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Kubord-fasttext - Aftonbladet 2010–2024 - lemma
No full textKubord-fasttext is a collection of fasttext models, developed within a collaboration between
KBLab and Språkbanken Text, that have
been trained on the same underlying data as Kubord 2.
The models have been trained on the token and the lemma level. The tool that has been used for the training is
Gensim, with the following parameter settings:
min_n 4, max_n 7, 20 epoker, dim 300, and lr .05.Kubord-fasttext är en samling fasttext-modeller, framtagna inom ett samarbete mellan
KB-labb och Språkbanken Text, som tränats på
samma underliggande data som Kubord 2. Modellerna är
tränade på token- och lemmanivå. Verktyget som använts vid träning är
Gensim, med följande parameterinställningar:
min_n 4, max_n 7, 20 epoker, dim 300 och lr .05
Kubord-fasttext - Göteborgsposten 2013–2024 - token
No full textKubord-fasttext is a collection of fasttext models, developed within a collaboration between
KBLab and Språkbanken Text, that have
been trained on the same underlying data as Kubord 2.
The models have been trained on the token and the lemma level. The tool that has been used for the training is
Gensim, with the following parameter settings:
min_n 4, max_n 7, 20 epoker, dim 300, and lr .05.Kubord-fasttext är en samling fasttext-modeller, framtagna inom ett samarbete mellan
KB-labb och Språkbanken Text, som tränats på
samma underliggande data som Kubord 2. Modellerna är
tränade på token- och lemmanivå. Verktyget som använts vid träning är
Gensim, med följande parameterinställningar:
min_n 4, max_n 7, 20 epoker, dim 300 och lr .05
Röding- och öringdata från ett helsjöexperiment med kompensatorisk näringstillsats i ett oligotrofierat vattenkraftsmagasin
No full textThis is a data set with length (fork lengt, mm), wet weight (g), condition (g/cm3x100) and age (+years) of Arctic charr (Salvelinus alpinus) and brown trout (Salmo trutta) from a whole lake experiment in two hydropower reservoirs in Jämtland region, Sweden. Nutrients (phosphorus and nitrogen) were added to Stor-Mjölkvattnet and upstream Burvattnet was a reference system. The study cover the years 2001-2009 and 2016, and nutrients were added to Stor-Mjölkvattnet during 8 consecutive years (2002-2009). For detailed method description, see Milbrink et al. (2025), https://doi.org/10.1080/02705060.2025.2511868Detta är ett dataset med längd (standardlängd, mm), våtvikt (g), kondition (g/cm3x100) och ålder (+år) hos röding (Salvelinus alpinus) och öring (Salmo trutta) från ett helsjöförsök i två vattenkraftsmagasin i Jämtland. Näring (fosfor och kväve) tillsattes i Stor-Mjölkvattnet och uppströms liggande Burvattnet var referenssystem. Studien omfattar åren 2001-2009 och 2016, och näringsämnen tillfördes Stor-Mjölkvattnet under 8 på varandra följande år (2002-2009). En detaljerad metodbeskrivning finns i Milbrink et al. (2025), https://doi.org/10.1080/02705060.2025.251186
Data för: "Spatial evidence for carcinoma in situ (CIS) as an entity in human papillomavirus (HPV)-associated tonsillar squamous cell carcinoma (TSCC)"
No full textHuman papillomavirus (HPV)-associated tonsillar squamous cell carcinoma (TSCC) is suggested to arise in tonsillar crypts. They also constitute a rare exception in the literature of carcinoma development, as carcinoma in situ (CIS) is not a recognized entity and dysplastic stages are not evident. Here we used spatial transcriptomics (10x Visium) on HPV-associated TSCC, cervical and HPV-independent oral cancer cases on morphological normal, dysplastic and invasive epithelium. Files included were:
- histpopathological annotations
- spatial data/images as a zip-file
- filtered_feautre_bc_matrix.h5-file per sampleHumant papillomvirus (HPV) associerade tonsillkarcinom anses ha sitt ursprung från tonsillkryptor och utgör ett undantag i cancerutvecklingsmodellerna, eftersom de inte anses företrädas av in-situförändringar. Här använder vi oss av spatialtranskriptomik (10X Visium) på HPV-associerade tonsill- cervix och HPV-oberoende orala karcinom och undersöker morfologiskt normala, dysplastiska och invasiva epitelceller. Filer som inkluderas i analysen är:
- histopatologiska annoteringar
- spatialdata/bilder i zip-format
- filtered_feautre_bc_matrix.h5 per pro
Single-cell morphological profiling reveals insights into cell death
No full textDataset description:The data Organization of files:
1) Features: features.tar.gz
- singlecell_features_CellProfiler.parquet: This file contains the single-cell profiles extracted with CellProfiler used for the analysis in this publication. Features are normalised and filtered according to Fig. 1B, C in the paper.
