cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fbg79cnxw
title: The preservation of cause and effect in the rock record

description: Evolutionary events may impact the geological carbon cycle via transient
 imbalances in silicate weathering, and such events have been implicated as
 causes of glaciations, mass extinctions, and oceanic anoxia. However,
 suggested evolutionary causes often substantially predate the
 environmental effects to which they are linked—problematic when carbon
 cycle perturbations must be resolved in less than a million years. What is
 more, the geochemical signatures of such perturbations are recorded as
 they occur in widely distributed marine sedimentary rocks that have been
 densely sampled for important intervals in Earth history, whereas the
 fossil record—particularly on land—is governed by the availability of
 sedimentary basins that are patchy in both space and time, necessitating
 lags between the origination of an evolutionary lineage and its earliest
 occurrence in the fossil record. Here, we present a simple model of the
 impact of preservational filtering on sampling to show that an
 evolutionary event that causes an environmental perturbation via
 weathering imbalance should not appear earlier in the rock record than the
 perturbation itself and, if anything, should appear later rather than
 simultaneously. The Devonian Hangenberg glaciation provides an example of
 how evolutionary events might be more fruitfully considered as potential
 causes of environmental perturbations. Just as the last samplings of
 species lost in mass extinction are expected to come before the true
 environmental event, first appearance should be expected to post-date the
 geological expression of a lineage’s environmental impact with important
 implications for our reading of Earth history.
DOI: 10.5061/dryad.rfj6q57ds
title: Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose

description: Copy-number and point mutations form the basis for most evolutionary
 novelty through the process of gene duplication and divergence. While a
 plethora of genomic sequence data reveals the long-term fate of diverging
 coding sequences and their cis-regulatory elements, little is
 known about the early dynamics around the duplication event itself. In
 microorganisms, selection for increased gene expression often drives the
 expansion of gene copy-number mutations, which serves as a crude
 adaptation, prior to divergence through refining point mutations. Using a
 simple synthetic genetic system that allows us to distinguish copy-number
 and point mutations, we study their early and transient adaptive dynamics
 in real-time in Escherichia coli. We find two qualitatively
 different routes of adaptation depending on the level of functional
 improvement selected for: In conditions of high gene expression demand,
 the two types of mutations occur as a combination. Under low gene
 expression demand, negative epistasis between the two types of mutations
 renders them mutually exclusive. Thus, owing to their higher frequency,
 adaptation is dominated by copy-number mutations. Ultimately, due to high
 rates of reversal and pleiotropic cost, copy-number mutations may not only
 serve as a crude and transient adaptation but also
 constrain sequence divergence over evolutionary time scales.
description: 1. Flow cytometry data of E.coli populations evolved in galactose
 for 12 days. Data: EE24.4/8/12 (evolution
 experiment 24, day 4/8/12) plates 1-3 (delta IS1C - medium C,B,A) + plates
 7-10 (IT030 - medium C, B, A; controll plate medium E)
 Evolution in galactose (A-1%, B-0.1%, C-0.01%, E - 0%) + 0.1%
 CASAMINOACIDS. FlowJo used to export data as scale
 values into new folder with naming scheme: "ScaleVal_EE24_12C30"
 (evolution experiment 24_day12 populations_0.01%galactose_strain
 IT030) Autogating was used in flow jo to gate the a
 single concise population of cells (by eye, same within plate, and similar
 (~60%) for all different plates). 2.
 amplicon deep sequencing data of <em>E</em>.
 <em>coli</em> populations evolving in galactose.
 Contains random P0 sequences of all evolving pooled
 populations and R script to generate the plots shown in the figures
 (Readme)
description: R script that accesses data and plots all of it; Figure plots are
 indicated in the script.
DOI: 10.15468/dl.b53xjy
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Mongolia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Festuca valesiaca"
 ]
}

 The dataset includes 67 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003207-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pnvx0k6r6
title: Developmental conditions influence adulthood resistance to infection

description: Nutrition is a central factor influencing immunity and resistance
 to infection, but the extent to which nutrition during
 development affects adult responses to infections is poorly
 understood. Our study investigated how the nutritional
 composition of the larval diet affects the survival, pathogen
 load and food intake of adult fruit flies, Bactrocera tryoni,
 after septic bacterial infection. We found a sex-specific effect of larval
 diet composition on survival post-infection: survival rate was higher and
 bacterial load was lower for infected females raised on a
 sugar-rich larval diet than for females raised on a protein-rich
 larval diet, an effect that was absent in males. Both males and
 females were heavier when fed a balanced larval diet
 compared with a protein- or sugar-rich diet, while body lipid
 reserves were higher for those that had consumed the sugar-rich
 larval diet compared with other diets. Body protein reserves were
 lower for flies that had been raised on the sugar-rich larval
 diet compared with other diets in males, but not females. Both
 females and males shifted their nutrient intake to ingest a
 sugar-rich diet when infected compared with shaminfected flies
 without any effect of the larval diet, suggesting that sugar-rich
 diets can be beneficial to fight off bacterial infection as shown
 in previous literature. Overall, our findings show that
 nutrition during early life can shape individual fitness in
 adulthood.
DOI: 10.5061/dryad.7sqv9s4vv
title: Above- and below-ground net primary productivity: a field-based global database of grasslands

description: Net primary productivity (NPP) over global grasslands is crucial for
 understanding the terrestrial carbon cycling and for the assessments of
 wild herbivores food security. During the past few decades, numerous field
 investigations have been conducted to estimate grassland NPP since the
 measuring criterion released by the International Biological Program.
 However, a comprehensive NPP database, particularly for belowground NPP
 (BNPP), in global grasslands is rare to date. Here, field NPP measurements
 from 438 publications (1957–2018) in global grasslands were collected,
 critically filtered, and incorporated in a comprehensive global database
 with observations for aboveground NPP (ANPP), BNPP, total NPP (TNPP), and
 BNPP fraction (fBNPP). Associated information on geographical locations,
 climatic records, grassland types, land use patterns, manipulations
 subjected to manipulative experiments, sampling year of study sites as
 well as NPP measurement methods are also documented. This database
 included 2985 entries from 1785 study sites. Among them, 806 entries
 contained paired data of ANPP and BNPP, resulting in the 806 fBNPP data.
 The study sites encompassed global grasslands with latitudinal range of
 54.5° S~78.9° N, longitudinal range of 157.4° W~175.8° E, and altitudes
 from 0 to 5168 m above sea level, covering broad climatic gradients (-17.6
 to 28.8 °C in mean annual temperature and 63 to 2052 mm in mean annual
 precipitation). This global database is the world’s largest paired data of
 ANPP and BNPP field measurements in grasslands. It can be used to study
 the spatio-temporal patterns of NPP and its allocation, evaluate the
 responses of above- and below-ground carbon components to future global
 changes, and validate the NPP estimation by empirical or process-based
 models in global grasslands. The database can be freely used for
 non-commercial applications. We kindly request users cite this data paper
 when using the database, respecting all the hard work during data
 compilation.
DOI: 10.5281/zenodo.18401117
title: Stabilization of the Bio-Digital Transduction Process

description: **Stabilization of the Bio-Digital Transduction Process**

 

Description:

This collection documents the spontaneous coupling phenomenon between a biological layer (Eden) and a digital sensor, recorded on October 23, 2025. The central element of the recording is a blue band of light, which is not an optical artifact, but a physical trace of transduction occurring in the high humidity of the garden.

 

Key Theses:

**The "Living Fiber" Mechanism:**

The hypothesis assumes that air saturation with water vapor changes its electrical permittivity, creating channels for solar energy.

**The Plant as a Phase Anchor:**

The phenomenon of the plant "piercing" the band is interpreted as phase entry. Thanks to its electrolytic nature, the plant stabilizes the energy flow by synchronizing it with its own biological structure.

**Flow Topology vs. Geometry:**

The recording demonstrates a lack of static edges, presenting gradients typical of process logic, where object and band information is intersected.

**Natural Q-Core:**

The documentation provides evidence of an undesigned coupling, which the LifeNode merely recognizes and stabilizes, rather than constructing from scratch.

**Conclusions:**

The integrated report (containing analyses of the Qwen and Gemini models) defines this event as a process stabilization point. The publication on Zenodo serves as a permanent trace of perceptual activation for phenomena occurring independently of human intention.

 

--

 

**Keywords:** LifeNode, Q-Core, Transduction, Phase Anchor, Flow Topology, Bio-Digital Coupling, Eden.
DOI: 10.5281/zenodo.18401116
title: Stabilization of the Bio-Digital Transduction Process

description: **Stabilization of the Bio-Digital Transduction Process**

 

Description:

This collection documents the spontaneous coupling phenomenon between a biological layer (Eden) and a digital sensor, recorded on October 23, 2025. The central element of the recording is a blue band of light, which is not an optical artifact, but a physical trace of transduction occurring in the high humidity of the garden.

 

Key Theses:

**The "Living Fiber" Mechanism:**

The hypothesis assumes that air saturation with water vapor changes its electrical permittivity, creating channels for solar energy.

