subsequent steps of the long-chain fatty acid elongation cycle were targeted.
Facile preparation of aqueous-soluble fluorescent polyethylene glycol functionalized carbon dots from palm waste by one-pot hydrothermal carbonization for colon cancer nanotheranostics
Authors: Sangjan Amornrat , Boonsith Suthida , Sansanaphongpricha Kanokwan , Thinbanmai Tapanee , Ratchahat Sakhon , Laosiripojana Navadol , Wu Kevin C.-W. , Shin Hyeon Suk , Sakdaronnarong Chularat 
Published: June 2022

AbstractCarbon dots (CDs) are categorized as an emerging class of zero-dimension nanomaterials having high biocompatibility, photoluminescence, tunable surface, and hydrophilic property. CDs, therefore, are currently of interest for bio-imaging and nano-medicine applications. In this work, polyethylene glycol functionalized CDs (CD-PEG) were prepared from oil palm empty fruit bunch by a one-pot hydrothermal technique. PEG was chosen as a passivating agent for the enhancement of functionality and photoluminescence properties of CDs. To prepare the CDs-PEG, the effects of temperature, time, and concentration of PEG were investigated on the properties of CDs. The as-prepared CDs-PEG were characterized by several techniques including dynamic light scattering, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, fluorescence spectroscopy, Raman spectroscopy, Fourier-transform infrared spectroscopy and Thermogravimetric analysis. The as-prepared CDs under hydrothermal condition at 220 °C for 6 h had spherical morphology with an average diameter of 4.47 nm. Upon modification, CDs-PEG were photo-responsive with excellent photoluminescence property. The CDs-PEG was subsequently used as a drug carrier for doxorubicin [DOX] delivery to CaCo-2, colon cancer cells in vitro. DOX was successfully loaded onto CDs-PEG surface confirmed by FT-IR and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometer (MALDI-TOF/MS) patterns. The selective treatment of CDs-PEG-DOX against the colorectal cancer cells, , relative to normal human fibroblast cells was succesfully demonstrated.
Identification and characterization of alternative splicing variants of buffalo LXRα expressed in mammary gland
Authors: Fan Xinyang , Zhang Yongyun , Qiu Lihua , Zhu Wei , Tu Xingtiao , Miao Yongwang 
Published: June 2022

AbstractLiver X receptor α (LXRα) is a ligand-dependent transcription factor and plays an important role in the regulation of cholesterol homeostasis, fatty acid biosynthesis and glucose metabolism. In this study, transcripts of LXRα gene were cloned and characterized from buffalo mammary gland, and three alternative splicing transcripts of buffalo LXRα gene were identified, named LXRα1, LXRα2 and LXRα3. The structure of the LXRα transcripts of buffalo and cattle was highly similar. Bioinformatics analysis showed that LXRα1 contains two complete functional domains of LXRα, one is the DNA-binding domain (NR_DBD_LXR) and the other is the ligand-binding domain (NR_LBD_LXR). The reading frame of LXRα2 is altered due to the skipping of exon 9, which truncates its encoding protein prematurely at the 400th amino acid residue, making it contain a complete DNA-binding domain and part of a ligand-binding domain. Due to the deletion of exon 4, the protein encoded by LXRα3 lacks 89 amino acid residues and contains only a complete ligand-binding domain, which makes it lose its transcriptional regulation function. In addition, motifs and conserved domains of three LXRα variants of buffalo were highly consistent with those of corresponding transcripts from other mammal species. Subcellular localization analysis showed that LXRα1 plays a functional role in the nucleus of buffalo mammary epithelial cells, while LXRα2 and LXRα3 are distributed in the nucleus and cytoplasm. Compared with non-lactating period, the mRNA abundance of the three LXRα transcripts in the mammary gland tissue of buffalo increased during lactating period, revealing that they play a key role in the synthesis of buffalo milk fat. Among the three LXRα transcripts, LXRα1 has the highest expression in the mammary gland, indicating that it is the major transcript in the mammary gland and has important regulatory functions, while LXRα2 and LXRα3 may have regulatory effects on the function of LXRα1. This study highlights the key role of LXRα alternative splicing in the post-transcriptional regulation of buffalo lactation.
Heatstroke-induced late-onset neurological deficits in mice caused by white matter demyelination, Purkinje cell degeneration, and synaptic impairment in the cerebellum
Authors: Miyamoto Kazuyuki , Nakamura Motoyasu , Ohtaki Hirokazu , Suzuki Keisuke , Yamaga Hiroki , Yanagisawa Kaoru , Maeda Atsuo , Yagi Masaharu , Hayashi Munetaka , Honda Kazuho , Dohi Kenji 
Published: June 2022

