bluuebunny/crossref_metadata_2025_split huggingface dataset:
NuInsSeg: A fully annotated dataset for nuclei instance segmentation in H&E-stained histological images
Authors: Mahbod Amirreza , Polak Christine , Feldmann Katharina , Khan Rumsha , Gelles Katharina , Dorffner Georg , Woitek Ramona , Hatamikia Sepideh , Ellinger Isabella 
Published: March 2024

AbstractIn computational pathology, automatic nuclei instance segmentation plays an essential role in whole slide image analysis. While many computerized approaches have been proposed for this task, supervised deep learning (DL) methods have shown superior segmentation performances compared to classical machine learning and image processing techniques. However, these models need fully annotated datasets for training which is challenging to acquire, especially in the medical domain. In this work, we release one of the biggest fully manually annotated datasets of nuclei in Hematoxylin and Eosin (H&E)-stained histological images, called NuInsSeg. This dataset contains 665 image patches with more than 30,000 manually segmented nuclei from 31 human and mouse organs. Moreover, for the first time, we provide additional ambiguous area masks for the entire dataset. These vague areas represent the parts of the images where precise and deterministic manual annotations are impossible, even for human experts. The dataset and detailed step-by-step instructions to generate related segmentation masks are publicly available on the respective repositories.
Dataset of the suitability of major food crops in Africa under climate change
Authors: Chemura Abel , Gleixner Stephanie , Gornott Christoph 
Published: March 2024

AbstractUnderstanding the extent and adapting to the impacts of climate change in the agriculture sector in Africa requires robust data on which technical and policy decisions can be based. However, there are no publicly available comprehensive data of which crops are suitable where under current and projected climate conditions for impact assessments and targeted adaptation planning. We developed a dataset on crop suitability of 23 major food crops (eight cereals, six legumes & pulses, six root & tuber crops, and three in banana-related family) for rainfed agriculture in Africa in terms of area and produced quantity. This dataset is based on the EcoCrop model parameterized with temperature, precipitation and soil data and is available for the historical period and until mid-century. The scenarios used for future projections are SSP1:RCP2.6, SSP3:RCP7.0 and SSP5:RCP8.5. The dataset provides a quantitative assessment of the impacts of climate change on crop production potential and can enable applications and linkages of crop impact studies to other socioeconomic aspects, thereby facilitating more comprehensive understanding of climate change impacts and assessment of options for building resilience.
Conventional extraction of fucoidan from Irish brown seaweed Fucus vesiculosus followed by ultrasound-assisted depolymerization
Authors: Ummat Viruja , Sivagnanam Saravana Periaswamy , Rai Dilip K. , O’Donnell Colm , Conway Gillian E. , Heffernan Shane M. , Fitzpatrick Stephen , Lyons Henry , Curtin James , Tiwari Brijesh Kumar 
Published: March 2024

AbstractFucoidan has attracted considerable attention from scientists and pharmaceutical companies due to its antioxidant, anticoagulant, anti-inflammatory, anti-tumor, and health-enhancing properties. However, the extraction of fucoidan from seaweeds often involves the use of harsh chemicals, which necessitates the search for alternative solvents. Additionally, the high viscosity and low cell permeability of high molecular weight (Mw) fucoidan can limit its effectiveness in drug action, while lower Mw fractions exhibit increased biological activity and are also utilized as dietary supplements. The study aimed to (1) extract fucoidan from the seaweed Fucus vesiculosus (FV) using an environmentally friendly solvent and compare it with the most commonly used extraction solvent, hydrochloric acid, and (2) assess the impact of ultrasound-assisted depolymerization on reducing the molecular weight of the fucoidan extracts and examine the cytotoxic effect of different molecular weight fractions. The findings indicated that the green depolymerization solvent, in conjunction with a brief ultrasound treatment, effectively reduced the molecular weight. Moreover, a significant decrease in cell viability was observed in selected samples, indicating potential anticancer properties. As a result, ultrasound was determined to be an effective method for depolymerizing crude fucoidan from Fucus Vesiculosus seaweed.
Identifying delay in glymphatic clearance of labeled protons post-acute head trauma utilizing 3D ASL MRI (arterial spin labeling): a pilot study
Authors: Joseph Charles R. , Lim Jubin Kang , Grohol Bryce N. , Zivcevska Marija , Lencke Joshua , Rich Ethan Dean , Arrasmith Connor James , Dorman Ian Shepherd , Clark Bradley Waman , Love Kim , Ferry Ben , Rolfs Mark E. 
Published: March 2024

