bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepDOF-SE: affordable deep-learning microscopy platform for slide-free histology
Authors: Jin Lingbo , Tang Yubo , Coole Jackson B. , Tan Melody T. , Zhao Xuan , Badaoui Hawraa , Robinson Jacob T. , Williams Michelle D. , Vigneswaran Nadarajah , Gillenwater Ann M. , Richards-Kortum Rebecca R. , Veeraraghavan Ashok 
Published: April 2024

AbstractHistopathology plays a critical role in the diagnosis and surgical management of cancer. However, access to histopathology services, especially frozen section pathology during surgery, is limited in resource-constrained settings because preparing slides from resected tissue is time-consuming, labor-intensive, and requires expensive infrastructure. Here, we report a deep-learning-enabled microscope, named DeepDOF-SE, to rapidly scan intact tissue at cellular resolution without the need for physical sectioning. Three key features jointly make DeepDOF-SE practical. First, tissue specimens are stained directly with inexpensive vital fluorescent dyes and optically sectioned with ultra-violet excitation that localizes fluorescent emission to a thin surface layer. Second, a deep-learning algorithm extends the depth-of-field, allowing rapid acquisition of in-focus images from large areas of tissue even when the tissue surface is highly irregular. Finally, a semi-supervised generative adversarial network virtually stains DeepDOF-SE fluorescence images with hematoxylin-and-eosin appearance, facilitating image interpretation by pathologists without significant additional training. We developed the DeepDOF-SE platform using a data-driven approach and validated its performance by imaging surgical resections of suspected oral tumors. Our results show that DeepDOF-SE provides histological information of diagnostic importance, offering a rapid and affordable slide-free histology platform for intraoperative tumor margin assessment and in low-resource settings.
Decoding early stress signaling waves in living plants using nanosensor multiplexing
Authors: Ang Mervin Chun-Yi , Saju Jolly Madathiparambil , Porter Thomas K. , Mohaideen Sayyid , Sarangapani Sreelatha , Khong Duc Thinh , Wang Song , Cui Jianqiao , Loh Suh In , Singh Gajendra Pratap , Chua Nam-Hai , Strano Michael S. , Sarojam Rajani 
Published: April 2024

AbstractIncreased exposure to environmental stresses due to climate change have adversely affected plant growth and productivity. Upon stress, plants activate a signaling cascade, involving multiple molecules like H2O2, and plant hormones such as salicylic acid (SA) leading to resistance or stress adaptation. However, the temporal ordering and composition of the resulting cascade remains largely unknown. In this study we developed a nanosensor for SA and multiplexed it with H2O2 nanosensor for simultaneous monitoring of stress-induced H2O2 and SA signals when Brassica rapa subsp. Chinensis (Pak choi) plants were subjected to distinct stress treatments, namely light, heat, pathogen stress and mechanical wounding. Nanosensors reported distinct dynamics and temporal wave characteristics of H2O2 and SA generation for each stress. Based on these temporal insights, we have formulated a biochemical kinetic model that suggests the early H2O2 waveform encodes information specific to each stress type. These results demonstrate that sensor multiplexing can reveal stress signaling mechanisms in plants, aiding in developing climate-resilient crops and pre-symptomatic stress diagnoses.
A metasurface-based full-color circular auto-focusing Airy beam transmitter for stable high-speed underwater wireless optical communications
Authors: Hu Junhui , Guo Zeyuan , Shi Jianyang , Jiang Xiong , Chen Qinmiao , Chen Hui , He Zhixue , Song Qinghai , Xiao Shumin , Yu Shaohua , Chi Nan , Shen Chao 
Published: April 2024