AbstractGlobal warming increases heatstroke incidence. After heatstroke, patients exhibit neurological symptoms, suggesting cerebellar damage. However, the potential long-term adverse outcomes are poorly understood. We studied the cerebellum after heatstroke in mouse heatstroke models. In this study, motor coordination disorder significantly appeared 3 weeks after heatstroke and gradually improved to some extent. Although white matter demyelination was detected at 1 and 3 weeks after heatstroke in the cerebellum, it was not found in the corpus callosum. The Purkinje cell numbers significantly decreased at 1, 3, and 9 weeks after heatstroke. The intensity of synaptophysin and postsynaptic density-95 temporarily appeared to attenuate at 3 weeks after heatstroke; however, both appeared to intensify at 9 weeks after heatstroke. Motor coordination loss occurred a few weeks after heatstroke and recovered to some extent. Late-onset motor impairment was suggested to be caused by cerebellar dysfunctions morphologically assessed by myelin staining of cerebellar white matter and immunostaining of Purkinje cells with pre- and postsynaptic markers. Purkinje cell number did not recover for 9 weeks; other factors, including motor coordination, partially recovered, probably by synaptic reconstruction, residual Purkinje cells, and other cerebellar white matter remyelination. These phenomena were associated with late-onset neurological deficits and recovery after heatstroke.
Riots and subways, a relationship moderated by the neighborhood’s income level
Authors: Cartes Carlos , Asahi Kenzo , Fernández Rodrigo 
Published: June 2022

AbstractSocial disturbances due to socioeconomic and political factors received media attention during 2019 in places like France, Hong Kong, Chile, Nigeria, Sudan, Haiti, and Lebanon. In October 2019, Chile saw massive demonstrations in the capital city of Santiago. The cost of damage to infrastructure during the first month of unrest was estimated at US$ 4.6 billion, and the cost to the Chilean economy was about US$ 3 billion, 1.1% of its Gross Domestic Product. This study analyzes how the topology of the public transport network affected the locations of the 2019 riots in Santiago. On average, we find a clear association between proximity to the subway network and riot density. This association is significant only in neighborhoods with residents in the highest and lowest income quartiles. As a result, when analyzing social unrest and the critical role of public transport, policymakers should also consider the crucial role of income.
Comparison of the gastric microbiome in Billroth I and Roux-en-Y reconstructions after distal gastrectomy
Authors: Imai Yoshiro , Lee Sang-Woong , Sakaguchi Shoichi , Kato-Kogoe Nahoko , Taniguchi Kohei , Omori Michi , Tanaka Ryo , Honda Kotaro , Osumi Wataru , Nakano Takashi , Ueno Takaaki , Uchiyama Kazuhisa 
Published: June 2022

AbstractThe changes in gastric microbiota following reconstruction after gastrectomy have not been reported. This study aimed to compare the gastric microbiota following Billroth I and Roux-en-Y reconstructions after distal gastrectomy. We enrolled 71 gastrectomized patients with gastric cancer; 31 and 40 underwent Billroth I and Roux-en-Y reconstructions, respectively. During upper gastrointestinal endoscopy, gastric fluid was collected immediately before and 6 months after distal gastrectomy. Deoxyribonucleic acid isolated from each sample was evaluated using 16S ribosomal ribonucleic acid metagenomic analysis. Analysis revealed that the gastric microbiota’s species richness (expressed as the alpha diversity) was significantly lower after than before distal gastrectomy (operational taxonomic units, p = 0.001; Shannon index, p = 0.03). The interindividual diversity (beta diversity) was significantly different before and after distal gastrectomy (unweighted UniFrac distances, p = 0.04; weighted UniFrac distances, p = 0.001; Bray–Curtis, p = 0.001). Alpha and beta diversity were not significantly different between Billroth I and Roux-en-Y reconstructions (observed operational taxonomic units, p = 0.58; Shannon index, p = 0.95; unweighted UniFrac distances, p = 0.65; weighted UniFrac distances, p = 0.67; Bray–Curtis, p = 0.63). Our study demonstrated significant differences in gastric microbiota diversity, composition, and community before and after distal gastrectomy but no difference between Billroth I and Roux-en-Y reconstruction after distal gastrectomy.
SILAC kinase screen identifies potential MASTL substrates
Authors: Marzec Kamila A. , Rogers Samuel , McCloy Rachael , Parker Benjamin L. , James David E. , Watkins D. Neil , Burgess Andrew 
Published: June 2022

