bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sperm motility assessed by deep convolutional neural networks into WHO categories
Authors: Haugen Trine B. , Witczak Oliwia , Hicks Steven A. , Björndahl Lars , Andersen Jorunn M. , Riegler Michael A. 
Published: September 2023

AbstractSemen analysis is central in infertility investigation. Manual assessment of sperm motility according to the WHO recommendations is the golden standard, and extensive training is a requirement for accurate and reproducible results. Deep convolutional neural networks (DCNN) are especially suitable for image classification. In this study, we evaluated the performance of the DCNN ResNet-50 in predicting the proportion of sperm in the WHO motility categories. Two models were evaluated using tenfold cross-validation with 65 video recordings of wet semen preparations from an external quality assessment programme for semen analysis. The corresponding manually assessed data was obtained from several of the reference laboratories, and the mean values were used for training of the DCNN models. One model was trained to predict the three categories progressive motility, non-progressive motility, and immotile spermatozoa. Another model was used in predicting four categories, where progressive motility was differentiated into rapid and slow. The resulting average mean absolute error (MAE) was 0.05 and 0.07, and the average ZeroR baseline was 0.09 and 0.10 for the three-category and the four-category model, respectively. Manual and DCNN-predicted motility was compared by Pearson’s correlation coefficient and by difference plots. The strongest correlation between the mean manually assessed values and DCNN-predicted motility was observed for % progressively motile spermatozoa (Pearson’s r = 0.88, p < 0.001) and % immotile spermatozoa (r = 0.89, p < 0.001). For rapid progressive motility, the correlation was moderate (Pearson’s r = 0.673, p < 0.001). The median difference between manual and predicted progressive motility was 0 and 2 for immotile spermatozoa. The largest bias was observed at high and low percentages of progressive and immotile spermatozoa. The DCNN-predicted value was within the range of the interlaboratory variation of the results for most of the samples. In conclusion, DCNN models were able to predict the proportion of spermatozoa into the WHO motility categories with significantly lower error than the baseline. The best correlation between the manual and the DCNN-predicted motility values was found for the categories progressive and immotile. Of note, there was considerable variation between the mean motility values obtained for each category by the reference laboratories, especially for rapid progressive motility, which impacts the training of the DCNN models.
Development and in-vivo validation of a portable phosphorescence lifetime-based fiber-optic oxygen sensor
Authors: Witthauer Lilian , Roussakis Emmanuel , Cascales Juan Pedro , Goss Avery , Li Xiaolei , Cralley Alexis , Yoeli Dor , Moore Hunter B. , Wang Zhaohui , Wang Yong , Li Bing , Huang Christene A. , Moore Ernest E. , Evans Conor L. 
Published: September 2023

AbstractOxygenation is a crucial indicator of tissue viability and function. Oxygen tension ($$\hbox {pO}_2$$

pO
2

), i.e. the amount of molecular oxygen present in the tissue is a direct result of supply (perfusion) and consumption. Thus, measurement of $$\hbox {pO}_{{2}}$$

pO
2

is an effective method to monitor tissue viability. However, tissue oximetry sensors commonly used in clinical practice instead rely on measuring oxygen saturation ($$\hbox {StO}_2$$

StO
2

), largely due to the lack of reliable, affordable $$\hbox {pO}_2$$

pO
2

sensing solutions. To address this issue we present a proof-of-concept design and validation of a low-cost, lifetime-based oxygen sensing fiber. The sensor consists of readily-available off-the shelf components such as a microcontroller, a light-emitting diode (LED), an avalanche photodiode (APD), a temperature sensor, as well as a bright in-house developed porphyrin molecule. The device was calibrated using a benchtop setup and evaluated in three in vivo animal models. Our findings show that the new device design in combination with the bright porphyrin has the potential to be a useful and accurate tool for measuring $$\hbox {pO}_2$$

pO
2

in tissue, while also highlighting some of the limitations and challenges of oxygen measurements in this context.
Sustainable mining of natural vein graphite via acid-extraction from waste attached to rock pieces of vein banks
Authors: Medagedara Asiri D. T. , Dahanayake Poornima , Pitawala Herath Mudiyanselage T. G. A. , Karunarathne Buddika , De Silva K. Kanishka H. , Yoshimura Masamichi , Walikannage Kosala P. , Bandara Thennakoon Mudiyanselage W. J. , Rajapakse Rajapakse Mudiyanselage G. , Kumara Gamaralalage R. A. 
Published: September 2023

