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opencc-zeroMay 2024View details →

Diatom cell-size composition as a novel tool for quantitative estimates of water table in peatlands

Diatom cell-size composition is an indicator of aquatic environmental changes, but has been rarely investigated, especially in semi-terrestrial peatlands. In this study, both taxonomic composition and cell-size composition of diatoms were analyzed in 41 samples from two montane peatlands, northeastern China. Redundancy analyses revealed that diatom taxonomic composition was significantly related to the depth to the water table (DWT) and Ca2+, while cell-size composition was significantly associated with DWT and Si. DWT was the most important factor and its sole effect explained 26.2% and 17.9% of the total variance in taxonomic composition and cell-size composition, respectively. Accordingly, diatom-based water-table transfer functions were developed based on taxonomic composition and cell-size composition, respectively. The maximum likelihood (ML) model based on diatom taxonomic composition had the best performance, with the correlation coefficient value (R2) of 0.78 and the root mean squared error of prediction (RMSEP) of 6.66 cm. The ML model based on cell-size composition had similar performance, with the R2 of 0.78 and the RMSEP of 6.87cm, suggesting that diatom cell-size composition can be a new quantitative means to track past water-table changes.

Testing novel climate accounting identifies animal agriculture as the leading emissions sector

Data and spreadsheet supporting the paper "Testing novel climate accounting identifies animal agriculture as the leading emissions sector" G Wedderburn-Bisshop, 2024

opencc-by-4.0Apr 2024View details →

Novel radiocontrast agent dataset

A newly synthesised and characterized diiodine-substituted natural eudesmic acid - 2,6-DiIodo-3,4,5-TriMethoxyBenzoic Acid (DITMBA) and its water soluble sodium salt (NaDITMB) is investigated in respect to commonly applied radiocontrast media in medical practice (Omnipaque®). A phantom with the iodine solutions was scanned with Philips Juno DRF system at different imaging conditions: 46 kV, 80 kV, 95 kV and 100 kV.

opencc-zeroMay 2024View details →

Data from: Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform

The majority of cancer deaths are caused by solid tumors, where the four most prevalent cancers (breast, lung, colorectal and prostate) account for more than 60% of all cases (1). Tumor cell heterogeneity driven by variable cancer microenvironments, such as hypoxia, is a key determinant of therapeutic outcome. We developed a novel culture protocol, termed the Long-Term Hypoxia (LTHY) time course, to recapitulate the gradual development of severe hypoxia seen in vivo to mimic conditions observed in primary tumors. Cells subjected to LTHY underwent a non-canonical epithelial to mesenchymal transition (EMT) based on miRNA and mRNA signatures as well as displayed EMT-like morphological changes. Concomitant to this, we report production of a novel truncated isoform of WT1 transcription factor (tWt1), a non-canonical EMT driver, with expression driven by a yet undescribed intronic promoter through hypoxia-responsive elements (HREs). We further demonstrated that tWt1 initiates translation from an intron-derived start codon, retains proper subcellular localization and DNA binding. A similar tWt1 is also expressed in LTHY-cultured human cancer cell lines as well as primary cancers and predicts long-term patient survival. Our study not only demonstrates the importance of culture conditions that better mimic those observed in primary cancers, especially with regards to hypoxia, but also identifies a novel isoform of WT1 which correlates with poor long-term survival in ovarian cancer.

opencc-by-4.0Apr 2024View details →

SemEval-2024 Task 9: BRAINTEASER: A Novel Task Defying Common Sense

<h3>Data  for the SemEval 2024 paper "SemEval-2024 Task 9: BRAINTEASER: A Novel Task Defying Common Sense"</h3>   The data of the two subtasks is saved in the data folder, BTDATA.zip, which contains the data for the sentence puzzle and word puzzle. The data contained in BTDATA.zip are as follows: <ul> <li>Semeval Competition <ul> <li>Training Data <ul> <li><code>SP_train.npy</code> (Semeval training data)</li> <li><code>WP_train.npy</code> (Semeval training data)</li> </ul> </li> <li>Test Data <ul> <li><code>SP_test.npy</code> (Semeval test data)</li> <li><code>WP_test.npy</code> (Semeval test data)</li> <li><code>SP_test_answer.npy</code> (Semeval test data answer)</li> <li><code>WP_test_answer.npy</code> (Semeval test data answer)</li> </ul> </li> </ul> </li> </ul> <div> <h3>Relation to EMNLP 2023 Paper</h3> <a href="https://github.com/1171-jpg/BrainTeaser#2-relation-to-semeval2024-task9"></a></div> The relationship between EMNLP and SemEval involves using the same dataset but with different data splitting and utilization methods. In EMNLP, the entire dataset is employed for testing, while in SemEval, the dataset is divided into training and testing sets, with the training set comprising a significant majority. Our EMNLP paper results on GitHub are tested on the entire data in a zero-shot manner. In the SemEval2024-Task9, although the whole dataset is the same as our EMNLP paper, we allow people to train on 80% of the whole dataset, and we evaluate the system on the 20% left. <ul> <li>EMNLP Zero-Shot Experiment <ul> <li><code>sentence_puzzle.npy</code> (on all sentence puzzle data)</li> <li><code>word_puzzle.npy</code> (on all word puzzle data)</li> </ul> </li> </ul> Note: To prevent automatic data crawlers, BTDATA.zip needs a password: brainteaser