- singlecell_features_DeepProfiler.parquet: This file contains the single-cell profiles extracted with DeepProfiler used for the analysis in this publication. Features are normalised and filtered according to Fig. 1B, C in the paper.
- singlecell_features_DINO.parquet: This file contains the single-cell profiles extracted with DINO used for the analysis in this publication. Features are normalised and filtered according to Fig. 1B, C in the paper (number of profiles here is smaller than in the other two approaches as outlined in the paper).
- aggregate_profiles_DINO_adjusted.parquet, aggregate_profiles_CP_aggregated.parquet, aggregated_profiles_DP_adjusted.parquet: Aggregated profile parquets for the three feature extractors.
2) Metadata: metadata_celldeath_paper.csv. This file contains the metadata used in the orgiinal cell painting experiment. It contains, plate, well, site (field-of-view), compounds, moa as well used concentrations and treatment conditions.
3). Grit scores: grit_scores.tar.gz. This zipped folder contains the grit scores for the compound concentrations for all three feature extractors. This info is provided for all the compounds concentrations for which grit could be computed. One file each for CellProfiler, DeepProfiler and DINO.
4.) E-distance: edistance.tar.gz. This zipped folder contains the edistances and etest results for the compound concentrations for all three feature extractors. This info is provided for all the compounds concentrations for which they could be computed. One file each for CellProfiler, DeepProfiler, and DINO. The file names indicate the number of samples and permutations used in the permutation test.
5.) Splits: splits.tar.gz. This zipped folder contains the splits used in the supervised model training. One file for each CellProfiler, DeepProfiler, and DINO. As described in the paper, splits were performed based on the wells of plates. Each file contains moa, compound, plate, well as well as split and the fraction of cells in each well.
6.) map: map.tar.gz. This zipped folder contains map results for the compound concentrations for all three feature extractors. This info is provided for all the compounds concentrations for which they could be computed. One file each for CellProfiler, DeepProfiler, and DINO. The file names indicate the number of samples and permutations used in the permutation test.
7) Embeddings: embeddings.tar.gz contains .h5ad with anndata files of calculated single-cell embeddings for CellProfiler, DeepProfiler, and DINO features. Each anndata file contains features, metadata as well as calculated UMAP, and PCA embeddings used in the figures. Additionally contains one anndata file with the DINO apoptosis embedding used to generate Fig. 3.
8) QC: qc_df.csv, File containing quality control flags used to filter out images and calculated viability values from cell counts.
9) Classification splits: classification_splits.tar.gz contains specific datasets used in training of supervised models for DINO, CellProfiler, and DeepProfiler on both aggregated and single-cell level.
Publication:The data in this repository supports the following publication:"Single-cell morphological profiling reveals insights into programmed cell death" by Frey et al.