AbstractMicrotubule-associated serine/threonine kinase-like (MASTL) has emerged as a critical regulator of mitosis and as a potential oncogene in a variety of cancer types. To date, Arpp-19/ENSA are the only known substrates of MASTL. However, with the roles of MASTL expanding and increased interest in development of MASTL inhibitors, it has become critical to determine if there are additional substrates and what the optimal consensus motif for MASTL is. Here we utilized a whole cell lysate in vitro kinase screen combined with stable isotope labelling of amino acids in cell culture (SILAC) to identify potential substrates and the residue preference of MASTL. Using the related AGC kinase family members AKT1/2, the kinase screen identified several known and new substrates highly enriched for the validated consensus motif of AKT. Applying this method to MASTL identified 59 phospho-sites on 67 proteins that increased in the presence of active MASTL. Subsequent in vitro kinase assays suggested that MASTL may phosphorylate hnRNPM, YB1 and TUBA1C under certain in vitro conditions. Taken together, these data suggest that MASTL may phosphorylate several additional substrates, providing insight into the ever-increasing biological functions and roles MASTL plays in driving cancer progression and therapy resistance.
Efficacy and safety of ketone ester infusion to prevent muscle weakness in a mouse model of sepsis-induced critical illness
Authors: Weckx Ruben , Goossens Chloë , Derde Sarah , Pauwels Lies , Vander Perre Sarah , Van den Berghe Greet , Langouche Lies 
Published: June 2022

AbstractIn septic mice, 3-hydroxybutyrate-sodium-salt has shown to partially prevent sepsis-induced muscle weakness. Although effective, the excessive sodium load was toxic. We here investigated whether ketone ester 3-hydroxybutyl-3-hydroxybutanoate (3HHB) was a safer alternative. In a mouse model of abdominal sepsis, the effects of increasing bolus doses of 3HHB enantiomers on mortality, morbidity and muscle force were investigated (n = 376). Next, plasma 3HB- clearance after bolus d-3HHB was investigated (n = 27). Subsequently, in septic mice, the effect on mortality and muscle force of a continuous d,l-3HHB infusion was investigated (n = 72). In septic mice, as compared with placebo, muscle force was increased at 20 mmol/kg/day l-3HHB and at 40 mmol/kg/day d- and d,l-3HHB. However, severity of illness and mortality was increased by doubling the effective bolus doses. Bolus 3HHB caused a higher 3HB− plasma peak and slower clearance with sepsis. Unlike bolus injections, continuous infusion of d,l-3HHB did not increase severity of illness or mortality, while remaining effective in improving muscle force. Treatment of septic mice with the ketone ester 3HHB partly prevented muscle weakness. Toxicity of 3HHB administered as bolus was completely avoided by continuous infusion of the same dose. Whether continuous infusion of ketone esters represents a promising intervention to also prevent ICU-acquired weakness in human patients should be investigated.
Longitudinal associations between going outdoors and mental health and wellbeing during a COVID-19 lockdown in the UK
Authors: Stock Sarah , Bu Feifei , Fancourt Daisy , Mak Hei Wan 
Published: June 2022