Towards Discovery: An End-to-End System for Uncovering Novel Biomedical Relations

This contains the embeddings as specified in the work: "Towards Discovery: An End-to-End System for Uncovering Novel Biomedical Relations". The embeddings are created from 4 seperate knowledge bases: <ul> <li><a href="https://ftp.expasy.org/databases/cellosaurus/" target="_blank" rel="noopener">Cellosaurus: </a>Concepts</li> <li><a href="https://ctdbase.org/downloads/" target="_blank" rel="noopener">CTD-Disease</a>: Concepts, Definitions, Synonyms</li> <li><a href="https://www.nlm.nih.gov/databases/download/mesh.html" target="_blank" rel="noopener">MeSH</a>: Concepts, Definitions, Synonyms. This includes embeddings for both the main and supplementary files, for Concepts and Definitions. </li> <li><a href="https://ftp.ncbi.nih.gov/gene/" target="_blank" rel="noopener">NCBI-Gene</a>: Concepts. Due ot the large size of the NCBI-cGene corpus we only provide the embeddings for the following top 7 organisms most prevalent in the corpus: <ul> <li>10090: house mouse </li> <li>10116: Norway Rat</li> <li>11676: human immunodeficiency virus (HIV)</li> <li>12814: Respiratory syncytial virus</li> <li>3702: thale cress</li> <li>7955: zebrafish</li> <li>9606: and human</li> </ul> </li> <li><a href="https://ftp.ncbi.nih.gov/pub/taxonomy/" target="_blank" rel="noopener">NCBI-Taxonomy</a>: Names</li> </ul> The embeddings supplied were created using the <a target="_blank" rel="noopener">SapBERT</a> model, for the knowledge bases as of March 2024. The exact files used to generate the embeddings are provided as jsonl files.

Replication package of "Higher Fault Detection Through Novel Density Estimators in Unit Test Generation"

Replication package for the paper "Higher Fault Detection Through Novel Density Estimators in Unit Test Generation" accepted at the Symposium on Search-based Software Engineering (SSBSE) 2024.

Data from: Osmia3DNest – novel designed 3D printed artificial nest for solitary cavity-nesting bees

The availability and appropriateness of nesting sites significantly influence the reproductive success and overall welfare of wild bees. Human-induced factors contribute to the destruction of natural nesting habitats. To address these limitations, innovative solutions such as the development of artificial nests, as indicated in recent studies, offer alternative nest sites to support wild bee populations. We designed the Osmia3DNest, a 3D printed standardized nest tube for solitary cavity-nesting bees, aiming to provide a safety for the environment life-long, time-saving, and biodegradable product that anyone can print. We proudly present the two Osmia3DNest models for mason bees – closed and open – using PLA filament. We demonstrate the effectiveness of Osmia3DNest on mason bee reproduction parameters compared with traditional reed nests. Osmia3DNest can be an alternative to the other artificial nests, which people can customize for their necessity depending on their place of living (rural or urban area), and they can also be washed and reused several times and then decomposed. Osmia3DNest holds potential for wildlife biologists, management of pollinators, and educational outreach, offering adaptability for different bee species and experimental needs.

Data from: Extreme mitochondrial reduction in a novel group of free-living metamonads

Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway through lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.

Urban and rural chickadee response to novel object and simulated predator

Urbanization is changing natural landscapes worldwide, pushing species to quickly acclimate or adapt if they are to survive in urban environments. Mountain chickadees (Poecile gambeli) readily nest in both urban and rural environments without suffering apparent reproductive costs. However, whether urban-nesting chickadees are successful in these environments due to differences in behaviour between urban and rural birds remains untested. We examined the behavioural responses of urban and rural nesting mountain chickadee females when presented with a novel object (red plastic cup) or simulated predator (imitation squirrel model) at the nest. Behavioural responses depended on both the type of model and the habitat. As expected, mountain chickadees responded more strongly to squirrel models than novel objects; however, the magnitude of the difference in response depended on habitat. Urban birds seemingly ignored the novel object, spending little time investigating, and re-entering the nest box quickly. In contrast, rural birds spent more time reacting to the novel object and alarm calling within 5 m of the nest. When presented with a predator model, the urban birds reacted relatively more strongly (compared to the novel stimulus) than rural birds, spending more time within 5 m of the nest and alarm calling. These results suggest that either mountain chickadees in urban environments quickly acclimatize to the presence of novel objects or, potentially, that less neophobic birds disproportionately settle in urban environments or experience positive selection in urban areas. Either way, reduced neophobia may aid in mountain chickadees' ability to readily and successfully nest in such habitats.

