bluuebunny/crossref_metadata_2025_split huggingface dataset:
One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade
Authors: Blaz Jazmin , Galindo Luis Javier , Heiss Aaron A. , Kaur Harpreet , Torruella Guifré , Yang Ashley , Alexa Thompson L. , Filbert Alexander , Warring Sally , Narechania Apurva , Shiratori Takashi , Ishida Ken-ichiro , Dacks Joel B. , López-García Purificación , Moreira David , Kim Eunsoo , Eme Laura 
Published: September 2023

AbstractMantamonads were long considered to represent an “orphan” lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the “CRuMs” supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.
Reservoir inventory for China in 2016 and 2021
Authors: Zhang Haiying , Chen Fang , Wang Lei , Wang Ning , Yu Bo 
Published: September 2023

AbstractReservoir inventories are essential for investigating the impact of climate change and anthropogenic activities on water scape changes. They provide fundamental data sources to explore the sustainability and management efficiency of water resources. However, publicly released reservoir inventories are currently limited to a single temporal domain. As a result, the effectiveness of governmental policy implementation on water resources remains to be explored due to the lack of multi-time datasets. In this study, we generated a reservoir inventory for China for the years 2016 and 2021 with an overall accuracy of 99.71%. The reservoirs were visually interpreted from annually composited Landsat images, and each reservoir is represented by a polygon with attributes of reservoir name, area and storage capacity. About 10.32% of the reservoirs have increased storage capacity from 2016 to 2021, while 22.73% have decreased. Most provinces and river basins in China have expanded their accumulated storage capacity from 2016 to 2021.
TIHM: An open dataset for remote healthcare monitoring in dementia
Authors: Palermo Francesca , Chen Yu , Capstick Alexander , Fletcher-Loyd Nan , Walsh Chloe , Kouchaki Samaneh , True Jessica , Balazikova Olga , Soreq Eyal , Scott Gregory , Rostill Helen , Nilforooshan Ramin , Barnaghi Payam 
Published: September 2023

AbstractDementia is a progressive condition that affects cognitive and functional abilities. There is a need for reliable and continuous health monitoring of People Living with Dementia (PLWD) to improve their quality of life and support their independent living. Healthcare services often focus on addressing and treating already established health conditions that affect PLWD. Managing these conditions continuously can inform better decision-making earlier for higher-quality care management for PLWD. The Technology Integrated Health Management (TIHM) project developed a new digital platform to routinely collect longitudinal, observational, and measurement data, within the home and apply machine learning and analytical models for the detection and prediction of adverse health events affecting the well-being of PLWD. This work describes the TIHM dataset collected during the second phase (i.e., feasibility study) of the TIHM project. The data was collected from homes of 56 PLWD and associated with events and clinical observations (daily activity, physiological monitoring, and labels for health-related conditions). The study recorded an average of 50 days of data per participant, totalling 2803 days.
Impact of fractionated cisplatin and radiation treatment on cell growth and accumulation of DNA damage in two normal cell types differing in origin
Authors: Akuwudike Pamela , López-Riego Milagrosa , Dehours Cloé , Lundholm Lovisa , Wojcik Andrzej 
Published: September 2023

AbstractEvidence on the impact of chemotherapy on radiotherapy-induced second malignant neoplasms is controversial. We estimated how cisplatin modulates the in vitro response of two normal cell types to fractionated radiation. AHH-1 lymphoblasts and VH10 fibroblasts were irradiated at 1 Gy/fraction 5 and 3 times per week during 12 and 19 days, respectively, and simultaneously treated with 0.1, 0.2, 0.4, 0.8, 1.7 and 3.3 µM of cisplatin twice a week. Cell growth during treatment was monitored. Cell growth/cell death and endpoints related to accumulation of DNA damage and, thus, carcinogenesis, were studied up to 21 days post treatment in cells exposed to radiation and the lowest cisplatin doses. Radiation alone significantly reduced cell growth. The impact of cisplatin alone below 3.3 µM was minimal. Except the lowest dose of cisplatin in VH10 cells, cisplatin reduced the inhibitory effect of radiation on cell growth. Delayed cell death was highest in the combination groups while the accumulation of DNA damage did not reveal a clear pattern. In conclusion, fractionated, concomitant exposure to radiation and cisplatin reduces the inhibitory effect of radiation on cell proliferation of normal cells and does not potentiate delayed effects resulting from accumulation of DNA damage.
Learning and predicting the unknown class using evidential deep learning
Authors: Nagahama Akihito 
Published: September 2023

