cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48370/ofd/hh53gf
title: Apodemus flavicollis - 35367, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1964-05-08, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/och2t0
title: Apodemus flavicollis - 10800, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-07-15, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/au7dnm
title: Apodemus flavicollis - 140247, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1981-10-01, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/vhguep
title: Apodemus flavicollis - 30803, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1962-10-21, in: Białowieża National Park, Poland. Material type:
DOI: 10.25982/65526.69/1755438
title: Substrate-explicit Modeling Tutorial

description: This tutorial Narrative demonstrates how to apply thermodynamic theory, also known as lambda theory, to convert molecular formulas of compounds (derived from FTICR-MS peaks using Formulatiry and R codes) into stoichiometric and kinetic forms of biogeochemical reactions and how to use the resulting kinetic equations to simulate dynamic conversion of compounds in batch and continuous stirred tank reactors. It will address under what conditions respiration rates are driven by thermodynamics, and how respiration rates respond to the variations in parameters and input variables and how to interpret the results.
DOI: 10.48370/ofd/aho0pu
title: Apodemus flavicollis - 40013, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1964-09-01, in: Białowieża National Park, Poland. Material type:
DOI: 10.6073/pasta/cc17b24a88c32eee8c9132f9a19c82c3
title: Particulate organic carbon and nitrogen measurements at selected depths in the water column from CalCOFI-CCE Augmented cruises in the California Current System, 2004 - July 2020.

description: Water column bottle samples at multiple depths are taken during CalCOFI cruises (since 2004, ongoing) at various CTD stations, filtered, and stored at -20°C. Measurements of particulate organic carbon (POC) and nitrogen (PON) are performed onshore in the lab where samples are acidified, dried and analyzed by high-temperature combustion. The sample and tin capsule react with oxygen and combust at 1000°C, and the sample is broken down, thus converting organic carbon to CO2 and reducing nitrogen oxides to N2 gas. Both gases are measured by thermal conductivity. Samples analyzed within the CCE constrain the mean C:N ratio of small particulates and by difference relative to measured living biomass, the biomass of suspended detritus.
DOI: 10.48370/ofd/7cnkdw
title: Apodemus flavicollis - 1480, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1953-06-09, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/vdxwhh
title: Apodemus flavicollis - 160695, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1990-10-02, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/vprbbn
title: Apodemus flavicollis - 10653, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-07-13, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/pov0zl
title: Apodemus flavicollis - 152960, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1986-07-15, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/zrppnk
title: Apodemus flavicollis - 153800, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1986-10-29, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/lplqys
title: Apodemus flavicollis - 72090, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1968-03-17, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/3dk8pd
title: Apodemus flavicollis - 137766, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1980-10-03, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/k5iypd
title: Apodemus flavicollis - 66625, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1967-11-15, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/tfbrzc
title: Apodemus flavicollis - 152784, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1986-07-04, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/j1ndlb
title: Apodemus flavicollis - 134298, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1979-10-24, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/h6sja2
title: Apodemus flavicollis - 152893, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1986-07-12, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/vduauz
title: Apodemus flavicollis - 152824, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1986-07-08, in: Białowieża National Park, Poland. Material type:
DOI: 10.25982/67335.259/1773074
title: Case Study: Can you find Delftia?

description: Delftia is a genus of bacteria with a bunch of cool features! The best studied species, Delftia acidovorans can produce gold nanoparticles from gold ions in solution. This bacteria has been found living in biofolms with Cupriavidis metallidurans on gold nuggets. It is also found in soil, in sinks and in rhizospheres of different plants where it promotes their growth.Delftia acidovorans forms gold nuggets by producing a short nonribosomal peptide called delftibactin. The 16 genes responsible for the production of delftibactin are called the del cluster (delA-delP). These genes were originally discovered in Delftia acidovorans SPH-1, but our research shows that the del cluster appears to be present across the genus.We'll start with a number of raw reads, clean them up and do a little taxonomy to figure out what we might be able to assemble. Next, we'll assemble the reads using 4 different methods and pick out the best assembly. Then we'll take those reads and sort them by genome and assess the quality of those genomes. We'll select the high quality genomes to annotate and insert into phylogenetic trees to find relatives.
DOI: 10.48370/ofd/mastan
title: Apodemus flavicollis - 1304, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1953-06-05, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/ag1v69
title: Apodemus flavicollis - 45411, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1965-08-14, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/1tpuqz
title: Apodemus flavicollis - 118837, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1976-05-30, in: Białowieża National Park, Poland. Material type:
DOI: 10.25982/73221.117/1777993
title: Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium

description: This narrative was used for the 3-member community modeling using R2A medium for the bacteria isolated from Populus deltoides (PD). 10 bacteiral strains isolated from PD were co-cultured as a synthetic microbial community in R2A complex medium. After 15 passages, there were 3 members survived in R2A medium.The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using R2A medium. The FBA modeling was performed and the metabolites exchange among community members was proposed.The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.​1016/​j.​csbj.​2021.​03.​034
DOI: 10.48370/ofd/xfvkph
title: Apodemus flavicollis - 99203, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1971-09-19, in: Białowieża National Park, Poland. Material type:
DOI: 10.25982/73218.75/1777998
title: Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium

description: This narrative was used for the 4-member community modeling using MOPS medium for the bacteria isolated from Populus deltoides (PD). 10 bacterial strains isolated from PD were co-cultured as a synthetic microbial community in MOPS minimal medium. After 15 passages there were 4 members survived in MOPS medium.The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using MOPS medium. The FBA modeling was performed and the metabolites exchange among community members was proposed.The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.​1016/​j.​csbj.​2021.​03.​034
DOI: 10.48370/ofd/binj33
title: Apodemus flavicollis - 12163, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-08-05, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/bbvibs
title: Apodemus flavicollis - 125715, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1977-10-04, in: Białowieża National Park, Poland. Material type:
DOI: 10.25982/69990.6/1778232
title: Leisingera sp. ANG59 & Pseudoalteromonas sp. JC28 Genomes Overview

description: The Hawaiian bobtail squid, Euprymna scolopes, has a symbiotic bacterial consortium in the accessory nidamental gland (ANG), a female reproductive organ that protects eggs against fouling microorganisms. To test the antibacterial activity of ANG community members, 19 bacterial isolates were screened for their ability to inhibit Gram-negative and Gram-positive bacteria, of which two strains were inhibitory. These two antibacterial isolates, Leisingera sp. ANG59 and Pseudoalteromonas sp. JC28, were subjected to further genomic characterization. Genomic analysis of Leisingera sp. ANG59 revealed a biosynthetic gene cluster encoding the antimicrobial compound indigoidine. The genome of Pseudoalteromonas sp. JC28 had a 14-gene cluster with &gt;95% amino acid identity to a known bromoalterochromide (BAC) cluster. Chemical analysis confirmed production of known BACs, BAC-A/A′ (compounds 1a/1b), as well as two new derivatives, BAC-D/D′ (compounds 2a/2b). Extensive nuclear magnetic resonance (NMR) analyses allowed complete structural elucidation of compounds 2a/2b, and the absolute stereochemistry was unambiguously determined using an optimized Marfey’s method. The BACs were then investigated for in vitro antibacterial, antifungal, and nitric oxide (NO) inhibitory activity. Compounds 1a/1b were active against the marine bacteria Bacillus algicola and Vibrio fischeri, while compounds 2a/2b were active only against B. algicola. Compounds 1a/1b inhibited NO production via lipopolysaccharide (LPS)-induced inflammation in RAW264.7 macrophage cells and also inhibited the pathogenic fungus Fusarium keratoplasticum, which, coupled with their antibacterial activity, suggests that these polyketide-nonribosomal peptides may be used for squid egg defense against potential pathogens and/or fouling microorganisms. These results indicate that BACs may provide Pseudoalteromonas sp. JC28 an ecological niche, facilitating competition against nonsymbiotic microorganisms in the host’s environment.​
DOI: 10.48370/ofd/xq47jk
title: Apodemus flavicollis - 120630, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1976-10-05, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/zfnvn8
title: Apodemus flavicollis - 160807, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1990-10-14, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/oorzgo
title: Apodemus flavicollis - 104635, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1972-05-10, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/fkepoe
title: Apodemus flavicollis - 162758, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1993-07-13, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/6z2sfv
title: Apodemus flavicollis - 81203, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1968-09-19, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/fky21k
title: Apodemus flavicollis - 87333, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1969-09-21, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/wr99gy
title: Apodemus flavicollis - 107807, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1972-10-16, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/esylcp
title: Apodemus flavicollis - 15521, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-11-05, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/ycvdg4
title: Apodemus flavicollis - 44522, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1965-07-04, in: Białowieża National Park, Poland. Material type:
DOI: 10.25982/90997.49/1783189
title: Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform

description: Over the past year, biology educators and staff at the Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free and easily accessible data science platform that integrates many bioinformatics resources into a graphical user interface built upon reproducible analysis notebooks. KBase held conversations with college and high school instructors to understand how KBase could potentially support their educational goals. These conversations morphed into a working group of biological and data science instructors that adapted the KBase platform to their curriculum needs, specifically around concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. The KBase Educators Working Group developed modular, adaptable, and customizable instructional units. Each instructional module contains teaching resources, publicly available data, analysis tools, and markdown capability to tailor instructions and learning goals for each class. The online user interface enables students to conduct hands-on data science research and analyses without requiring programming skills or their own computational resources (these are provided by KBase). Alongside these resources, KBase continues to work with instructors, supporting the development of additional curriculum modules. For anyone new to the platform, KBase, and the growing KBase Educators Organization, provides a community network, accompanied by community-sourced guidelines, instructional templates, and peer support to use KBase within a classroom whether virtual or in-person.
DOI: 10.48370/ofd/rvhdq8
title: Apodemus flavicollis - 81561, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1968-10-02, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/lrvl4s
title: Apodemus flavicollis - 66089, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1967-10-09, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/oznyvt
title: Apodemus flavicollis - 45562, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1965-09-02, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/w3ngat
title: Apodemus flavicollis - 25316, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1961-07-25, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/a7t9z8
title: Apodemus flavicollis - 66093, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1967-10-09, in: Białowieża National Park, Poland. Material type:
DOI: 10.25982/58799.728/1798340
title: Osur_paper

description: Glyphosate is widely used as a herbicide, but recent studies begin to reveal its detrimental side effects on animals by targeting the shikimate pathway of associated gut microorganisms. However, its impact on nutritional endosymbionts in insects remains poorly understood. Here, we sequenced the tiny, shikimate pathway encoding symbiont genome of the sawtoothed grain beetle Oryzaephilus surinamensis. Decreased titers of the aromatic amino acid tyrosine in symbiont-depleted beetles underscore the symbionts’ ability to synthesize prephenate as the precursor for host tyrosine synthesis and its importance for cuticle sclerotization and melanization. Glyphosate exposure inhibited symbiont establishment during host development and abolished the mutualistic benefit on cuticle synthesis in adults, which could be partially rescued by dietary tyrosine supplementation. Furthermore, phylogenetic analyses indicate that the shikimate pathways of many nutritional endosymbionts likewise contain a glyphosate sensitive 5-enolpyruvylshikimate-3-phosphate synthase. These findings highlight the importance of symbiont-mediated tyrosine supplementation for cuticle biosynthesis in insects, but also paint an alarming scenario regarding the use of glyphosate in light of recent declines in insect populations.
DOI: 10.48370/ofd/zspzrj
title: Apodemus flavicollis - 24302, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1961-04-17, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/hfpu4g
title: Apodemus flavicollis - 85556, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1969-06-02, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/cnnwgx
title: Apodemus flavicollis - 159591, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1990-07-06, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/b8ylge
title: Apodemus flavicollis - 24847, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1961-06-07, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/68bdoj
title: Apodemus flavicollis - 155873, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1987-09-23, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/zfzxqh
title: Apodemus flavicollis - 35073, Zoological collection of the Mammal Research Institute, PAS

description: Apodemus flavicollis (Yellow-necked mouse) from Zoological collection of the Mammal Research Institute, PAS. Collected 1964-04-09, in: Białowieża National Park, Poland. Material type: