cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/gdhpxjpsp5.1
title: Gahlot et al. Mol Cell 2024_Part 6: Suppl Fig 2D-E (n2)

description: Raw data for the manuscript "Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH" by Gahlot et al.
Original microscopy imaging files, uncropped western blots, uncropped Coomassie gels and automated image analysis pipelines used for the quantification of microscopy data.
The set is split into 8 parts because of data size (max upload per set is 10 GB).
Part 1: Figures 1A-G and S2C
Part 2: Figure 1F-G
Part 3: Figures 2-5 and S8A-B
Part 4: Figures 6, S1 and S9A
Part 5: Figure S2
Part 6: Figure S2D-E (n2)
Part 7: Figures S3-S7
Part 8: Figures S8-S10
DOIs for other parts:
Part 1: DOI: 10.17632/6kfbpr73w6.1
Part 2: DOI: 10.17632/3fjzxbr679.1
Part 3: DOI: 10.17632/988rrt5dk8.1
Part 4: DOI: 10.17632/8bjbtwc2fp.1
Part 5: DOI: 10.17632/pvz62pdt4n.1
Part 7: DOI: 10.17632/k5grf4464j.1
Part 8: DOI: 10.17632/mhzfnvnfws.1
DOI: 10.17632/8bjbtwc2fp.1
title: Gahlot et al. Mol Cell 2024_Part 4: Figure 6, Suppl Fig 1 and 9A

description: Raw data for the manuscript "Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH" by Gahlot et al.
Original microscopy imaging files, uncropped western blots, uncropped Coomassie gels and automated image analysis pipelines used for the quantification of microscopy data.
The set is split into 8 parts because of data size (max upload per set is 10 GB).
Part 1: Figures 1A-G and S2C
Part 2: Figure 1F-G
Part 3: Figures 2-5 and S8A-B
Part 4: Figures 6, S1 and S9A
Part 5: Figure S2
Part 6: Figure S2D-E (n2)
Part 7: Figures S3-S7
Part 8: Figures S8-S10
DOIs for other parts:
Part 1: DOI: 10.17632/6kfbpr73w6.1
Part 2: DOI: 10.17632/3fjzxbr679.1
Part 3: DOI: 10.17632/988rrt5dk8.1
Part 5: DOI: 10.17632/pvz62pdt4n.1
Part 6: DOI: 10.17632/gdhpxjpsp5.1
Part 7: DOI: 10.17632/k5grf4464j.1
Part 8: DOI: 10.17632/mhzfnvnfws.1
DOI: 10.17632/y4znm8mgz3.1
title: Raw dataset Predation of Asian weaver ant on Metisa plana bagworms

description: Field observations and monitoring of the foraging-predation of Oecophylla smaragdina major workers on pupae-larvae of the invasive bagworms species Metisa plana in oil palm plantations in Malaysia. The relationship between foraging-predation behaviors with air temperature AT and relative humidity RH was examined as well. 
A large plantation comparative biological control strategy trial with trunk systemic chemical injection to monitor the monthly, yearly yield productivity of Fresh Fruit Bunches FFB, the quality of fruit by the Oil Extraction Rate OER and the monthly, yearly incomes-profit: assessment of the effectiveness between both treatment methods. 
The Biological control strategy by weaver ants BC ant was significantly much higher, hence more effective than chemical trunk injection for all the variables of the study: Monthly-yearly yield; OER and Incomes. This is the first study ever conducted using the Asian weaver ants colonies towards the control of M. plana in a critically affected-infested large oil palm plantations in Asia.
DOI: 10.17632/6dc3yb8h5c.1
title: Design Fluency is Related to Dual Task Treadmill Gait Variability in Healthy Adults