AbstractA procedure based on acid extraction using a mixture of conc. sulfuric and nitric acids (8:1) to recover graphite attached to rock pieces of the vein contact zones of graphite mines, is developed as a sustainable mining practice. When the extracted graphite is heated at 600 °C for 15 min, it is converted to a highly expanded form resembling worm-like structures. The unique properties of this graphite and expanded graphite are presented by characterizing using FT-IR, Raman, SEM–EDX and XRD. This expanded graphite has the oil absorption capacity of 120 g of oil per 1 g of expanded graphite, making it the material so far known to have the highest oil absorption capacity. For comparison purpose, properties of ball-milled graphite powder which was obtained from the middle of the vein is prepared and characterized. However, the ball-milled graphite does not expand upon heat-treatment at 600 °C for 15 min. The acid-extracted graphite (AEG) has lower purity than that of ball-milled graphite (BMG), but heat-treatment increases the purity of the AEG while BMG shows opposite results. The purity of AEG has increased considerably upon heat-treatment by lowering the O wt% (weight percentage) by 6.07% to half of its original value while increasing C wt% by 8.05%. On the contrary, the C wt% of BMG has decreased by 3.71% and O wt% increased by 3.84%. The increase of purity upon heat treatment of AEG is due to the removal of some carbon and sulfur impurities as their volatile oxides. The ball-milled graphite absorbs carbon dioxide from the atmosphere when heat-treated at 600 °C. As such, the ball-milled graphite powder can be used to extract carbon dioxide from the atmosphere. The crystallite size of AEG is 1.25 times larger than that of BMG and it has been increased by 8 and 2.9 times, respectively, upon heat-treatment at 600 °C for 15 min. This is a clear evidence to expanded nature of AEG compared to BMG.
Are sex and gender considered in head and neck cancer clinical studies?
Authors: Gaeta Aurora , Tagliabue Marta , D’Ecclesiis Oriana , Ghiani Lavinia , Maugeri Paolo , De Berardinis Rita , Veneri Camilla , Gaiaschi Camilla , Cacace Marina , D’Andrea Luciano , Ansarin Mohssen , Gandini Sara , Chiocca Susanna 
Published: September 2023

AbstractWe analyzed the inclusion of sex and/or gender (S/G) in Head and Neck Cancer (HNC) clinical studies, through inspecting ClinicalTrials.gov (AACT) and the mention of Human Papilloma Virus (HPV) on a specific subgroup, namely oral cavity, larynx and oropharynx. Only 5% of HNC studies mention S/G as a planned analytical variable. Proportionally more observational studies treated S/G as an analytical variable than interventional studies (10% vs 5%, P-value ≤ 0.001), 8% of studies that mentioned S/G involved more than 100 subjects while 4% less than 100 (P-value ≤ 0.001). In randomized protocols, S/G was mentioned more in studies with a planned sample of more than 100 patients and including HPV status (P-value < 0.05). Small controlled studies have lower mention of S/G as an analytical variable than uncontrolled studies (4% and 10%, respectively among studies with less than 100 subjects). Significantly greater mention of S/G as an analytical variable is observed in controlled and randomized studies with a sample size greater than 100 subjects. HPV was mentioned in only 18% of oral cavity-larynx-oropharynx studies. Interventional studies do not regularly account for S/G during HNC study design. Thus, although fundamental, in studies concerning HNC the S/G variable is often not considered. In trials published in scientific journals (P-value = 0.01) and in more recent clinical trials (P-value = 0.002), S/G is taken more into account suggesting an increasing awareness on its importance. However, the need to systematically include S/G in study design clearly emerges, to better highlight sex-related differences in disease incidence and prognosis and best imbue science and medicine with the proper biological and cultural differences.
Principles for transformative ocean governance
Authors: Lombard Amanda T. , Clifford-Holmes Jai , Goodall Victoria , Snow Bernadette , Truter Hannah , Vrancken Patrick , Jones Peter J. S. , Cochrane Kevern , Flannery Wesley , Hicks Christina , Gipperth Lena , Allison Edward H. , Diz Daniela , Peters Kimberley , Erinosho Bolanle , Levin Phillip , Holthus Paul , Szephegyi María Nube , Awad Adnan , Golo Harrison , Morgera Elisa 
Published: September 2023