Abstract:Analysis at the single-cell level is a powerful approach to study biological processes and responses to perturbations. However, its application in morphological profiling with phenomics remains underexplored. Here, we use the Cell Painting assay to investigate morphological effects of 53 small molecule compounds, associated with six distinct cell death mechanisms, across six concentrations in MCF7 cells. To compare single-cell and aggregated analysis strategies, we conduct both supervised and unsupervised evaluations aimed at identifying features linked to programmed cell death. We apply an energy distance as a metric to quantify morphological perturbation strength, enabling efficient filtering. Among three tested feature extraction methods, self-supervised DINO embeddings applied to single-cell data captured high-resolution morphological patterns. Focused analyses of apoptosis-inducing compounds revealed biological heterogeneity attributable to specific molecular targets and concentration-dependent effects, which were not apparent in aggregated profiles. In contrast, multi-class classification models for the six programmed cell death mechanisms trained on single-cell features achieved F1 scores of 79.86\%, while models trained on aggregated features reached F1 scores of up to 89.97\%.
Our results highlight the advantages of single-cell data for unsupervised exploration and show that aggregated representations yield more robust and accurate performance in supervised models
Temperaturmätningar av mikro- och makroklimat samt artdata för vedlevande skalbaggar från svenska skogar
No full textFrom May until September 2020, micro- and macroclimatic temperature were measured along a 1200 km latitudinal gradient in Sweden. Microclimatic temperature was measured hourly under the bark of spruce logs, while macroclimatic temperature refers to measured air temperature 1.3 m above the ground at the same study sites. From April until September 2021, saproxylic beetles were collected at these study sites.
The data set "boreal_forest_climate_data" contains 12 columns and 88 rows.
Block: six different study sites are distributed from southern (1) to northern Sweden (6).
Plot: five study plots that contains one study site.
Block 1: Plot 11-15
Block 2: Plot 6-10
Block 3: 16-20
Block 4: 21-25
Block 5: 1-5
Block 6: 26-30
Shade: three different shade level at one plot. 1: sun-exposed, 2: intermediately shaded and 3: fully-shaded.
Mikro- and makrotemp: mean temperatures per Block, plot and shade.
CTI: community temperature index per Block, plot, and shade.
Bark: Remaining bark at every spruce log.
Diameter: Diameter of the spruce logs.
Regional climate: Average temperature measured by nearby weather stations
for every block over the period from May-September 1990-2020 in °C.
Aspect: Aspect in degrees of every plot.
Species richness: Species richness per Block, plot, and shade.
Totalab: Abundance per Block, plot, and shade.
Dataset "specieslist_xylo" contains 6 columns and 3460 rows.
Log: 15 Spruce logs distributed over different shade levels on every plot. Spruce logs 1,4,7,10 and 13 on shade level 1; spruce logs 2,5,8,11 and 14 on shade level 2 and spruce logs 3,6,9,12, and 15 on shade level 3.
Sampling_date: Date, when beetle species were collected.
Species: Name of saproxylic beetle species found in each spruce log.
Number: Number of each species found in each spruce log.
STI: Species temperature index for every beetle species.Temperaturmätningar av mikro- och makroklimat har gjorts på sex skogslokaler i Sverige längs en 1200 km lång latitudinell gradient från maj till september 2020. Mikroklimatets temperatur mättes varje timme under barken på granstockar, och makroklimatets temperatur mättes som lufttemperaturen 1,3 m ovanför marknivå på samma platser.
Från april till september 2021 samlades vedlevande skalbaggar in från granstockar på skogslokalerna.
boreal_forest_climate_data.csv innehåller temperaturdata från mätningar av mikro- och makroklimat, och specieslist_xylo.csv innehåller artdata. Filerna använder sig av semikolon som separatortecken.
Se den engelska versionen av databeskrivningen samt dokumentationsfilen readme.txt för detaljerade kolumnbeskrivningar
Kubord 2: Ordrelationer Expressen 2024
No full textKubord 2 is an updated version of Kubord and contains both token frequencies and word relations from modern newspaper texts from the The National Library of Sweden.Kubord 2 är en uppdaterad version av Kubord och innehåller utöver ordfrekvenser även ordrelationer från moderna tidningstexter från Kungliga biblioteket
Meteorological data from Skogaryd Central, Mast-1
No full textAutomatic weather station data from locations within the distributed Swedish research infrastructure SITES. Check preview or file for the specific parameters included at this location. Data has been quality controlled and cleaned from outliers and other events producing unrealistic data. Gaps have not been filled.