description: Evidence supporting a link between gait and cognition is accumulating. However, the relation between executive functioning and spatiotemporal gait parameters has received little attention. This is surprising since these gait variables are related to falls. The goal of the current study was to determine whether performance on measures of inhibition, reasoning, and fluency is related to variability in stride length and step width during dual task treadmill walking in a sample of healthy adults. Nineteen healthy adults averaging 40 years of age were evaluated. Results indicated that processing speed was reduced, t(18) = 6.31, p = .0001, step width increased, t(18) = -8.00, p = .0001, and stride length decreased, t(18) = 3.06, p = .007, while dual tasking, but variability in gait parameters did not significantly change, consistent with a gait/posture first approach. As hypothesized, better performance on a visual design fluency task which assesses cognitive flexibility was associated with less dual task stride length variability, r = -.62, p = .002, and step width variability, r = -.56, p = .006. The results extend previous findings with older adults walking over ground and additionally suggest that cognitive flexibility may be important for gait maintenance while dual tasking.
DOI: 10.17632/4hwv29mhcb.1
title: Gamma-butyrobetaine hydroxylase 1 confers metastatic advantage by shielding cancer cells from natural killer cell immunosurveillance

description: Primary tumors constantly shed cancer cells into the circulation, yet only a fraction of these cells manage to give rise to metastatic tumors. Success appears to depend on metabolic changes within metastatic tumor cells, but few details are known. Here we report that expression of the enzyme γ-butyrobetaine hydroxylase 1 (BBOX1) under the control of a super enhancer allows a subset of cells in various types of tumors to produce the metabolite cartinine, which inhibits the small GTPase RhoA in natural killer cells, preventing immunological synapse formation and thereby protecting the metastatic cells from destruction. Knocking down γ-butyrobetaine hydroxylase 1 in tumor cells promoted their destruction by natural killer cells in vitro and improved the efficacy of natural killer cell adoptive transfer therapy in vivo. These findings illustrate how a subpopulation of tumor cells hijacks the metabolite carnitine to evade immune surveillance in the tumor microenvironment. Targeting γ-butyrobetaine hydroxylase 1 may be a powerful anti-metastatic strategy.
DOI: 10.17632/9h9xcdz7pz.1
title: DFT data, Electronic Inductive and Resonance Effects of Substituents on Concerted Two-proton-coupled Electron Transfer between Electrogenerated Superoxide and Hydroquinone Derivatives in N,N-Dimethylformamide

description: DFT data for this study was calculated using with two hybrid functionals, the Becke three-parameter Lee–Yang–Parr (B3LYP) and the meta exchange-correlated functional (Minnesota 06, M06-2X), implemented in the Gaussian 16 Program package.
DOI: 10.17632/p4bspsn369.1
title: Spatially Resolved Transcriptomes of CD30+-transformed Mycosis Fungoides and Cutaneous Anaplastic Large-cell Lymphoma

description: Metadata and matrix
DOI: 10.17632/44kjgc4gkc.1
title: GYMNSA dataset

description: Annotated image dataset with different stages of European pear rust in orchards for UAV-based automatic symptom detection. 

The evaluation of fruit genetic resources regarding a resistance to pathogens is an essential basis for subsequent selection in fruit breeding. Both genetic analysis and phenotyping of defined traits are important tools and provide decision data in the evaluation process. However, the phenotyping of plants is often carried out "by hand" and remains the bottleneck in fruit breeding and fruit growing. The development of a digital and UAV (unmanned aerial vehicle)-based phenotyping method for the assessment of genotype-specific susceptibility or resistance against diseases in orchards would significantly increase the efficiency of plant breeding. In this framework, a workflow for drone-based monitoring of pathogens in orchards was developed using the European pear rust (Gymnosporangium sabinae) as model pathogen. We provide a dataset with expert-annotated high-resolution RGB images with pear rust symptoms. The UAV images present different pear genotypes, including varieties, wild species and progeny from breeding. The dataset contains manually labelled images with a size of 768 x 768 pixels of leaves infected with pear rust at different stages of development, labelled as class GYMNSA, as well as background images without symptoms. A total of 584 annotated images and 162 background images, organized into a training and validation set, are included in the GYMNSA dataset. This dataset can be used as a resource for researchers and developers working on drone-based plant disease monitoring systems.
DOI: 10.17632/6jxk38k96t.1
title: LINF_220013800

description: Translation initiation factor SUI1; Leishmania infantum (strain JPCM5)
DOI: 10.17632/vk8zvrm25g.1
title: LINF_220014600

description: Protein of unknown function (DUF3184); Leishmania infantum (strain JPCM5)
DOI: 10.17632/c3trp7jt3n.1
title: Comparison of Yarrowia lipolytica growth and rProt synthesis when cultured in different vessels

description: 1. Introduction
The aim of this experiment was to quantitatively describe the costs of culturing Y. lipolytica strain synthesizing a fluorescent reporter protein (rProt) in different volumes / different vessels.