Novel Activation Modulating Sites in a GPCR Identified with a Large-Scale Alchemical Mutation Scan

This dataset contains the starting configurations and mdp files for the alchemical free energy calculations using pmx. The MD parameter files (*.mdp) for the forward reaction (lambda 0 to 1, wt to mutant) and reverse reaction (lambda 1 to 0, mutant to wt) start with f (forward) and r (reverse). Mdp files are available for the energy minimization (em), npt (npt), equilibrium run (equilibrium) and non equilibrium alchemical transition (nonequilibrium).  The starting configurations for mutants of the DRD2 receptor can be found in WT7jvr and WT6cm4 for the active and inactive state respectively. Mutant folders are labeled with the residue number and the amino acid it is mutated to.

To Trust or Not to Trust: Towards a novel approach to measure trust for XAI systems

Experimental data from unpublished work To Trust or Not to Trust: Towards a novel approach to measure trust for XAI systems

Diagnosis of tuberculosis infection in children with a novel skin test and the traditional tuberculin skin test: an observational study

Codebook of a minimal data set that can be accessed through the MF-DAC of the Universtiy Basel, Switzerland.

opencc-by-4.0Nov 2023View details →

Reevaluating the Little Ice Age: Novel insights from oceanic and terrestrial records on unexpected warm winters

Open the record for dataset details and reuse information.

A Novel Surface Energy Balance Method for Thermal Inertia Studies of Terrestrial Analogs

Thermophysical data collected from Woodhouse Mesa, AZ, USA in May 2021 and Sept 2022

opencc-by-4.0Dec 2023View details →

Figure 8 in Microbial diversity of ticks and a novel typhus group Rickettsia species (Rickettsiales bacterium Ac37b) in Inner Mongolia, China

Figure 8. The composition of bacteria and pathogenic bacteria with a high abundance.

Positive correlation between Ammospiza caudacuta (Saltmarsh Sparrow) capture and productivity supports use of a novel rapid assessment monitoring protocol

Salt marshes in the northeastern United States provide critical breeding habitat for tidal marsh specialist birds like the Saltmarsh Sparrow (Ammospiza caudacuta). The Saltmarsh Sparrow population has declined by nine percent annually, necessitating immediate conservation actions for this vulnerable species. However, estimating species vital rates across a large geographic region is logistically challenging and cost prohibitive. Therefore, we developed and tested a rapid assessment monitoring protocol focused on reproductive metrics to enhance future conservation planning. We used three years of intensive demographic data from 12 sites to estimate daily nest survival, nest period success, fledglings produced per female, and successful broods per female. We implemented the rapid assessment protocol co-located at intensive sites in the same years to estimate the number of captured females and juveniles. We used Pearson's correlation analyses to determine the association of intensive metrics with rapid metrics. We found that the sum of Saltmarsh Sparrow female and juvenile captures was positively correlated with daily nest survival, nest period success, fledglings produced per female, and successful broods per female. Our results demonstrate that fixed-effort mist-netting from our rapid assessment protocol is an informative and time-efficient sampling method that can aid in making informed management decisions related to Saltmarsh Sparrow conservation.

A novel ChlF-free leaf spectra dataset and the PROSPECT-DP model code

A novel ChlF-free leaf spectra dataset (n = 849, species = 95) collected at three sites in Beijing, China during June and August 2023. Directional-directional reflectance and transmittance spectra with or without ChlF contributions were simultaneously measured using an ASD FieldSpec 3 spectrometer coupled with an FluoWat leaf clip. PROSPECT-DP, a coupled leaf optical properties model, in which a principal component analysis approach was applied on the training dataset to derive the spectral vectors for leaf spectra reconstruction, while the coefficients of spectral vectors were determined by leveraging the simulated leaf spectra derived from the PROSPECT-D model.

opencc-by-4.0May 2023View details →

Novel stereological method for estimation of cell counts in 3D collagen scaffolds

Dataset provides all images used for cell number evaluation. The used macros are the part of Supplementary of the article.

Reorganisation of circadian activity and the pacemaker circuit under novel light regimes

Many environmental features are cyclic, with predictable changes across the day, seasons and latitudes. Additionally, anthropogenic, artificial light-induced changes in photoperiod or shiftwork-driven novel light/dark cycles also occur. Endogenous timekeepers or circadian clocks help organisms cope with such changes. The remarkable plasticity of clocks is evident in the waveforms of behavioural and molecular rhythms they govern. Despite detailed mechanistic insights into the functioning of the circadian clock, practical means to manipulate activity waveform are lacking. Previous studies using a nocturnal rodent model showed that novel light regimes caused locomotor activity to bifurcate such that mice showed two bouts of activity restricted to the dimly lit phases. Here, we explore the generalizability of these findings and leverage the genetic toolkit of Drosophila melanogaster to obtain mechanistic insights into this unique phenomenon. We find that dim scotopic illumination of specific durations induces circadian photoreceptor CRYPTOCHROME-dependent activity bifurcation in male flies. We show circadian re-organisation of the pacemaker circuit wherein the 'evening' neurons regulate the timing of both bouts of activity under novel light regimes. Our findings indicate that environmental regimes can be exploited to design light regimes to ease the circadian waveform into synchronising with challenging conditions.