AbstractThis study correlated mild traumatic brain injury (mTBI) cognitive changes with ASL-MRI glymphatic clearance rates (GCRs) and recovery with GCR improvement. mTBI disrupts the blood brain barrier (BBB), reducing capillary mean transit time and GCRs. mTBI is clinically diagnosed utilizing history/examination findings with no physiologic biomarkers. 3D TGSE (turbo-gradient spin-echo) pulsed arterial spin-labeling 3T MRI with 7 long inversion times (TIs) assessed the signal clearance of labeled protons 2800–4000 ms postlabeling in bifrontal, bitemporal, and biparietal regions within 7 days of mTBI and once clinically cleared to resume activities. The Sport Concussion Assessment Tool Version 5 (SKAT5) and Brief Oculomotor/Vestibular Assessment evaluated injured athletes’ cognitive function prior to MRIs. The pilot study demonstrated significant GCRs improvement (95% CI − 0.06 to − 0.03 acute phase; to CI—recovery CI 0.0772 to − 0.0497; P < 0.001 in frontal lobes; and parietal lobes (95% CI − 0.0584 to − 0.0251 acute; CI − 0.0727 to − 0.0392 recovery; P = 0.024) in 9 mTBI athletes (8 female, 1 male). Six age/activity-matched controls (4 females, 2 males) were also compared. mTBI disrupts the BBB, reducing GCR measured using the 3D ASL MRI technique. ASL MRI is a potential noninvasive biomarker of mTBI and subsequent recovery.
Knowledge, attitudes, and associated factors towards HIV pre-exposure prophylaxis among health care providers
Authors: Mekonnen Getachew , Liknaw Tiliksew , Anley Alemayehu , Afenigus Abebe Dilie 
Published: March 2024

AbstractThe knowledge and attitudes of health care providers were limited as reviewed in many studies. Attitudes and knowledge about pre-exposure prophylaxis among healthcare providers have not been investigated in Ethiopia even though pre-exposure prophylaxis is a novel healthcare topic. The aim was to assess knowledge, attitudes, and associated factors towards pre-exposure prophylaxis among healthcare providers in Gojjam health facilities, North West Ethiopia, 2022. An institutional-based cross-sectional study was conducted from June 1–30 among 410 healthcare providers in public health facilities in the East Gojjam zone. A simple random sampling technique was used to recruit the required study participants. The statistical program EPI Data version 4.6 was used to enter the data, and statistical packages for Social science version 25 was used for analysis. Variables with a p-value less than 0.25 in the bivariable analysis were included in the multivariable logistic regression analysis. Statistical significance was determined with a p-value less than 0.05. The good knowledge and the favorable attitude of healthcare providers toward HIV pre-exposure prophylaxis were 55.7% (50.6–60.2%) and 60.2% (55.0–65.0%) respectively. male participant (AOR 1.67; 95% CI (1.01–2.55), service year ≥ 10 years (AOR 2.52; 95% CI (1.23–5.17), favorable attitudes (AOR 1.92; 95%CI (1.25–2.95), and providers good sexual behavior (AOR 1.85; 95%CI (1.21–2.82) were significantly associated with the good knowledge, and training (AOR 2.15; 95% CI (1.23–3.76), reading the guideline (AOR 1.66; 95% CI (1.02–2.70), and good knowledge (AOR 1.78; 95% CI (1.16–2.75) was significantly associated with the favorable attitudes. In general, the finding of this study shows that the knowledge and attitudes of healthcare providers were low. Since this is a new initiative their knowledge is lower than their attitudes. Male, service year 10 years, and good provider sexual behavior were factors significantly associated with good knowledge. Training, reading the guidelines, and good knowledge were factors significantly associated with a favorable attitudes. As a result, healthcare facilities intervention programs and strategies better target these factors to improve the knowledge and attitudes of healthcare providers. Preparing training programs to enhance knowledge and attitudes towards PrEP is recommended.
Interface frictional anisotropy of dilative sand
Authors: Nawaz Muhammad Naqeeb , Lee Seung-Hun , Chong Song-Hun , Ku Taeseo 
Published: March 2024