2. Methodology
The Yarrowia lipolytica strain used in this experiment was JMY2810 (genotype: MATa, ura3::pTEF-RedStar2-LEU2-Zeta-URA3ex-pTEF-empty, leu2-270, xpr2-322; phenotype: ΔAEP, ΔAXP, suc+, ura+, leu+, intracellular RedStarII, Zeta platform). The YPG medium was composed as follows [g L-1]: yeast extract, 10 (BTL, Lodz, Poland); peptone 20 (BTL); glycerol, 35 (POCH). Precultures were developed in standard YPG medium. All the media were autoclaved. Technical parameters of the culturing vessels used and shaking parameters are presented in Table 1 (pdf). 
The main cultures were continued for 48 h and samples were collected at the end of the cultivation time. Precultures were developed for 18h at 28 °C in the 300mL shake flasks. The main cultures were inoculated at 5% (v/v).
Samples were analyzed for growth and fluorescence from the reporter protein (RedStar2) following dilution in 0.75% NaCl (POCH) to match a linear range of the methods. Absorbance was measured at 600 nm in transparent 96-well plates (Costar; Merck). FL was determined under at ex/em 550/595 nm in black opaque plates (Thermo Fisher Scientific). Both measurements were done using a Tecan Spark automatic plate reader (Tecan Group Ltd., Mannedorf, Switzerland). pH level at the end of cultures was determined in the supernatant using indicatory strips (POCh, Poland).
The concentration of the carbon source and the main metabolites was analyzed through HPLC, under the following conditions: Agilent Technologies 1200 series (Agilent Technologies, Santa Clara, USA), equipped with a refractive-index detector (G1362A) and a Rezex ROA-Organic Acid H+ column (Phenomenex, Torrance, USA), and 0.005 N H2SO4 as eluent at a flow rate of 0.6 [mL/min], at 40 °C. The 96-well plate cultures were pooled to obtain sufficient amounts of the supernatant. The analysis was conducted in technical duplicate.
Statistical significance of the difference in a given measure was assessed by analysis of variance (ANOVA) test, with a significance level set at p-value &lt; 0.05 (RStudio and Visual Studio Code, Microsoft), and equality of variances was checked with the Levene test. The homogenous groups were calculated using Tukey HSD post-hoc analysis (RStudio with relevant packages). The results were calculated based on 5 – 48 biological repetitions.

3. Results
The raw results from fluorescence and optical density measurements, as well as the HPLC data, are presented in the Table S1 (xlsx) excel file. 
A graphical presentation of the data processed using statistical analysis is given in the main manuscript as Figures 1 to 4.
DOI: 10.17632/gtyrsvwjbh.1
title: LINF_220012100

description: prefoldin-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/d6t83hpj8v.1
title: LINF_220015800

description: protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/zv3wjtk8cv.1
title: LINF_220015300

description: AAA+ ATPase; Leishmania infantum (strain JPCM5)
DOI: 10.17632/4xkft5g9r5.1
title: Herpesvirus reactivation and immunemodulations in ME/CFS and long COVID

description: Myalgic Encephalomyelitis/ Chronic Fatigue syndrome (ME/CFS) is a complex, debilitating, long-term illness without a diagnostic biomarker. ME/CFS patients share overlapping symptoms with long COVID patients, an observation which has strengthened the infectious origin hypothesis of ME/CFS. However, the exact sequence of events leading to disease development is largely unknown for both clinical conditions. Here we show antibody response to herpesvirus dUTPases, particularly to that of Epstein-Barr virus (EBV) and HSV-1, increased circulating fibronectin (FN1) levels in serum and depletion of natural IgM against fibronectin ((n)IgM-FN1) are common factors for both severe ME/CFS and long COVID. We provide evidence for herpesvirus dUTPases-mediated alterations in host cell cytoskeleton, mitochondrial dysfunction and OXPHOS. Our data show altered active immune complexes, immunoglobulin-mediated mitochondrial fragmentation as well as adaptive IgM production in ME/CFS patients. Our findings provide mechanistic insight into both ME/CFS and long COVID development. Finding of increased circulating FN1 and depletion of (n)IgM-FN1 as a biomarker for the severity of the disease has an immediate implication in diagnostics and development of treatment modalities.
DOI: 10.17632/5ths67sb4v
title: Peng_2024_GCA_Data