AbstractWith a focus on oceans, we collaborated across ecological, social and legal disciplines to respond to the United Nations call for transformation in the ‘2030 Agenda for Sustainable Development’. We developed a set of 13 principles that strategically and critically connect transformative ocean research to transformative ocean governance (complementing the UN Decade for Ocean Science). We used a rigorous, iterative and transparent consensus-building approach to define the principles, which can interact in supporting, neutral or sometimes conflicting ways. We recommend that the principles could be applied as a comprehensive set and discuss how to learn from their interactions, particularly those that reveal hidden tensions. The principles can bring and keep together partnerships for innovative ocean action. This action must respond to the many calls to reform current ocean-use practices which are based on economic growth models that have perpetuated inequities and fuelled conflict and environmental decline.
High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries
Authors: Balarezo-Cisneros Laura N. , Timouma Soukaina , Hanak Alistair , Currin Andrew , Valle Fernando , Delneri Daniela 
Published: September 2023

AbstractKazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals including organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing long read sequencing we report a high-quality phased genome assembly for three strains of K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14 Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array and mating type locus. This high-quality reference genome provides a resource to advance our fundamental knowledge of biotechnologically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts in biotechnological processes.
Persister cell phenotypes contribute to poor patient outcomes after neoadjuvant chemotherapy in PDAC
Authors: Zhou Xu , An Jingyu , Kurilov Roma , Brors Benedikt , Hu Kai , Peccerella Teresa , Roessler Stephanie , Pfütze Katrin , Schulz Angela , Wolf Stephan , Hohmann Nicolas , Theile Dirk , Sauter Max , Burhenne Jürgen , Ei Shigenori , Heger Ulrike , Strobel Oliver , Barry Simon T. , Springfeld Christoph , Tjaden Christine , Bergmann Frank , Büchler Markus , Hackert Thilo , Fortunato Franco , Neoptolemos John P. , Bailey Peter 
Published: September 2023

AbstractNeoadjuvant chemotherapy can improve the survival of individuals with borderline and unresectable pancreatic ductal adenocarcinoma; however, heterogeneous responses to chemotherapy remain a significant clinical challenge. Here, we performed RNA sequencing (n = 97) and multiplexed immunofluorescence (n = 122) on chemo-naive and postchemotherapy (post-CTX) resected patient samples (chemoradiotherapy excluded) to define the impact of neoadjuvant chemotherapy. Transcriptome analysis combined with high-resolution mapping of whole-tissue sections identified GATA6 (classical), KRT17 (basal-like) and cytochrome P450 3A (CYP3A) coexpressing cells that were preferentially enriched in post-CTX resected samples. The persistence of GATA6hi and KRT17hi cells post-CTX was significantly associated with poor survival after mFOLFIRINOX (mFFX), but not gemcitabine (GEM), treatment. Analysis of organoid models derived from chemo-naive and post-CTX samples demonstrated that CYP3A expression is a predictor of chemotherapy response and that CYP3A-expressing drug detoxification pathways can metabolize the prodrug irinotecan, a constituent of mFFX. These findings identify CYP3A-expressing drug-tolerant cell phenotypes in residual disease that may ultimately inform adjuvant treatment selection.
The land and sea routes to 2030: a call for greater attention on all small islands in global environmental policy
Authors: Ortiz Andrea Monica D. , Jamero Ma. Laurice , Crespin Silvio Javier , Smith Ramirez Cecilia , Matias Denise Margaret S. , Reyes Jameela Joy , Pauchard Aníbal , La Viña Antonio G. M. 
Published: September 2023