AbstractUnderstanding direction-dependent friction anisotropy is necessary to optimize interface shear resistance across soil-structure. Previous studies estimated interface frictional anisotropy quantitatively using contractive sands. However, no studies have explored how sand with a high dilative tendency around the structural surface affects the interface shear response. In this study, a series of interface direct shear tests are conducted with selected French standard sand and snakeskin-inspired surfaces under three vertical stresses (50, 100, and 200 kPa) and two shearing directions (cranial → caudal or caudal → cranial). First, the sand-sand test observes a higher dilative response, and a significant difference between the peak and residual friction angles (ϕpeak − ϕres = 8°) is obtained at even a lower initial relative density Dr = 40%. In addition, the interface test results show that (1) shearing against the scales (cranial shearing) mobilizes a larger shear resistance and produces a dilative response than shearing along the scales (caudal shearing), (2) a higher scale height or shorter scale length exhibits a higher dilative tendency and produces a higher interface friction angle, and (3) the interface anisotropy response is more pronounced during cranial shearing in all cases. Further analysis reveals that the interface friction angle and dilation angle are decreased with the scale geometry ratio (L/H). For L/H values between 16.67 and 60, the interface dilation angle varies between 9° and 4° for cranial first shearing and 3.9°–2.6° for caudal first shearing. However, the difference in dilation angle within the same shearing direction is less than 1°.
An experimental investigation and flow-system simulation about the influencing of silica–magnesium oxide nano-mixture on enhancing the rheological properties of Iraqi crude oil
Authors: Alhamd Salem Jawad , Manteghian Mehrdad , Dehaghani Amir Hossein Saeedi , Rashid Farhan Lafta 
Published: March 2024

AbstractThis study aims to investigate the effects of introducing a 50/50 mixture of silica and magnesium oxide nanoparticles (SNP + MgONP) to the viscosity of Al-Ahdab crude oil (Iraq) at varied concentrations and temperatures. It is observed that the viscosity value drops from 38.49 to 7.8 cP. The highest degree of viscosity reduction is measured to be 56.91% at the maximum temperature of 50 °C and the greatest concentration of 0.4 wt% SM4. The Bingham model can be used to classify the behavior of the crude oil before the Nano-mixture is added. The liquid behavior grew closer to Newtonian behavior once the Nano-mixture was added. Along with a rise in plastic and effective viscosity values, the yield stress value decreases as the concentration of the Nano-mixture increases. The numerical data demonstrate that when the volume proportion of nanoparticles increases, the pressure distribution decreases. Furthermore, as the nanoparticle volume fraction increases, the drag decrease would also increase. SM4 obtains a maximum drag reduction of 53.17%. It is discovered that the sample SM4 has a maximum flow rate increase of 2.408%. Because they reduce the viscosity of crude oil, nanoparticles also reduce the friction factor ratio.
Performance evaluation of automated scoring for the descriptive similarity response task
Authors: Oka Ryunosuke , Kusumi Takashi , Utsumi Akira 
Published: March 2024

AbstractWe examined whether a machine-learning-based automated scoring system can mimic the human similarity task performance. We trained a bidirectional encoder representations from transformer-model based on the semantic similarity test (SST), which presented participants with a word pair and asked them to write about how the two concepts were similar. In Experiment 1, based on the fivefold cross validation, we showed the model trained on the combination of the responses (N = 1600) and classification criteria (which is the rubric of the SST; N = 616) scored the correct labels with 83% accuracy. In Experiment 2, using the test data obtained from different participants in different timing from Experiment 1, we showed the models trained on the responses alone and the combination of responses and classification criteria scored the correct labels in 80% accuracy. In addition, human–model scoring showed inter-rater reliability of 0.63, which was almost the same as that of human–human scoring (0.67 to 0.72). These results suggest that the machine learning model can reach human-level performance in scoring the Japanese version of the SST.
A pipeline contributes to efficient identification of salivary proteins in short-headed planthopper, Epeurysa nawaii
Authors: Wang Xiao-Jing , Li Qiao , Ye Zhuang-Xin , Huang Hai-Jian 
Published: March 2024

AbstractSaliva, an oral secretion primarily originating from salivary glands (SGs), exert critical roles in the ongoing evolutionary interaction between insects and plants. However, identifying insect salivary components poses challenges due to the tiny size of insects, low secretion amounts, and the propensity for degradation after secretion. In this study, we developed a transcriptome-based approach to comprehensively analyze the salivary proteins of the short-headed planthopper, Epeurysa nawaii, a species with unique feeding habits on bamboo. A total of 165 salivary proteins were identified, with 114 secretory genes highly and specifically expressed in SGs. Consistent with most phloem-feeding insects, digestive enzymes, calcium-binding proteins, oxidoreductases, and a few previously reported salivary effectors were ubiquitously distributed in E. nawaii saliva. However, we also identified a substantial portion of salivary proteins exhibiting taxonomy specificity, including 60 E. nawaii-specific and 62 Delphacidae-specific proteins. These taxonomy-restricted proteins potentially play a role in insect adaptation to specific host plants. Our study provides an efficient pipeline for salivary protein identification and serves as a valuable resource for the functional characterization of effectors.
ERK pathway agonism for cancer therapy: evidence, insights, and a target discovery framework
Authors: Timofeev Oleg , Giron Philippe , Lawo Steffen , Pichler Martin , Noeparast Maxim 
Published: March 2024

AbstractAt least 40% of human cancers are associated with aberrant ERK pathway activity (ERKp). Inhibitors targeting various effectors within the ERKp have been developed and explored for over two decades. Conversely, a substantial body of evidence suggests that both normal human cells and, notably to a greater extent, cancer cells exhibit susceptibility to hyperactivation of ERKp. However, this vulnerability of cancer cells remains relatively unexplored. In this review, we reexamine the evidence on the selective lethality of highly elevated ERKp activity in human cancer cells of varying backgrounds. We synthesize the insights proposed for harnessing this vulnerability of ERK-associated cancers for therapeutical approaches and contextualize these insights within established pharmacological cancer-targeting models. Moreover, we compile the intriguing preclinical findings of ERK pathway agonism in diverse cancer models. Lastly, we present a conceptual framework for target discovery regarding ERKp agonism, emphasizing the utilization of mutual exclusivity among oncogenes to develop novel targeted therapies for precision oncology.
The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses
Authors: Qu Changfan , Cui Hao , Xiao Song , Dong Longlong , Lu Qianyi , Zhang Lei , Wang Peng , Xin Mengyu , Zhi Hui , Liu Chenyu , Ning Shangwei , Gao Yue 
Published: March 2024

AbstractLong non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) by cooperating with immunity genes in tumor immunization. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here we present an integrated framework that leverages network-based analyses and Bayesian network inference to identify the regulated relationships including lncRNA, ICP and immunity genes as ICP-related LncRNAs mediated Core Regulatory Circuitry Triplets (ICP-LncCRCTs) that can make robust predictions. Hub ICP-related lncRNAs such as MIR155HG and ADAMTS9-AS2 were highlighted to play central roles in immune regulation. Specific ICP-related lncRNAs could distinguish cancer subtypes. Moreover, the ICP-related lncRNAs are likely to significantly correlated with immune cell infiltration, MHC, CYT. Some ICP-LncCRCTs such as CXCL10-MIR155HG-ICOS could better predict one-, three- and five-year prognosis compared to single molecule in melanoma. We also validated that some ICP-LncCRCTs could effectively predict ICI-response using three kinds of machine learning algorithms follow five independent datasets. Specially, combining ICP-LncCRCTs with the tumor mutation burden (TMB) improves the prediction of ICI-treated melanoma patients. Altogether, this study will improve our grasp of lncRNA functions and accelerating discovery of lncRNA-based biomarkers in ICI treatment.
Directly visualizing individual polyorganophosphazenes and their single-chain complexes with proteins
Authors: Hlushko Raman , Pozharski Edwin , Prabhu Vivek M. , Andrianov Alexander K. 
Published: March 2024

AbstractPolyorganophosphazenes are water-soluble macromolecules with immunoadjuvant activity that self-assemble with proteins to enable biological functionality. Direct imaging by cryogenic electron microscopy uncovers the coil structure of those highly charged macromolecules. Here, we successfully visualize individual polymer chains within the vitrified state in the absence of additives for contrast enhancement which is attributed to the high mass contrast of the inorganic backbone. Upon assembly with proteins, multiple protein copies bind at the single polymer chain level resulting in structures reminiscent of compact spherical complexes or stiffened coils. The outcome depends on protein characteristics and cannot be deduced by commonly used characterization techniques, such as light scattering, thus revealing direct morphological insights crucial for understanding biological activity. Atomic force microscopy supports the morphology outcomes while advanced analytical techniques confirm protein-polymer binding. The chain visualization methodology provides tools for gaining insights into the processes of supramolecular assembly and mechanistic aspects of polymer-enabled vaccine delivery.
Synoptic and planetary-scale dynamics modulate Antarctic atmospheric river precipitation intensity
Authors: Baiman Rebecca , Winters Andrew C. , Pohl Benjamin , Favier Vincent , Wille Jonathan D. , Clem Kyle R. 
Published: March 2024