AbstractDue to its unique intensity distribution, self-acceleration, and beam self-healing properties, Airy beam holds great potential for optical wireless communications in challenging channels, such as underwater environments. As a vital part of 6G wireless network, the Internet of Underwater Things requires high-stability, low-latency, and high-capacity underwater wireless optical communication (UWOC). Currently, the primary challenge of UWOC lies in the prevalent time-varying and complex channel characteristics. Conventional blue Gaussian beam-based systems face difficulties in underwater randomly perturbed links. In this work, we report a full-color circular auto-focusing Airy beams metasurface transmitter for reliable, large-capacity and long-distance UWOC links. The metasurface is designed to exhibits high polarization conversion efficiency over a wide band (440-640 nm), enabling an increased data transmission rate of 91% and reliable 4 K video transmission in wavelength division multiplexing (WDM) based UWOC data link. The successful application of this metasurface in challenging UWOC links establishes a foundation for underwater interconnection scenarios in 6G communication.
Efficient bubble/precipitate traffic enables stable seawater reduction electrocatalysis at industrial-level current densities
Authors: Liang Jie , Cai Zhengwei , Li Zixiao , Yao Yongchao , Luo Yongsong , Sun Shengjun , Zheng Dongdong , Liu Qian , Sun Xuping , Tang Bo 
Published: April 2024

AbstractSeawater electroreduction is attractive for future H2 production and intermittent energy storage, which has been hindered by aggressive Mg2+/Ca2+ precipitation at cathodes and consequent poor stability. Here we present a vital microscopic bubble/precipitate traffic system (MBPTS) by constructing honeycomb-type 3D cathodes for robust anti-precipitation seawater reduction (SR), which massively/uniformly release small-sized H2 bubbles to almost every corner of the cathode to repel Mg2+/Ca2+ precipitates without a break. Noticeably, the optimal cathode with built-in MBPTS not only enables state-of-the-art alkaline SR performance (1000-h stable operation at –1 A cm−2) but also is highly specialized in catalytically splitting natural seawater into H2 with the greatest anti-precipitation ability. Low precipitation amounts after prolonged tests under large current densities reflect genuine efficacy by our MBPTS. Additionally, a flow-type electrolyzer based on our optimal cathode stably functions at industrially-relevant 500 mA cm−2 for 150 h in natural seawater while unwaveringly sustaining near-100% H2 Faradic efficiency. Note that the estimated price (~1.8 US$/kgH2) is even cheaper than the US Department of Energy’s goal price (2 US$/kgH2).
The effect of a political crisis on performance of community forests and protected areas in Madagascar
Authors: Neugarten Rachel A. , Rasolofoson Ranaivo A. , Barrett Christopher B. , Vieilledent Ghislain , Rodewald Amanda D. 
Published: April 2024

AbstractUnderstanding the effectiveness of conservation interventions during times of political instability is important given how much of the world’s biodiversity is concentrated in politically fragile nations. Here, we investigate the effect of a political crisis on the relative performance of community managed forests versus protected areas in terms of reducing deforestation in Madagascar, a biodiversity hotspot. We use remotely sensed data and statistical matching within an event study design to isolate the effect of the crisis and post-crisis period on performance. Annual rates of deforestation accelerated at the end of the crisis and were higher in community forests than in protected areas. After controlling for differences in location and other confounding variables, we find no difference in performance during the crisis, but community-managed forests performed worse in post-crisis years. These findings suggest that, as a political crisis subsides and deforestation pressures intensify, community-based conservation may be less resilient than state protection.
Origin and dispersal history of Hepatitis B virus in Eastern Eurasia
Authors: Sun Bing , Andrades Valtueña Aida , Kocher Arthur , Gao Shizhu , Li Chunxiang , Fu Shuang , Zhang Fan , Ma Pengcheng , Yang Xuan , Qiu Yulan , Zhang Quanchao , Ma Jian , Chen Shan , Xiao Xiaoming , Damchaabadgar Sodnomjamts , Li Fajun , Kovalev Alexey , Hu Chunbai , Chen Xianglong , Wang Lixin , Li Wenying , Zhou Yawei , Zhu Hong , Krause Johannes , Herbig Alexander , Cui Yinqiu 
Published: April 2024

AbstractHepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.
Activating reversible carbonate reactions in Nasicon solid electrolyte-based Na-air battery via in-situ formed catholyte
Authors: Park Heetaek , Kang Minseok , Lee Donghun , Park Jaehyun , Kang Seok Ju , Kang Byoungwoo 
Published: April 2024

AbstractOut of practicality, ambient air rather than oxygen is preferred as a fuel in electrochemical systems, but CO2 and H2O present in air cause severe irreversible reactions, such as the formation of carbonates and hydroxides, which typically degrades performance. Herein, we report on a Na-air battery enabled by a reversible carbonate reaction (Na2CO3·xH2O, x = 0 or 1) in Nasicon solid electrolyte (Na3Zr2Si2PO12) that delivers a much higher discharge potential of 3.4 V than other metal-air batteries resulting in high energy density and achieves > 86 % energy efficiency at 0.1 mA cm−2 over 100 cycles. This cell design takes advantage of moisture in ambient air to form an in-situ catholyte via the deliquescent property of NaOH. As a result, not only reversible electrochemical reaction of Na2CO3·xH2O is activated but also its kinetics is facilitated. Our results demonstrate the reversible use of free ambient air as a fuel, enabled by the reversible electrochemical reaction of carbonates with a solid electrolyte.
Modulation of subthalamic beta oscillations by movement, dopamine, and deep brain stimulation in Parkinson’s disease
Authors: Mathiopoulou Varvara , Lofredi Roxanne , Feldmann Lucia K. , Habets Jeroen , Darcy Natasha , Neumann Wolf-Julian , Faust Katharina , Schneider Gerd-Helge , Kühn Andrea A. 
Published: April 2024

AbstractSubthalamic beta band activity (13–35 Hz) is known as a real-time correlate of motor symptom severity in Parkinson’s disease (PD) and is currently explored as a feedback signal for closed-loop deep brain stimulation (DBS). Here, we investigate the interaction of movement, dopaminergic medication, and deep brain stimulation on subthalamic beta activity in PD patients implanted with sensing-enabled, implantable pulse generators. We recorded subthalamic activity from seven PD patients at rest and during repetitive movements in four conditions: after withdrawal of dopaminergic medication and DBS, with medication only, with DBS only, and with simultaneous medication and DBS. Medication and DBS showed additive effects in improving motor performance. Distinct effects of each therapy were seen in subthalamic recordings, with medication primarily suppressing low beta activity (13–20 Hz) and DBS being associated with a broad decrease in beta band activity (13–35 Hz). Movement suppressed beta band activity compared to rest. This suppression was most prominent when combining medication with DBS and correlated with motor improvement within patients. We conclude that DBS and medication have distinct effects on subthalamic beta activity during both rest and movement, which might explain their additive clinical effects as well as their difference in side-effect profiles. Importantly, subthalamic beta activity significantly correlated with motor symptoms across all conditions, highlighting its validity as a feedback signal for closed-loop DBS.
An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments
Authors: Schadt Christopher , Martin Stanton , Carrell Alyssa , Fortner Allison , Hopp Dan , Jacobson Dan , Klingeman Dawn , Kristy Brandon , Phillips Jana , Piatkowski Bryan , Miller Mark A. , Smith Montana , Patil Sujay , Flynn Mark , Canon Shane , Clum Alicia , Mungall Christopher J. , Pennacchio Christa , Bowen Benjamin , Louie Katherine , Northen Trent , Eloe-Fadrosh Emiley A. , Mayes Melanie A. , Muchero Wellington , Weston David J. , Mitchell Julie , Doktycz Mitchel 
Published: April 2024

AbstractBridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.
A chromosome-level genome assembly of the spider mite Tetranychus piercei McGregor
Authors: Chen Lei , Yu Xin-Yue , Zhang Feng , Zhang Hua-Meng , Guo Li-Xue , Ren Lu , Hong Xiao-Yue , Sun Jing-Tao 
Published: April 2024