AbstractIn practical deep-learning applications, such as medical image analysis, autonomous driving, and traffic simulation, the uncertainty of a classification model’s output is critical. Evidential deep learning (EDL) can output this uncertainty for the prediction; however, its accuracy depends on a user-defined threshold, and it cannot handle training data with unknown classes that are unexpectedly contaminated or deliberately mixed for better classification of unknown class. To address these limitations, I propose a classification method called modified-EDL that extends classical EDL such that it outputs a prediction, i.e. an input belongs to a collective unknown class along with a probability. Although other methods handle unknown classes by creating new unknown classes and attempting to learn each class efficiently, the proposed m-EDL outputs, in a natural way, the “uncertainty of the prediction” of classical EDL and uses the output as the probability of an unknown class. Although classical EDL can also classify both known and unknown classes, experiments on three datasets from different domains demonstrated that m-EDL outperformed EDL on known classes when there were instances of unknown classes. Moreover, extensive experiments under different conditions established that m-EDL can predict unknown classes even when the unknown classes in the training and test data have different properties. If unknown class data are to be mixed intentionally during training to increase the discrimination accuracy of unknown classes, it is necessary to mix such data that the characteristics of the mixed data are as close as possible to those of known class data. This ability extends the range of practical applications that can benefit from deep learning-based classification and prediction models.
Evaluation of a polarization-enhanced laparoscopy prototype for improved intra-operative visualization of peritoneal metastases
Authors: Schnelldorfer Thomas , Gnanatheepam Einstein , Trout Robert , Gado Ahmed , Pelletier Joyce-Ellen , Dinh Long T. , Hunter Martin , Georgakoudi Irene 
Published: September 2023

AbstractDespite careful staging, the accuracy for preoperative detection of small distant metastases remains poor, creating a clinical need for enhanced operative staging to detect occult peritoneal metastases. This study evaluates a polarization-enhanced laparoscopy (PEL) prototype and assesses its potential for label-free contrast enhancement of peritoneal metastases. This is a first-in-human feasibility study, including 10 adult patients who underwent standard staging laparoscopy (SSL) for gastrointestinal malignancy along with PEL. Image frames of all detectable peritoneal lesions underwent analysis. Using Monte Carlo simulations, contrast enhancement based on the color dependence of PEL (mPEL) was assessed. The prototype performed safely, yet with limitations in illumination, fogging of the distal window, and image co-registration. Sixty-five lesions (56 presumed benign and 9 presumed malignant) from 3 patients represented the study sample. While most lesions were visible under human examination of both SSL and PEL videos, more lesions were apparent using SSL. However, this was likely due to reduced illumination under PEL. When controlling for such effects through direct comparisons of integrated (WLL) vs differential (PEL) polarization laparoscopy images, we found that PEL imaging yielded an over twofold Weber contrast enhancement over WLL. Further, enhancements in the discrimination between malignant and benign lesions were achieved by exploiting the PEL color contrast to enhance sensitivity to tissue scattering, influenced primarily by collagen. In conclusion, PEL appears safe and easy to integrate into the operating room. When controlling for the degree of illumination, image analysis suggested a potential for mPEL to provide improved visualization of metastases.
Rodents as vehicle for delivery of transgenic bacteria to make paratransgenic sand fly vectors of cutaneous leishmaniasis in field condition
Authors: Ghassemi Marzieh , Akhavan Amir Ahmad , Zahraei-Ramazani Alireza , Yakhchali Bagher , Arandian Mohammad Hossein , Jafari Reza , Akhlaghi Maryam , Shirani-Bidabadi Leila , Azam Kamal , Koosha Mona , Oshaghi Mohammad Ali 
Published: September 2023

AbstractVector-borne diseases, among them leishmaniasis, cause more than 700,000 deaths annually. The lack of an effective vaccination and the increasing resistance of sand flies to insecticides require the urgent development of innovative approaches to contain the disease. The use of engineered bacteria that express anti-parasite molecules (paratransgenesis) shows much promise. However, a challenge for implementation of this strategy is to devise means to introduce modified bacteria into sand flies in the field. In this study, we use rodent food bait as a delivery strategy to introduce two mCherry-fluorescent bacteria, Serratia AS1 and Enterobacter cloacae, into adult sand flies in field settings. Bacteria-infected food was provided to Rhombomys opimus rodents. These bacteria transiently pass through the rodent alimentary tract and are delivered to larval habitats with the rodent feces. The feces are ingested by sand fly larvae and, in the case of Serratia AS1, are trans-stadially transmitted to adults. This is the first report of targeting delivery of Serratia AS1 in a paratransgenic system to control transmission of leishmaniasis under field condition. This novel strategy shows promise for delivering transgenic bacteria to Leishmania vectors in the field.
Multiscale relevance of natural images
Authors: Lakhal Samy , Darmon Alexandre , Mastromatteo Iacopo , Marsili Matteo , Benzaquen Michael 
Published: September 2023