AbstractIslands have unique vulnerabilities to biodiversity loss and climate change. Current Nationally Determined Contributions under the Paris Agreement are insufficient to avoid the irreversible loss of critical island ecosystems. Existing research, policies, and finance also do not sufficiently address small islands’ social-environmental challenges. For instance, the new Global Biodiversity Framework (GBF) mentions islands in the invasive species management target. This focus is important, as islands are at high risk to biological invasions; however, this is the only GBF target that mentions islands. There are threats of equal or greater urgency to small islands, including coastal hazards and overexploitation. Ecosystems such as coral reefs and mangroves are crucial for biodiversity, coastal protection, and human livelihoods, yet are unaddressed in the GBF. While research and global policy, including targeted financial flows, have a strong focus on Small Island Developing States (SIDS), the situation of other small islands has been largely overlooked. Here, through a review of policy developments and examples from islands in the Philippines and Chile, we urge that conservation and climate change policies place greater emphasis on acknowledging the diversity of small islands and their unique governance challenges, extending the focus beyond SIDS. Moving forward, global policy and research should include the recognition of small islands as metacommunities linked by interacting species and social-ecological systems to emphasize their connectivity rather than their isolation. Coalition-building and knowledge-sharing, particularly with local, Indigenous and traditional knowledge-holders from small islands, is needed to meet global goals on biodiversity and sustainable development by 2030.
Robust packet loss compensation in the cloud‐based TT&C receiver using a predictive tracking loop with RBF network identification
Authors: Fan Yimin , Liu Tian , Li Ting , Zhang Yi , Liu Liu , Liu Yang 
Published: September 2023

AbstractIn recent years, ground‐based aerospace tracking, telemetry and control (TT&C) systems have been shifting towards an IP‐based cloud TT&C network architecture to improve signal transmission efficiency and system flexibility. However, this new architecture presents new challenges for the performance of tracking loops in the cloud‐based TT&C receiver. The authors present a predictive compensation tracking loop that addresses the problem of packet loss. The loop utilises radial basis function (RBF) online network identification for robust carrier and code frequency offset tracking. To account for packet loss, the phenomenon is modelled as a Bernoulli random process, and the predictive compensation loop uses the trained RBF network to maintain the system's tracking state. When normal data are received again, the loop can track the received information well and align the frequency offset locking state. The authors compare the performance of the proposed predictive compensation tracking loop with traditional loop tracking performance using data hold strategies under different packet loss rates. The results demonstrate the effectiveness of the proposed approach in maintaining stable tracking and solving in the discontinuous reception of the loop under packet loss environments. The proposed predictive compensation tracking loop offers a practical solution for addressing packet loss, which is a common issue in real‐world applications.
Magnetite supported on different zeolites as highly efficient heterogeneous Fenton catalysts for methylene blue removal
Authors: Quynh Ho Gia , Thanh Huynh Van , Phuong Nguyen Thi Truc , Hung Lam Hoa , Dung Nguyen Van , Long Nguyen Quang 
Published: September 2023