AbstractDespite the rapid advances in sequencing technology, limited genomic resources are currently available for phytophagous spider mites, which include many important agricultural pests. One of these pests is Tetranychus piercei (McGregor), a serious banana pest in East Asia exhibiting remarkable tolerance to high temperature. In this study, we assembled a high-quality genome of T. piercei using a combination of PacBio long reads and Illumina short reads sequencing. With the assistance of chromatin conformation capture technology, 99.9% of the contigs were anchored into three pseudochromosomes with a total size of 86.02 Mb. Repetitive elements, accounting for 14.16% of this genome (12.20 Mb), are predominantly composed of long-terminal repeats (30.7%). By combining evidence of ab initio prediction, transcripts, and homologous proteins, we annotated 11,881 protein-coding genes. Both the genome and proteins have high BUSCO completeness scores (>94%). This high-quality genome, along with reliable annotation, provides a valuable resource for investigating the high-temperature tolerance of this species and exploring the genomic basis that underlies the host range evolution of spider mites.
Datascape: exploring heterogeneous dataspace
Authors: Rolland Jakez , Boutin Ronan , Eveillard Damien , Delahaye Benoit 
Published: April 2024

AbstractData science is a powerful field for gaining insights, comparing, and predicting behaviors from datasets. However, the diversity of methods and hypotheses needed to abstract a dataset exhibits a lack of genericity. Moreover, the shape of a dataset, which structures its contained information and uncertainties, is rarely considered. Inspired by state-of-the-art manifold learning and hull estimations algorithms, we propose a novel framework, the datascape, that leverages topology and graph theory to abstract heterogeneous datasets. Built upon the combination of a nearest neighbor graph, a set of convex hulls, and a metric distance that respects the shape of the data, the datascape allows exploration of the dataset’s underlying space. We show that the datascape can uncover underlying functions from simulated datasets, build predictive algorithms with performance close to state-of-the-art algorithms, and reveal insightful geodesic paths between points. It demonstrates versatility through ecological, medical, and simulated data use cases.
Comparative studies of four cumin landraces grown in Egypt
Authors: Ahmed Abeer A. , Ghoneim Marwa , Ali Mahmoud A. A. , Amer Alia , Głowacka Aleksandra , Ahmed Mohamed A. A. 
Published: April 2024

AbstractOne of the significant aromatic plants applied in food and pharma is cumin. Despite its massive trading in Egypt, there are no comprehensive reports on cumin landraces profile screening. This study aimed to investigate the variation in seeds’ physical and biochemical profiles and genetic diversity as well as assess the efficiency of seeds’ germination under salinity stress. Consequently, during the 2020/2021 growing season, four common cumin seed landraces were gathered from various agro-climatic regions: El Gharbia, El Menia, Assiut, and Qena. Results showed a significant variation in physical profile among the four seeds of landraces. In addition, Assiut had the highest percentage of essential oil at 8.04%, whilst Qena had the largest amount of cumin aldehyde, the primary essential oil component, at 25.19%. Lauric acid was found to be the predominant fatty acid (54.78 to 62.73%). According to ISSR amplification, El Menia presented a negative unique band, whereas other landraces offered a positive band. Additionally, the cumin genotypes were separated into two clusters by the dendrogram, with El Gharbia being located in an entirely separate cluster. There were two sub-clusters within the other cluster: El Menia in one and Assiut and Qena in the other. Moreover, the germination sensitivity to the diverse salinity concentrations (control, 4, 8, 12, and 16 dS/m) findings showed that landraces exhibited varying responses to increased salinity when El Gharbia and El Menia showed a moderate response at four dS/m. Whilst, Qena landraces showed supreme values among other landraces under 12 and 16 dS/m. The majority of the examined features had strong positive associations over a range of salinity levels, according to phenotypic correlation coefficient analysis. To accomplish the aims of sustainable agriculture in Egypt, it would be imperative that the potential breeding program for cumin landraces consider this screening study.
Ozone pollution contributes to the yield gap for beans in Uganda, East Africa, and is co-located with other agricultural stresses
Authors: Sharps K. , Foster J. , Vieno M. , Beck R. , Hayes F. 
Published: April 2024