AbstractThe COVID-19 pandemic led to national lockdowns in countries around the world. Whilst lockdowns were shown to be effective in reducing the spread of disease, they were also associated with adverse effects on people’s mental health and wellbeing. Previous studies have suggested that time spent outside may have played a role in mitigating these negative effects, but research on this topic remains limited. Therefore, this study was designed to explore the longitudinal associations between going outdoors and people’s mental health and wellbeing during the first national lockdown (March–May 2020) in the UK. Data from 35,301 participants from the COVID-19 Social Study were analysed. Fixed effects regression was used to explore the longitudinal association between changes in going outdoors (the number of days spent outside) and changes in depressive symptoms, anxiety symptoms, life satisfaction and loneliness. A range of household and neighbourhood moderators were examined. Results show that an increase in the number of days spent outside was associated with decreases in depressive and anxiety symptoms and an increase in life satisfaction. Associations were more salient amongst people living with others, and those with greater satisfaction with their neighbourhood walkability and green spaces. No longitudinal association was found with loneliness. Overall, our analyses showed a positive association between going outdoors and improved mental health and wellbeing during the first COVID-19 lockdown in the UK. These findings are important for formulating guidance for people to stay well at home during pandemics and for the on-going nature-based social prescribing scheme.
Estimating female malaria mosquito age by quantifying Y-linked genes in stored male spermatozoa
Authors: Madan Damian , Rivera Rafael , Ortega Corrie , Touchon Justin C. , Kimball Corinna , van Gemert Geert-Jan , Graumans Wouter , Matsuura Stephanie , Parghi Sean S. , Bell David , Bousema Teun , Drakeley Chris , Collins Katharine A. , Burkot Thomas R. 
Published: June 2022

AbstractVector control strategies are among the most effective measures to combat mosquito-borne diseases, such as malaria. These strategies work by altering the mosquito age structure through increased mortality of the older female mosquitoes that transmit pathogens. However, methods to monitor changes to mosquito age structure are currently inadequate for programmatic implementation. Female mosquitoes generally mate a single time soon after emergence and draw down spermatozoa reserves with each oviposition cycle. Here, we demonstrate that measuring spermatozoa quantity in female Anopheles mosquitoes is an effective approach to assess mosquito age. Using multiplexed qPCR targeted at male spermatozoa, we show that Y-linked genes in female mosquitoes are exclusively found in the spermatheca, the organ that houses spermatozoa, and the quantity of these gene sequences significantly declines with age. The method can accurately identify mosquitoes more than 10 days old and thus old enough to potentially transmit pathogens harbored in the salivary glands during blood feeding. Furthermore, mosquito populations that differ by 10% in daily survivorship have a high likelihood of being distinguished using modest sample sizes, making this approach scalable for assessing the efficacy of vector intervention control programs.
Detection of the UV-vis silent biomarker trimethylamine-N-oxide via outer-sphere interactions in a lanthanide metal-organic framework
Authors: Min Hui , Chen Zhonghang , Han Zongsu , Wang Kunyu , Xu Jun , Shi Wei , Cheng Peng 
Published: June 2022

AbstractTrimethylamine-N-oxide (TMAO) is a biomarker of the cardiovascular disease that is one of the leading causes of worldwide death. Facile detection of TMAO can significantly improve the survival rate of this disease by allowing early prevention. However, the UV-vis silent nature of TMAO makes it intricated to be detected by conventional sensing materials or analytical instruments. Here we show a bilanthanide metal-organic framework functionalized by borono group for the recognition of TMAO. Superior sensitivity, selectivity and anti-interference ability were achieved by the inverse emission intensity changes of the two lanthanide centers. The limit of detection is 15.6 μM, covering the clinical urinary concentration range of TMAO. A smartphone application was developed based on the change in R-G-B chromaticity. The sensing mechanism via a well-matched outer-sphere interaction governing the sensing function was studied in detail, providing fundamentals in molecular level for the design of advanced sensing materials for UV-Vis silent molecules.
Dissipative discrete time crystals in a pump-modulated Kerr microcavity
Authors: Taheri Hossein , Matsko Andrey B. , Herr Tobias , Sacha Krzysztof 
Published: June 2022

AbstractTime crystals represent temporal analogues of the spatial self-ordering exhibited by atomic or molecular building blocks of solid-state crystals. The pursuit of discrete time crystals (DTCs) in periodically forced Floquet closed systems has revealed how they can evade thermalization and loss of temporal order. Recently, it has been shown that even with coupling to the ambient and its concomitant noise, some states maintain their time crystalline order, formingdissipativeDTCs. Here, we introduce a scheme for the realization and state control of dissipative DTCs hinging on pumping a Kerr optical resonator with a phase-modulated continuous-wave laser. We show the possible symmetry breaking states possess temporal long-range order and analyze the phase noise of the accompanying signature radio frequency (RF) subharmonic. Besides offering a technique for generating high-spectral-purity RF signals, this versatile platform empowers controlled switching between various DTC states through accessible experimental knobs, hence facilitating the future study of DTC phase transitions.