cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10304494
title: Dataset - Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics

description: Dataset Summary

Lysine deacetylase inhibitors (KDACis) are approved for cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), and multiple myeloma. Despite the mechanism of action(s) (MoA) remains elusive, these inhibitors lead to increasing acetylation levels of histones and other proteins, altered gene expression and cell death. To characterize the MoA of these drugs in more detail, we systematically measured dose-dependent changes in protein expression, acetylation, and phosphorylation in response to 21 clinical and pre-clinical KDACis. MV4-11 cells were treated for 6 h with 1 vehicle control and 10 increasing doses of the respective drug (from 100 pM to 30 mM). Proteins were digested with trypsin, and the resulting 11 peptide preparations corresponding to one drug dose each were encoded by stable isotopes (tandem mass tags, TMT-11plex) and combined. Acetylated peptides were subsequently enriched by immunoprecipitation and phosphopeptides by immobilized metal affinity chromatography (IMAC). PTM-carrying and unmodified peptides were analyzed separately by liquid chromatography tandem mass spectrometry (LC-MS/MS) for peptide and protein identification and quantification. Additionally, Vorinostat and Panobinostat were also recorded as time-dependent experiments at their pEC50 concentration, respectively. 

Dataset structure

Here, we provide all curve data processed with CurveCurator v0.4.0 (https://github.com/kusterlab/curve_curator). Each drug is a zip folder containing acetylome, phosphoproteome, and fullproteome data. Next to each data set is the toml parameter file used to generate the curves.txt and dashboard.html files. Time-dependent data is indicated by "td" and dose-dependent data is indicated by "dd".
DOI: 10.5281/zenodo.10304495
title: Dataset - Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics

description: Dataset Summary
Lysine deacetylase inhibitors (KDACis) are approved for cutaneous T-cell lymphoma (CTCL) and multiple myeloma. Despite the mechanism of action(s) (MoA) remains elusive, these inhibitors lead to increasing acetylation levels of histones and other proteins, altered gene expression and cell death. To characterize the MoA of these drugs in more detail, we systematically measured dose-dependent changes in protein expression, acetylation, and phosphorylation in response to 21 clinical and pre-clinical KDACis. MV4-11 cells were treated for 6 h with vehicle control and 10 increasing doses of the respective drug (from 100 pM to 30 mM). Proteins were digested with trypsin, and the resulting 11 peptide preparations corresponding to one drug dose each were encoded by stable isotopes (tandem mass tags, TMT-11plex) and combined. Acetylated peptides were subsequently enriched by immunoprecipitation and phosphopeptides by immobilized metal affinity chromatography (IMAC). PTM-carrying and unmodified peptides were analyzed separately by liquid chromatography tandem mass spectrometry (LC-MS/MS) for peptide and protein identification and quantification. Additionally, Vorinostat and Panobinostat were also recorded as time-dependent experiments at their pEC50 concentration, respectively. 
Dataset structure
Here, we provide all curve data processed with the decryptM pipeline (https://github.com/kusterlab/decryptM). Each drug is a zip folder containing acetylation, phosphorylation, and fullproteome data, as well as a combined pdf folder displaying the curves. Next to the data is the toml parameter file used to generate the curves.txt file. Time-dependent data is indicated by "td" and dose-dependent data is indicated by "dd".
DOI: 10.5063/f11v5cfn
title: Behavior, body mass, and sex: how intraspecific variation influences seed dispersal by a scatterhoarding rodent

description: 1. Intraspecific variation plays a pivotal role in shaping ecological dynamics.As the dispersal of seeds of most woody plants is mediated by animals, individual variation within the animal dispersers holds considerable implications for plant population and ecology. 2. We explored how individual traits (such as sex, body mass, and exploration levels) of yellow-necked mice (Apodemus flavicollis) impact the dispersal of common oak (Quercus robur) acorns. Over three years, we collected data on seed fate and the specific mice responsible for their dispersal.3. The relationship between individual traits and seed dispersal was not static, but influenced by yearly environmental conditions. Heavier individuals tended to carry seeds farther, yet contrary to our expectations, sex had no effect on the distance of seed dispersal. Moreover, the exploration rate showed an inconsistent association with seed consumption and dispersal distance, while it positively impacted the distance of dispersal from the nearest tree. 4. Synthesis. Our findings suggest a more nuanced role of individual traits in seed dispersal than often assumed, with noticeable annual variation significantly influencing these impacts. Consequently, it appears there is no single, universally beneficial individual type to ensure maximal benefits to plants. Rather, the traits conferring advantages in seed dispersal are dynamic, subject to change over time in response to environmental context.
DOI: 10.15468/8yh6j6
title: Prieskum drobných zemných cicavcov Chopok juh, lyžiarske stredisko