description: Research data for all figures and tables in the manuscript by Peng et al. to be published by Geochimica et Cosmochimica Acta as "ReaxFF molecular dynamics simulation study on the solubility and dissolution of water in the silica melt".
DOI: 10.17632/5ths67sb4v.1
title: Peng_2024_GCA_Data

description: Research data for all figures and tables in the manuscript by Peng et al. to be published by Geochimica et Cosmochimica Acta as "ReaxFF molecular dynamics simulation study on the solubility and dissolution of water in the silica melt".
DOI: 10.17632/7zvbswfdw7.1
title: LINF_220016900

description: CRAL/TRIO domain containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/wt8t5kxzbs.1
title: Compressible turbulent plane channel DNS database

description: The database contains detailed turbulence statistics of compressible turbulent plane channel (TPC) flow, obtained from direct numerical simulation (DNS), solving the compressible Navier-Stokes equations [1,2]. The database contains 25 flow-conditions determined by the corresponding Reynolds and Mach numbers (Retau*, MCLx), covering the range 100 &lt; Retau* &lt;1000 , 0.3&lt; MCLx &lt;2.5.

The directory corresponding to each flow-condition contains 4 subdirectories:
0_GD_global_data
1_PBs_profiles_and_budgets
2_pdfsq_single_variable_pdfs
3_pdfs2q_two_variable_joint_pdfs
each of which contains plain text (.txt.) files. Detailed comments in each file describe its contents, which are space-separated columns. All data can be directly plotted from the files using gnuplot.

Detailed description of the computations and initial physical analysis of the data can be found in [1,2] (both are open access).

[1] Gerolymos G.A, Vallet I.: J. Fluid Mech. 958 (2023) A19; doi:10.1017/jfm.2023.42
[2] Gerolymos G.A, Vallet I.: J. Fluid Mech. 978 (2024) A25; doi:10.1017/jfm.2023.1034
DOI: 10.17632/48y47rv4ym.1
title: Cell Cycle Imaging: Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis

description: The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations and multi-contact 3C, and propose that, in contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a Topoisomerase II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias Topoisomerase II activity towards decatenation. At the second stage, the loops are released, and formation of new entanglements is prevented by lower Topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed, in experiment and models, a normal interphase state cannot be acquired. 

Original microscopy images supporting this dataset are included in this repository.
DOI: 10.17632/ccd42j5jxr.1
title: Confocal Imaging: Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis

description: The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations and multi-contact 3C, and propose that, in contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a Topoisomerase II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias Topoisomerase II activity towards decatenation. At the second stage, the loops are released, and formation of new entanglements is prevented by lower Topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed, in experiment and models, a normal interphase state cannot be acquired. 

Original microscopy images supporting this dataset are included in this repository.
DOI: 10.17632/ns77shhvw7.2
title: Effects of Ozone and Biological Degradation on the Removal and Transformation of Highly Hydrophilic DOC in a Conventional Water Treatment Process