AbstractAlthough rare, atmospheric rivers substantially influence the interannual variability of Antarctic surface mass balance. Here we use MERRA-2 reanalysis to identify characteristics unique to atmospheric river environments by comparing (1) Analog (environments that feature high-low pressure couplets, similar to Atmospheric River environments, but no Atmospheric River), (2) Atmospheric River, and (3) Top Atmospheric River (highest precipitation) timesteps during 1980–2019 around Antarctica. We find significant differences between Atmospheric River and Analog environments including more intense and poleward-shifted mid-tropospheric geopotential height couplets as well as larger atmospheric moisture anomalies. We find similar significant enhancement in synoptic-scale dynamic drivers of Top Atmospheric Rivers compared to all Atmospheric River environments, but no significant difference in local integrated water vapor anomalies. Instead, our results highlight the importance of large-scale dynamic drivers during Top Atmospheric River timesteps, including amplified Rossby waves excited by tropical convection.
System characterization of a human-sized 3D real-time magnetic particle imaging scanner for cerebral applications
Authors: Thieben Florian , Foerger Fynn , Mohn Fabian , Hackelberg Niklas , Boberg Marija , Scheel Jan-Philipp , Möddel Martin , Graeser Matthias , Knopp Tobias 
Published: March 2024

AbstractSince the initial patent in 2001, the Magnetic Particle Imaging community has endeavored to develop a human-applicable Magnetic Particle Imaging scanner, incorporating contributions from various research fields. Here we present an improved head-sized Magnetic Particle Imaging scanner with low power consumption, operated by open-source software and characterize it with an emphasis on human safety. The focus is on the evaluation of the technical components and on phantom experiments for brain perfusion. We achieved 3D single- and multi-contrast imaging at 4 Hz frame rate. The system characterization includes sensitivity, resolution, perfusion and multi-contrast experiments as well as field measurements and sequence analysis. Images were acquired with a clinically approved tracer and within human peripheral nerve stimulation thresholds. This advanced scanner holds potential as a tomographic imager for diagnosing conditions such as ischemic stroke (different stages) or intracranial hemorrhage in environments lacking electromagnetic shielding, such as the intensive care unit.
Metabolic priming by multiple enzyme systems supports glycolysis, HIF1α stabilisation, and human cancer cell survival in early hypoxia
Authors: Grimm Fiona , Asuaje Agustín , Jain Aakriti , Silva dos Santos Mariana , Kleinjung Jens , Nunes Patrícia M , Gehrig Stefanie , Fets Louise , Darici Salihanur , MacRae James I , Anastasiou Dimitrios 
Published: March 2024

AbstractAdaptation to chronic hypoxia occurs through changes in protein expression, which are controlled by hypoxia-inducible factor 1α (HIF1α) and are necessary for cancer cell survival. However, the mechanisms that enable cancer cells to adapt in early hypoxia, before the HIF1α-mediated transcription programme is fully established, remain poorly understood. Here we show in human breast cancer cells, that within 3 h of hypoxia exposure, glycolytic flux increases in a HIF1α-independent manner but is limited by NAD+availability. Glycolytic ATP maintenance and cell survival in early hypoxia rely on reserve lactate dehydrogenase A capacity as well as the activity of glutamate-oxoglutarate transaminase 1 (GOT1), an enzyme that fuels malate dehydrogenase 1 (MDH1)-derived NAD+. In addition, GOT1 maintains low α-ketoglutarate levels, thereby limiting prolyl hydroxylase activity to promote HIF1α stabilisation in early hypoxia and enable robust HIF1α target gene expression in later hypoxia. Our findings reveal that, in normoxia, multiple enzyme systems maintain cells in a primed state ready to support increased glycolysis and HIF1α stabilisation upon oxygen limitation, until other adaptive processes that require more time are fully established.