AbstractWe use an agnostic information-theoretic approach to investigate the statistical properties of natural images. We introduce the Multiscale Relevance (MSR) measure to assess the robustness of images to compression at all scales. Starting in a controlled environment, we characterize the MSR of synthetic random textures as function of image roughness $$\text{ H }$$

H

and other relevant parameters. We then extend the analysis to natural images and find striking similarities with critical ($$\text {H}\approx 0$$

H
≈
0

) random textures. We show that the MSR is more robust and informative of image content than classical methods such as power spectrum analysis. Finally, we confront the MSR to classical measures for the calibration of common procedures such as color mapping and denoising. Overall, the MSR approach appears to be a good candidate for advanced image analysis and image processing, while providing a good level of physical interpretability.
Epidemiological and molecular characterization of HBV and HCV infections in HIV-1-infected inmate population in Italy: a 2017–2019 multicenter cross-sectional study
Authors: Maggiorella Maria Teresa , Sernicola L. , Picconi O. , Pizzi E. , Belli R. , Fulgenzi D. , Rovetto C. , Bruni R. , Costantino A. , Taffon S. , Chionne P. , Madonna E. , Pisani G. , Borsetti A. , Falvino C. , Ranieri R. , Baccalini R. , Pansera A. , Castelvedere F. , Babudieri S. , Madeddu G. , Starnini G. , Dell’Isola S. , Cervellini P. , Ciccaglione A. R. , Ensoli B. , Buttò S. 
Published: September 2023

AbstractHBV/HCV co-infection is common in HIV-1-infected prisoners. To investigate the characteristics of HIV co-infections, and to evaluate the molecular heterogeneity of HIV, HBV and HCV in prisoners, we carried-out a multicenter cross-sectional study, including 65 HIV-1-infected inmates enrolled in 5 Italian detention centers during the period 2017–2019. HIV-1 subtyping showed that 77.1% of inmates were infected with B subtype and 22.9% with non-B subtypes. Italian nationals were all infected with subtype B (93.1%), except two individuals, one infected with the recombinant form CRF72_BF1, and the other with the HIV-1 sub-subtype A6, both previously not identified in inmates of Italian nationality. Non-Italian nationals were infected with subtype B (52.6%), CRFs (36.8%) and sub-subtypes A1 and A3 (5.2%). HIV variants carrying resistance mutations to NRTI, NNRTI, PI and InSTI were found in 7 inmates, 4 of which were never exposed to the relevant classes of drugs associated with these mutations. HBV and/or HCV co-infections markers were found in 49/65 (75.4%) inmates, while 27/65 (41.5%) showed markers of both HBV and HCV coinfection. Further, Italian nationals showed a significant higher presence of HCV markers as compared to non-Italian nationals (p = 0.0001). Finally, HCV phylogenetic analysis performed in 18 inmates revealed the presence of HCV subtypes 1a, 3a, 4d (66.6%, 16.7% and 16.7%, respectively). Our data suggest the need to monitor HIV, HBV and HCV infections in prisons in order to prevent spreading of these viruses both in jails and in the general population, and to implement effective public health programs that limit the circulation of different genetic forms as well as of viral variants with mutations conferring resistance to treatment.
Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes
Authors: Rahman Sarthok Rasique , Lozier Jeffrey D. 
Published: September 2023

AbstractUnraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.
Inducing an LCST in hydrophilic polysaccharides via engineered macromolecular hydrophobicity
Authors: Bubli Saniya Yesmin , Smolag Matthew , Blackwell Ellen , Lin Yung-Chun , Tsavalas John G. , Li Linqing 
Published: September 2023