AbstractBy using a simple but upgraded impregnation– precipitation method, this study successfully synthesized the magnetite loaded on zeolite catalysts. The catalysts were characterized by X-ray diffraction (XRD) and scanning electron microscope (SEM) methods. Moreover, the study investigated their catalysis activity by using them for the methylene blue (MB) degradation via a heterogeneous Fenton process in the presence of an oxidizing agent (H2O2). The study discovered the effects of different parameters on the MB decolorization efficiency, such as the amounts of catalyst, the initial concentration of hydrogen peroxide, pH of the solution, and the durability of the catalysts. Experimental results revealed that an almost complete degradation was achieved with an initial methylene blue concentration of 50 ppm, a solution pH of 3, a H2O2concentration of 1.95 mM, and a catalyst dosage of 0.6 gL−1within 60 minutes. Furthermore, after four to five cycles, the Fe3O4/zeolite catalysts showed high stability for Fenton degradation of MB, indicating that these catalysts might be promising choices for wastewater remediation.
Effects of sodium silicate on the growth and starch content in seeds of Mungbean (Vigna radiate L.) under salt stress
Authors: Tran Thang Thanh 
Published: September 2023

Abstract
Mungbean is known as an essential legume with high nutritional value for human beings. They are not only a source of vegetable proteins but they are also rich in vitamins and minerals. Salinity stress affects negatively mungbean growth, especially at germination and seedling stages. Thus, finding measures to limit the impact of salinity stress will have positive effects on mungbean production. The present study investigates the effectiveness of sodium silicate application (6, 12, 18, 24 mM) in alleviating the negative impact of salinity stress on seed germination and seedling growth. Physiological and biochemical changes during the growth of mungbean were analyzed. Our experiments showed that salinity stress dramatically impeded the germination of mungbean seeds. Under the salinity condition (125 mM NaCl), the germination index decreased by approximately 65 % compared to control plants. Salinity stress caused a significant decrease in leaf chlorophyll and leaf relative water content, whereas respiration rate, leaf epicuticular wax and carotenoid content increased in comparison to control plants. The application of 12 mM sodium silicate improved plant performances under salinity stress, as indicated by the increase in fruit and seed number, seed weight (72.33 mg), and starch content (0.51 g g−1) in seeds. Moreover, sodium silicate treatment induced an increase in chlorophyll a content (4.00 mg g−1), carotenoid content (2.50 mg g−1), and epicuticular wax content (3.67 µg cm−2) in the leaves of plants under salt stress. These results were scientific evidence that might help us to understand the role of Si in the improvement of the salt tolerance of mungbean.
Fabrication of cellulose-based aerogel from banana stem for thermal insulation and water treatment
Authors: Chau Quyen N D , Le Quyen T M , Huynh Ha K P , Nguyen Son T 
Published: September 2023

Abstract
Herein banana stem was used as a source of cellulose to fabricate a novel material that can be used in thermal insulation and water treatment. Characterization of the fabricated aerogels was carried out. The results expressed morphology, appearances, and thermal stability of the aerogels. The cellulose-based aerogels expressed low density (about 0.043 g/cm3), super high porosity (up to 98.11%), high compressive Young’s Modulus value (up to 365.5 kPa), ultra-low thermal conductivity (0.0362 to 0.0367 W/mK), and the oil adsorption capability up to 17.42 g/g. By applying a simple and green procedure, our banana stem aerogel could be used for further applications in material industry as those for thermal insulation and oil adsorption.
Calculating groundwater recharge using saturated-unsaturated flow modeling
Authors: Thanh Hoa Nguyen Thi , Song Giang Le 
Published: September 2023

Abstract
Groundwater in the unpressurized aquifer is divided into saturated and unsaturated zones, which are separated by the water table. Calculating the groundwater flow in the saturation zone is performed by solving the Laplace equation. Whereas the movement of groundwater in an unsaturated zone requires solving Richards’ equation. The difficulty in calculating groundwater flows is not only due to the high nonlinearity of the Richards’ equation. The problem is even more difficult because the two equations Richards and Laplace have completely different mathematical natures. In addition, in the area near the water table, the two states of saturation and unsaturation alternately change. In this paper, an algorithm for solving one-dimensional Richards’ equations by the finite volume method is introduced. The algorithm allows the calculation of the distribution of moisture in the unsaturated zone and accurate determination of the position of the water table in the interaction with the saturated zone