AbstractAir quality negatively impacts agriculture, reducing the yield of staple food crops. While measured data on African ground-level ozone levels are scarce, experimental studies demonstrate the damaging impact of ozone on crops. Common beans (Phaseolus vulgaris), an ozone-sensitive crop, are widely grown in Uganda. Using modelled ozone flux, agricultural surveys, and a flux-effect relationship, this study estimates yield and production losses due to ozone for Ugandan beans in 2015. Analysis at this scale allows the use of localised data, and results can be presented at a sub-regional level. Soil nutrient stress, drought, flood risk, temperature and deprivation were also mapped to investigate where stresses may coincide. Average bean yield losses due to ozone were 17% and 14% (first and second growing season respectively), equating to 184 thousand tonnes production loss. However, for some sub-regions, losses were up to 27.5% and other crop stresses also coincided in these areas. This methodology could be applied widely, allowing estimates of ozone impact for countries lacking air quality and/or experimental data. As crop productivity is below its potential in many areas of the world, changing agricultural practices to mitigate against losses due to ozone could help to reduce the crop yield gap.
Leptin signalling regulates transcriptional differences in granulosa cells from genetically obese mice but not the activation of NLRP3 inflammasome
Authors: Adamowski Marek , Sharma Yashaswi , Molcan Tomasz , Wołodko Karolina , Kelsey Gavin , Galvão António M. 
Published: April 2024

AbstractObesity is associated with increased ovarian inflammation and the establishment of leptin resistance. We presently investigated the role of impaired leptin signalling on transcriptional regulation in granulosa cells (GCs) collected from genetically obese mice. Furthermore, we characterised the association between ovarian leptin signalling, the activation of the NOD-like receptor protein 3 (NLRP3) inflammasome and macrophage infiltration in obese mice. After phenotype characterisation, ovaries were collected from distinct group of animals for protein and mRNA expression analysis: (i) mice subjected to a diet-induced obesity (DIO) protocol, where one group was fed a high-fat diet (HFD) and another a standard chow diet (CD) for durations of 4 or 16 weeks; (ii) mice genetically deficient in the long isoform of the leptin receptor (ObRb; db/db); (iii) mice genetically deficient in leptin (ob/ob); and (iv) mice rendered pharmacologically hyperleptinemic (LEPT). Next, GCs from antral follicles isolated from db/db and ob/ob mice were subjected to transcriptome analysis. Transcriptional analysis revealed opposing profiles in genes associated with steroidogenesis and prostaglandin action between the genetic models, despite the similarities in body weight. Furthermore, we observed no changes in the mRNA and protein levels of NLRP3 inflammasome components in the ovaries of db/db mice or in markers of M1 and M2 macrophage infiltration. This contrasted with the downregulation of NLRP3 inflammasome components and M1 markers in ob/ob and 16-wk HFD-fed mice. We concluded that leptin signalling regulates NLRP3 inflammasome activation and the expression of M1 markers in the ovaries of obese mice in an ObRb-dependent and ObRb-independent manner. Furthermore, we found no changes in the expression of leptin signalling and NLRP3 inflammasome genes in GCs from db/db and ob/ob mice, which was associated with no effects on macrophage infiltration genes, despite the dysregulation of genes associated with steroidogenesis in homozygous obese db/db. Our results suggest that: (i) the crosstalk between leptin signalling, NLRP3 inflammasome and macrophage infiltration takes place in ovarian components other than the GC compartment; and (ii) transcriptional changes in GCs from homozygous obese ob/ob mice suggest structural rearrangement and organisation, whereas in db/db mice the impairment in steroidogenesis and secretory activity.