Skogaryd Research Catchment (2025). Meteorological data from Skogaryd Central, Mast-1, 2016-01-01–2016-12-31 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/Y_WBvABjvZiIsPGkvOg_YVT
CATSS18 - The Child and Adolescent Twin Study in Sweden (18 år)
No full textCATSS18 - The Child and Adolescent Twin Study in Sweden (18 years)
Overview CATSS
The Child and Adolescent Twin Study in Sweden (CATSS) is an ongoing longitudinal twin study that targets all twins born in Sweden since July 1, 1992. Since 2004, parents of twins have been interviewed about the children's somatic and mental health and social environment in connection with their 9th birthday (CATSS9). At ages 15 (CATSS15) and 18 (CATSS18), twins and parents complete a web questionnaire that, in addition to assessments of somatic and mental health, includes measures of personality development and psychosocial adaptation. At the age of 24 (CATSS24), only twins participate in a web survey that mainly focuses on mental health.
CATSS18:
CATSS18 started in 2011. The study includes all 18-year-old twins and their parents, regardless of their participation in CATSS9 or CATSS15. The response rate is 50% for the twin survey and 40% for the parent survey. The sample comprises both identical (monozygotic) and fraternal (dizygotic) twins, including same-sex and opposite-sex pairs. The total number of participating twins (through parent and/or twin participation) is currently 20,400 out of 35,800 invited twins (December 2024). The combined response rate is 57%. Participants who have not yet provided a DNA sample via saliva are requested to do so. The saliva sample is used for zygosity determination and genotyping. Currently, 12,700 twins have been genotyped in CATSS18 (December 2024).
The question areas in the CATSS18 surveys are listed below. For detailed information about variables, visit strdata.se.
Question areas in parent survey:
ABCL - Adult Behavior Checklist
A-TAC - Autism - Tics, ADHD and other Comorbidities inventory (only Autism-questions)
Demography
Asthma
Eating disorders
LEC - Life Events Checklist
LSC-R - Life Stressor Checklist
MDQ - Mood Disorder Questionnaire
PCR - Parent Child Relationship
PPCP - Parents' Perception of Child's Peers
PLE - Psychotic-like Experiences
Parents physical activity
Social Interventions
Spare Time Activities
Question areas in twin survey:
AUDIT - Alcohol Use Disorders Identification Test
A-TAC - Autism - Tics, ADHD and other Comorbidities inventory (only Autism-questions)
BOCS - Brief Obsessive Compulsive Scale
CES-D - Center for Epidemiologic Studies Depression Scale
CMRS- Child Mania Rating Scale
Demography
DAWBA - Development and Well-Being Assessment
DUDIT - Drug Use Disorders Identification Test
DSM-IV Criteria for Major Depressive Episode
DCQ - Dysmorphic Concerns Questionnaire
EDI-2 - Eating Disorder Inventory - 2
Friends' Behavior
HRS-I - Hoarding Rating Scale-Interview
LEC - Life Events Checklist
LHA - Life History of Aggression
LSC-R - Life Stressor Checklist- Revised
Love Relationship
MDQ - Mood Disorder Questionnaire
Nicotine Use
PCR - Parent Child Relationship
Phobias
Physical Activity
PLE - Psychotic-like Experiences
Premenstrual syndrome
Quality of Friendship
SCARED - Screen for Child Anxiety Related Emotional Disorders
SRD - Self-Reported Delinquency
Sexuality
Social Interventions
Spare Time Activities
Synesthesia
TCI - Temperament and Character Inventory
YPI - Youth Psychopathic Traits Inventory
Weight & heightCATSS18 - The Child and Adolescent Twin Study in Sweden (18 år)
Översikt CATSS
Tvillingstudien CATSS är en pågående longitudinell tvillingstudie som riktar sig till alla tvillingar födda i Sverige sedan 1 juli 1992. Sedan 2004 intervjuas tvillingföräldrar om barnens somatiska och psykiska hälsa och sociala miljö i samband med deras 9-årsdag (CATSS9). Vid 15 (CATSS15) och 18 (CATSS18) års ålder, fyller tvillingar och föräldrar i en webenkät som, förutom bedömningar av somatisk och mental hälsa, inkluderar mått på personlighetsutveckling och psykosocial anpassning. Vid 24 års ålder (CATSS24) fyller endast tvillingar i en webenkät som främst fokuserar på mental hälsa.