description: Teriologický (mammaliologický) výskum drobných zemných cicavcov (ďalej iba drobných cicavcov alebo mikromamálií) sme uskutočnili počas vegetačného obdobia roku 2022 (jún – september) v montánnom až alpínskom vegetačnom stupni orografického celku Nízke Tatry.
Na vzorkovanie druhových populácií (vzorkovací dizajn) a taxocenóz drobných cicavcov sme použili kvadrátovú metódu značkovania a opätovného odchytu označkovaných jedincov (CMR). Aplikovali sme nedeštruktívnu metódu odchytu živých jedincov, pri ktorej sme používali živolovné odchytávacie zariadenia (pasce) značky Sherman. Živolovné pasce sme na v teréne vytýčených pokusných kvadrátoch (PK) kládli v štvorcovej sieti 15 x 15 m, v jej priesečníkoch (chytacích bodoch) a to v počte 36 kusov na PK. Rozloha jednotlivých PK bola štandardne 0,56 ha. Pri odchytoch drobných cicavcov sme použili návnadu tvorenú zmesou koreňovej zeleniny (mrkva, petržlen a zeler), nesolených arašidov, lúpaných slnečnicových jadier a sardiniek konzervovaných v slnečnicovom oleji (zmes s preukázateľnou atraktivitou pre všetky potenciálne sa vyskytujúce potravné typy drobných cicavcov). Na zaistenie normálneho fungovania termoregulačných mechanizmov drobných cicavcov v živolovných pasciach sme tieto vystlali vrstvou buničinovej vaty. Okrem živolovných pascí sme na každý s odchytových bodov inštalovali tiež zemnú padaciu pascu bez konzervačnej tekutiny (preferované niektorými insektivornými/evertebratofágnymi drobnými cicavcami (piskorovité) alebo myšovkou horskou). Pasce boli na PK exponované kontinuálne 3 dni a 3 noci a kontrolované v 3 – 4 hodinových intervaloch. Odchytené jedince boli po determinácii druhu, pohlavia a vekovej kategórie (ad., sad., juv.) odvážené pomocou pružinovej váhy Pesola s presnosťou 0,5 g. Jedince boli pred vypustením označkované (drobné hlodavce ušnými značkami, insektivorné a evertebratofágne formy značkovacou farbou aplikovanou na srsť).
DOI: 10.15468/jatbgt
title: Bentické rozsievky, Chopok juh, lyžiarske stredisko

description: Pri odbere vzoriek bentických rozsievok sa postupovalo podľa STN 757715, ktorá špecifikuje, že odber vzoriek bentických rozsievok v tokoch sa vykonáva podľa STN EN 13946. Princíp odberu spočíva v tom, že sa na odberovom úseku nájde vhodný pevný substrát (najmä kamene, balvany) a z neho sa získava vzorka rozsievok. Základnou podmienkou vhodnosti substrátu pre odber vzorky je jeho výskyt v stabilných hydrologických podmienkach v toku počas doby minimálne 4 týždňov a dostatočné svetelné podmienky. Vzorky sa odoberajú vždy z minimálne 5 kameňov. Pokiaľ je to možné, tieto kamene sa vyberajú priamo z prúdnice. V hlbokých tokoch, kde nie je možné odobrať vzorky z prúdnice, sa vhodný substrát berie z ripálu, čo najbližšie k prúdivej zóne a nachádza sa v eufotickej zóne vodného stĺpca. Nárast sa zoškrabáva čistou kefkou do fotomisky, kefka sa po každom odbere dôkladne preperie v laboratóriu. Zoškrabaná vzorka sa prevedie do polyetylénovej vzorkovnice. Vzorka sa konzervuje chladením pri teplote 5 °C ± 3 °C a prevezie sa do laboratória, spracovanie je zahájené do 24 hodín po odbere. 
Následné spracovanie prebieha v laboratóriu. Zo vzorky je vytvorený trvalý mikroskopický preparát s využitím metódy horúceho peroxidu vodíka (podstatou metódy je vypálenie organického obsahu buniek). Následne sa v preparáte pri 1 000-násobnom zväčšení postupne determinujú prítomné taxóny rozsievok do najnižšej možnej taxonomickej úrovne a zároveň sa počítajú misky zaznamenaných taxónov. Základnou počítanou jednotkou je vždy miska (valva) rozsievky.
DOI: 10.5281/zenodo.10804895
title: Výkazy města Sedlčany 2019-2023
title: Materiály ke zpracování finanční analýzy

description: Přiložené výkazy z města Sedlčany 2019-2023 sloužily jako materiály ke zpracování finanční analýzy této obce v rámci bakalářské práce.
DOI: 10.5281/zenodo.10804894
title: Výkazy města Sedlčany 2019-2023
title: Materiály ke zpracování finanční analýzy

description: Přiložené výkazy z města Sedlčany 2019-2023 sloužily jako materiály ke zpracování finanční analýzy této obce v rámci bakalářské práce.
DOI: 10.5281/zenodo.10804643
title: Global patterns of tree wood density

description: Wood density is a fundamental property related to tree biomechanics and hydraulic function while playing a crucial role in assessing vegetation carbon stocks by linking volumetric retrieval and a mass estimate. This study provides a high-resolution map of the global distribution of tree wood density at the 0.01º (~1 km) spatial resolution, derived from four decision trees machine learning models using a global database of 28,822 tree-level wood density measurements. An ensemble of four top-performing models, combined with eight cross-validation strategies shows great consistency, providing wood density patterns with pronounced spatial heterogeneity. The global pattern shows lower wood density values in northern and northwestern Europe, Canadian forest regions, and slightly higher values in Siberia forests, western USA, and southern China. In contrast, tropical regions, especially wet tropical areas, exhibit high wood density. Climatic predictors explain 49~63% of spatial variations, followed by vegetation characteristics (25~31%) and edaphic properties (11~16%). Notably, leaf type (evergreen vs. deciduous) and leaf habit type (broadleaved vs. needleleaved) are the most dominant individual features among all selected predictive covariates. Wood density tends to be higher for angiosperm broadleaf trees compared to gymnosperm needleleaf trees, particularly for evergreen species. The distributions of wood density categorized by leaf types and leaf habit types have good agreement with the features observed in wood density measurements. This global map quantifying wood density distribution can help improve accurate predictions of forest carbon stocks, providing deeper insights into ecosystem functioning and carbon cycling such as forest vulnerability to hydraulic and thermal stresses in the context of future climate change. 

Research Funding



GlobBiomass DUE Project. Grant Number: 4000113100/14/I-NB

German Federal Ministry for Economic Affairs and Climate Action. Grant Number: 50EE1904

ESM2025

H2020 European Research Council. Grant Number: 855187

International Max Planck Research School for Biogeochemical Cycles

ESA IFBN project. Grant Number: 4000114425/15/NL/FF/gp

ESA FRM4BIOMASS. Grant Number: 4000142684/23/I-EF-bgh

Poland National Centre for Research and Development REMBIOFOR project. Grant Number: BIOSTRATEG1/267755/4/NCBR/2015
DOI: 10.5281/zenodo.10692058
title: Global patterns of tree wood density

description: Wood density is a fundamental property related to tree biomechanics and hydraulic function while playing a crucial role in assessing vegetation carbon stocks by linking volumetric retrieval and a mass estimate. This study provides a high-resolution map of the global distribution of tree wood density at the 0.01º (~1 km) spatial resolution, derived from four decision trees machine learning models using a global database of 28,822 tree-level wood density measurements. An ensemble of four top-performing models, combined with eight cross-validation strategies shows great consistency, providing wood density patterns with pronounced spatial heterogeneity. The global pattern shows lower wood density values in northern and northwestern Europe, Canadian forest regions, and slightly higher values in Siberia forests, western USA, and southern China. In contrast, tropical regions, especially wet tropical areas, exhibit high wood density. Climatic predictors explain 49~63% of spatial variations, followed by vegetation characteristics (25~31%) and edaphic properties (11~16%). Notably, leaf type (evergreen vs. deciduous) and leaf habit type (broadleaved vs. needleleaved) are the most dominant individual features among all selected predictive covariates. Wood density tends to be higher for angiosperm broadleaf trees compared to gymnosperm needleleaf trees, particularly for evergreen species. The distributions of wood density categorized by leaf types and leaf habit types have good agreement with the features observed in wood density measurements. This global map quantifying wood density distribution can help improve accurate predictions of forest carbon stocks, providing deeper insights into ecosystem functioning and carbon cycling such as forest vulnerability to hydraulic and thermal stresses in the context of future climate change. 

Research Funding



GlobBiomass DUE Project. Grant Number: 4000113100/14/I-NB

German Federal Ministry for Economic Affairs and Climate Action. Grant Number: 50EE1904

ESM2025

H2020 European Research Council. Grant Number: 855187

International Max Planck Research School for Biogeochemical Cycles

ESA IFBN project. Grant Number: 4000114425/15/NL/FF/gp

ESA FRM4BIOMASS. Grant Number: 4000142684/23/I-EF-bgh

Poland National Centre for Research and Development REMBIOFOR project. Grant Number: BIOSTRATEG1/267755/4/NCBR/2015
DOI: 10.5281/zenodo.10692059
title: Global patterns of tree wood density