description: The application of ozone followed by biological active filters (BAFs) for treating high dissolved organic carbon (DOC) waters has shown limited efficacy in DOC removal and controlling trihalomethanes (THMs). The following effects of ozone on DOC characteristics were extensively studied and documented: substantial and rapid decrease in UV254 absorbance and SUVA, increase in the hydrophilic (HPI) DOC content, and transformation of high MW compounds such as biopolymers (BP) and humic substances (HS) into low MW and building blocks (LMWs&BB). All these changes imposed by ozone could increase DOC biodegradability since HPI, low SUVA, and low MW compounds have been reported to be more biodegradable. While the effects of ozone on DOC characteristics have been extensively studied, these investigations often focused on source waters rather than coagulated/softened water.
Coagulated/softened water exhibits different chemical characteristics than source water, such as lower UV254 absorbance, lower hydrophobicity (HPO), and higher content of low MW DOC components. Given the prevalence of HPI DOC fractions in coagulated/softened water and the comparable THMFP of HPI and HPO DOC fractions in Manitoba, it is imperative to evaluate the impact of ozone treatment on the chemical characteristics and biodegradability of such water and to determine the required ozone dose for improved water quality in the following biological degradation process.
Therefore, we first examined the removal and transformation of total DOC (tDOC) and its HPI fraction through full-scale coagulation/softening, ozonation, and BAFs. Second, we investigated the effect of different ozone doses on the characteristics of tDOC and HPI fractions. Our results revealed that the HPI fractions after coagulation/softening had a higher percentage of low MW compounds (&lt; 1 kDa) and higher STHMFP than the raw HPI, indicating these treatment units induced distinct changes in characteristics of DOC fractions. Increasing the ozone dose from 0.4 to 1 mg O3/mg-C on highly-hydrophilic coagulated/softened water (HPI=73%) made all the DOC to be HPI, increased the DOC biodegradability from 5 to 27%, and reduced the STHMFP from 69.4 to 11.2 µg/mg-C. However, the 28-day biological degradation offset the impact of 1 mg O3/mg-C and increased the STHMFP to 60 ± 7 µg/mg-C, which was due to the formation of low-MW compounds.
DOI: 10.17632/t4kwhr99vw.1
title: Texture Imaging: Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis

description: The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations and multi-contact 3C, and propose that, in contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a Topoisomerase II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias Topoisomerase II activity towards decatenation. At the second stage, the loops are released, and formation of new entanglements is prevented by lower Topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed, in experiment and models, a normal interphase state cannot be acquired. 

Original microscopy images supporting this dataset are included in this repository.
DOI: 10.17632/k7twggfsdm.1
title: SWCNT Nanotrusses

description: Data accompanying the research paper: Čanađija, M., Košmerl, V., Zlatić, M., Vrtovšnik, D., Munjas, N.: A computational framework for nanotrusses: input convex neural networks approach, European Journal of Mechanics - A/Solids (2023)

Trained neural networks for true-stress vs. true strain uniaxial tension/compression curves and diameter vs. true strain for 818 different single-walled carbon nanotubes at 300 K. Datasets obtained by molecular dynamics (MD) are also enclosed. Results used in the second example in the above paper, obtained by MD are provided.
In the case you find this dataset useful, please cite the above paper. Full bibliographic data can be found at the DOI link:
https://doi.org/10.1016/j.euromechsol.2023.105195
DOI: 10.17632/y4znm8mgz3.2
title: Raw dataset Predation of Asian weaver ant on Metisa plana bagworms

description: Field observations and monitoring of the foraging-predation of Oecophylla smaragdina major workers on pupae-larvae of the invasive bagworms species Metisa plana in oil palm plantations in Malaysia. The relationship between foraging-predation behaviors with air temperature AT and relative humidity RH was examined as well. 
A large plantation comparative biological control strategy trial with trunk systemic chemical injection to monitor the monthly, yearly yield productivity of Fresh Fruit Bunches FFB, the quality of fruit by the Oil Extraction Rate OER and the monthly, yearly incomes-profit: assessment of the effectiveness between both treatment methods. 
The Biological control strategy by weaver ants BC ant was significantly much higher, hence more effective than chemical trunk injection for all the variables of the study: Monthly-yearly yield; OER and Incomes. This is the first study ever conducted using the Asian weaver ants colonies towards the control of M. plana in a critically affected-infested large oil palm plantations in Asia.
DOI: 10.17632/x8stnrtfrj.2
title: Salidroside project

description: The project tested primarily the influence of salidroside on cytochrome P450 metabolic activities and a possible mechanism of induced changes. The rats were treated with salidroside at the doses from 5 to 45 mg/kg/day for 7 consecutive days. The liver microsomes were isolated and tested for P450 metabolic activities with specific substrates. In vitro inhibition studies with human liver microsomes and naive rat liver microsomes were also performed.
DOI: 10.17632/zt2s3ynftd.1
title: LDHU3_03.0110

description: Leucine-rich repeat (LRR) domain-containing protein; Leishmania donovani (HU3 strain)