CATSS18:
CATSS18 startade 2011. Studien inkluderar alla 18-åriga tvillingar och deras föräldrar, oavsett om de tidigare deltagit i CATSS9 eller CATSS15. Svarsfrekvensen är 50% för tvillingarna och 40% för föräldrarna. Urvalet inkluderar enäggstvillingar samt tvåäggstvillingar av samma eller olika kön inom tvillingparet. Det totala antalet deltagande tvillingar (genom tvilling och/eller förälder) är för närvarande 20 400 av 35 800 inbjudna tvillingar (december 2024), vilket ger en kombinerad svarsfrekvens på 57%. De som inte tidigare lämnat DNA via salivprov erbjuds att göra det i samband med CATSS18. Salivprovet används för zygositetsbestämning och genotypning. Antalet genotypade tvillingar i CATSS18 är för närvarande 12 700 (december 2024).
De frågeområden som ingår i CATSS18 finns listade nedan. Detaljerad information om variabler finns på strdata.se.
Frågeområden föräldrar:
ABCL - Adult Behavior Checklist
A-TAC - Autism - Tics, ADHD and other Comorbidities inventory (endast Autism-frågorna)
Demografi
Astma
Ätstörningar
LEC - Life Events Checklist
LSC-R - Life Stressor Checklist- Revised
MDQ - Mood Disorder Questionnaire
PCR - Parent Child Relationship
PPCP - Parents' Perception of Child's Peers
PLE - Psychotic-like Experiences
Fysisk aktivitet hos föräldrar
Sociala insatser
Fritidsaktiviteter
Frågeområden tvillingar:
AUDIT - Alcohol Use Disorders Identification Test
A-TAC - Autism - Tics, ADHD and other Comorbidities inventory (endast Autism-frågor)
BOCS - Brief Obsessive Compulsive Scale
CES-D - Center for Epidemiologic Studies Depression Scale
CMRS - Child Mania Rating Scale
Demografi
DAWBA - Development and Well-Being Assessment
DUDIT - Drug Use Disorders Identification Test
DSM-IV Criteria for Major Depressive Episode
DCQ - Dysmorphic Concerns Questionnaire
EDI-2 - Eating Disorder Inventory - 2
Friends' Behavior
HRS-I - Hoarding Rating Scale-Interview
LEC - Life Events Checklist
LHA - Life History of Aggression
LSC-R - Life Stressor Checklist- Revised
Love Relationship
MDQ - Mood Disorder Questionnaire
Nikotinanvändning
PCR - Parent Child Relationship
Fobier
Premenstruellt syndrom
Fysisk aktivitet
PLE - Psychotic-like Experiences
Quality of Friendship
SCARED - Screen for Child Anxiety Related Emotional Disorders
SRD - Self-Reported Delinquency
Sexualitet
Sociala insatser
Synestesi
Fritidsaktiviteter
TCI - Temperament and Character Inventory
YPI - Youth Psychopathic Traits Inventory
Vikt och läng
Meteorological data from Mycklemossen, S-mast-2
No full textAutomatic weather station data from locations within the distributed Swedish research infrastructure SITES. Check preview or file for the specific parameters included at this location. Data has been quality controlled and cleaned from outliers and other events producing unrealistic data. Gaps have not been filled.
Skogaryd Research Catchment (2025). Meteorological data from Mycklemossen, S-mast-2, 2017 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/uIlBVIovUSnbIZGCpH5YzIW