description: Wood density is a fundamental property related to tree biomechanics and hydraulic function while playing a crucial role in assessing vegetation carbon stocks by linking volumetric retrieval and a mass estimate. This study provides a high-resolution map of the global distribution of tree wood density at the 0.01º (~1 km) spatial resolution, derived from four decision trees machine learning models using a global database of 28,822 tree-level wood density measurements. An ensemble of four top-performing models, combined with eight cross-validation strategies shows great consistency, providing wood density patterns with pronounced spatial heterogeneity. The global pattern shows lower wood density values in northern and northwestern Europe, Canadian forest regions, and slightly higher values in Siberia forests, western USA, and southern China. In contrast, tropical regions, especially wet tropical areas, exhibit high wood density. Climatic predictors explain 49~63% of spatial variations, followed by vegetation characteristics (25~31%) and edaphic properties (11~16%). Notably, leaf type (evergreen vs. deciduous) and leaf habit type (broadleaved vs. needleleaved) are the most dominant individual features among all selected predictive covariates. Wood density tends to be higher for angiosperm broadleaf trees compared to gymnosperm needleleaf trees, particularly for evergreen species. The distributions of wood density categorized by leaf types and leaf habit types have good agreement with the features observed in wood density measurements. This global map quantifying wood density distribution can help improve accurate predictions of forest carbon stocks, providing deeper insights into ecosystem functioning and carbon cycling such as forest vulnerability to hydraulic and thermal stresses in the context of future climate change.
DOI: 10.5281/zenodo.10803330
title: Temperature data on forest plots recorded with hourly measurements in LandKlif Project

description: Temperature data on forest plots in LandKlif project recorded with hourly measurements (EasyLOG USB, measured accurate to 0.5°C). Thermologgers were attached to the wildlife cameras within the forest. Due to battery leakage, corrosion, and programming errors, only 39 out of 56 loggers collected temperature data.

LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif).  Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.
DOI: 10.5281/zenodo.10803331
title: Temperature data on forest plots recorded with hourly measurements in LandKlif Project

description: Temperature data on forest plots in LandKlif project recorded with hourly measurements (EasyLOG USB, measured accurate to 0.5°C). Thermologgers were attached to the wildlife cameras within the forest. Due to battery leakage, corrosion, and programming errors, only 39 out of 56 loggers collected temperature data.

LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif).  Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.
DOI: 10.5281/zenodo.10803973
title: Plant diversity and indicator values within 200m radius of the Landklif plots

description: Species numbers of vascular plants as assessed in vegetation surveys inside and within 200m radius of the Landklif plots. Vegetation inside the plots was sampled between mid-May and end of July 2019 (seven subplots, 10m2 sampling area per plot). Cover values for each species were estimated following the Braun-Blanquet scale. Species pools within 200m radius around the plot were assessed between mid-May and begin of August 2020 by standardized transect walks (walking time proportional to area percentages of dominant habitat types within 200m radius, 60 minutes total walking time in each circle). The dataset contains average species numbers of the subplots, total species numbers of the plots, and total species numbers within 200m radius of the plots, as well as mean Ellenberg indicator values on plot and 200m scale.

LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif).  Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.
DOI: 10.5281/zenodo.10803974
title: Plant diversity and indicator values within 200m radius of the Landklif plots

description: Species numbers of vascular plants as assessed in vegetation surveys inside and within 200m radius of the Landklif plots. Vegetation inside the plots was sampled between mid-May and end of July 2019 (seven subplots, 10m2 sampling area per plot). Cover values for each species were estimated following the Braun-Blanquet scale. Species pools within 200m radius around the plot were assessed between mid-May and begin of August 2020 by standardized transect walks (walking time proportional to area percentages of dominant habitat types within 200m radius, 60 minutes total walking time in each circle). The dataset contains average species numbers of the subplots, total species numbers of the plots, and total species numbers within 200m radius of the plots, as well as mean Ellenberg indicator values on plot and 200m scale.

LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif).  Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.
DOI: 10.5281/zenodo.10804054
title: Local plot information observed on LandKlif plots during vegetation survey 2019

description: LandKlif local plot information observed on site during vegetation survey 2019, including vegetation height, slope, aspect, proximity to hedge / forest edge / water, intensity of use (only for meadows), and further information on plot habitat.

LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif).  Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.
DOI: 10.5281/zenodo.10804055
title: Local plot information observed on LandKlif plots during vegetation survey 2019

description: LandKlif local plot information observed on site during vegetation survey 2019, including vegetation height, slope, aspect, proximity to hedge / forest edge / water, intensity of use (only for meadows), and further information on plot habitat.

LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif).  Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.
DOI: 10.5281/zenodo.10804204
title: Cover percentages of vegetation layers within the Landklif plots

description: Cover percentages of vegetation layers within the Landklif plots, as assessed during the vegetation survey between mid-May and end of July 2019 (seven subplots, 10m2 sampling area per plot). 

LandKlif is funded by the Bavarian State Ministry of Science and the Arts within the Bavarian Climate Research Network (bayklif).  Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. LandKliF, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.