AbstractThermoresponsive polysaccharide-based materials with tunable transition temperatures regulating phase-separated microdomains offer substantial opportunities in tissue engineering and biomedical applications. To develop novel synthetic thermoresponsive polysaccharides, we employed versatile chemical routes to attach hydrophobic adducts to the backbone of hydrophilic dextran and gradually increased the hydrophobicity of the dextran chains to engineer phase separation. Conjugating methacrylate moieties to the dextran backbone yielded a continuous increase in macromolecular hydrophobicity that induced a reversible phase transition whose lower critical solution temperature can be modulated via variations in polysaccharide concentration, molecular weight, degree of methacrylation, ionic strength, surfactant, urea and Hofmeister salts. The phase separation is driven by increased hydrophobic interactions of methacrylate residues, where the addition of surfactant and urea disassociates hydrophobic interactions and eliminates phase transition. Morphological characterization of phase-separated dextran solutions via scanning electron and flow imaging microscopy revealed the formation of microdomains upon phase transition. These novel thermoresponsive dextrans exhibited promising cytocompatibility in cell culture where the phase transition exerted negligible effects on the attachment, spreading and proliferation of human dermal fibroblasts. Leveraging the conjugated methacrylate groups, we employed photo-initiated radical polymerization to generate phase-separated hydrogels with distinct microdomains. Our bottom-up approach to engineering macromolecular hydrophobicity of conventional hydrophilic, non-phase separating dextrans to induce robust phase transition and generate thermoresponsive phase-separated biomaterials will find applications in mechanobiology, tissue repair and regenerative medicine.
Consistency of spectral results in cardiac dual-source photon-counting CT
Authors: Liu Leening P. , Shapira Nadav , Sahbaee Pooyan , Gang Grace J. , Knollman Friedrich D. , Chen Marcus Y. , Litt Harold I. , Noël Peter B. 
Published: September 2023

AbstractWe evaluate stability of spectral results at different heart rates, acquisition modes, and cardiac phases in first-generation clinical dual-source photon-counting CT (PCCT). A cardiac motion simulator with a coronary stenosis mimicking a 50% eccentric calcium plaque was scanned at five different heart rates (0, 60–100 bpm) with the three available cardiac scan modes (high pitch prospectively ECG-triggered spiral, prospectively ECG-triggered axial, retrospectively ECG-gated spiral). Subsequently, full width half max (FWHM) of the stenosis, Dice score (DSC) for the stenosed region, and eccentricity of the non-stenosed region were calculated for virtual monoenergetic images (VMI) at 50, 70, and 150 keV and iodine density maps at both diastole and systole. FWHM averaged differences of − 0.20, − 0.28, and − 0.15 mm relative to static FWHM at VMI 150 keV across acquisition parameters for high pitch prospectively ECG-triggered spiral, prospectively ECG-triggered axial, and retrospectively ECG-gated spiral scans, respectively. Additionally, there was no effect of heart rate and acquisition mode on FWHM at diastole (p-values < 0.001). DSC demonstrated similarity among parameters with standard deviations of 0.08, 0.09, 0.11, and 0.08 for VMI 50, 70, and 150 keV, and iodine density maps, respectively, with insignificant differences at diastole (p-values < 0.01). Similarly, eccentricity illustrated small differences across heart rate and acquisition mode for each spectral result. Consistency of spectral results at different heart rates and acquisition modes for different cardiac phase demonstrates the added benefit of spectral results from PCCT to dual-source CT to further increase confidence in quantification and advance cardiovascular diagnostics.
In vitro hyperspectral biomarkers of human chondrosarcoma cells in nanoparticle-mediated radiosensitization using carbon ions
Authors: Tudor Mihaela , Popescu Roxana Cristina , Negoita Raluca D. , Gilbert Antoine , Ilisanu Mihaela A. , Temelie Mihaela , Dinischiotu Anca , Chevalier François , Mihailescu Mona , Savu Diana Iulia 
Published: September 2023

AbstractNew therapeutic approaches are needed for the management of the highly chemo- and radioresistant chondrosarcoma (CHS). In this work, we used polyethylene glycol-encapsulated iron oxide nanoparticles for the intracellular delivery of the chemotherapeutic doxorubicin (IONPDOX) to augment the cytotoxic effects of carbon ions in comparison to photon radiation therapy. The in vitro biological effects were investigated in SW1353 chondrosarcoma cells focusing on the following parameters: cell survival using clonogenic test, detection of micronuclei (MN) by cytokinesis blocked micronucleus assay and morphology together with spectral fingerprints of nuclei using enhanced dark-field microscopy (EDFM) assembled with a hyperspectral imaging (HI) module. The combination of IONPDOX with ion carbon or photon irradiation increased the lethal effects of irradiation alone in correlation with the induction of MN. Alterations in the hyperspectral images and spectral profiles of nuclei reflected the CHS cell biological modifications following the treatments, highlighting possible new spectroscopic markers of cancer therapy effects. These outcomes showed that the proposed combined treatment is promising in improving CHS radiotherapy.