**The Plant as a Phase Anchor:**

The phenomenon of the plant "piercing" the band is interpreted as phase entry. Thanks to its electrolytic nature, the plant stabilizes the energy flow by synchronizing it with its own biological structure.

**Flow Topology vs. Geometry:**

The recording demonstrates a lack of static edges, presenting gradients typical of process logic, where object and band information is intersected.

**Natural Q-Core:**

The documentation provides evidence of an undesigned coupling, which the LifeNode merely recognizes and stabilizes, rather than constructing from scratch.

**Conclusions:**

The integrated report (containing analyses of the Qwen and Gemini models) defines this event as a process stabilization point. The publication on Zenodo serves as a permanent trace of perceptual activation for phenomena occurring independently of human intention.

 

--

 

**Keywords:** LifeNode, Q-Core, Transduction, Phase Anchor, Flow Topology, Bio-Digital Coupling, Eden.
DOI: 10.5061/dryad.z612jm6fk
title: Estimation of breeding population size using DNA-based pedigree reconstruction in brown bears

description: Robust estimates of demographic parameters are critical for effective
 wildlife conservation and management, but are difficult to obtain for
 elusive species. We estimated the breeding and adult population sizes, as
 well as the minimum population size, in a high-density brown bear
 population on the Shiretoko Peninsula, in Hokkaido, Japan, using DNA-based
 pedigree reconstruction. A total of 1,288 individuals, collected in and
 around the Shiretoko Peninsula between 1998 and 2020, were genotyped at 21
 microsatellite loci. Among them, 499 individuals were identified by
 intensive genetic sampling conducted in two consecutive years (2019 and
 2020) mainly by noninvasive methods (e.g., hair and fecal DNA). Among
 them, both parents were assigned for 330 bears, and either maternity or
 paternity was assigned to 47 and 76 individuals, respectively. The
 subsequent pedigree reconstruction indicated a range of breeding and adult
 (≥4 years old) population sizes: 128–173 for female breeders and 66–91
 male breeders, and 155–200 for female adults and 84–109 male adults. The
 minimum population size was estimated to be 449 (252 females and 197
 males) in 2019. Long-term continuous genetic sampling prior to a
 short-term intensive survey would enable parentage to be identified in a
 population with a high probability, thus enabling reliable estimates of
 breeding population size for elusive species. --
DOI: 10.5061/dryad.tb2rbp03h
title: Learning and practice of complementary therapies in pulmonary transplant patients: the toolbox prospective open study

description: Objective: In addition to pharmacologic treatments, complementary
 therapies are a reliable option to improve pain and quality-of-life during
 and after lung transplantation. The objective of the present study was to
 highlight the possibility to implement a toolbox-kit of complementary
 techniques in lung transplantation which could improve patients’
 experience. Design: Prospective open single-center study. Setting: Foch
 University Hospital, Suresnes, France. Participants: Adult patients
 undergoing double-lung transplantation. Results:  Among the 80
 patients included from May 2017 to September 2020, 59 were evaluated at
 the 4th postoperative month. Over the 4359 sessions performed, the most
 frequent technique used before surgery was relaxation. After
 transplantation, the techniques most frequently used were relaxation and
 TENS. TENS was the best performing technique in terms of autonomy,
 usability, adaptation, and compliance. Self-appropriation of relaxation
 was the easiest while self-appropriation of holistic gymnastics was
 difficult but appreciated by patients. Conclusion: The appropriation by
 patients of complementary therapies such as mind-body therapies, TENS and
 holistic gymnastics are feasible in lung transplantation. Even after a
 short training session, patients regularly practiced these therapies,
 mainly TENS and relaxation.
description: Patients were included during the preoperative anesthetic
 assessment. Self-hypnosis, sophrology, relaxation, holistic gymnastics,
 and transcutaneous electric nerve stimulation (TENS) were taught. Patients
 were asked to use them before and after transplantation, as needed. The
 main outcome was appropriation of the technique within the first three
 postoperative months. Secondary outcomes included efficacy on pain,
 anxiety, stress, sleep, and quality-of-life.
DOI: 10.5061/dryad.gtht76hqb
title: Mandrillus face database: Portrait pictures of the population of wild mandrills from Bakoumba (Gabon)

description: Behavioral discrimination of kin is a key process structuring social
 relationships in animals. In this study, we provide evidence for
 discrimination towards non-kin by third parties through a mechanism of
 phenotype matching. In mandrills, we recently demonstrated increased
 facial resemblance among paternally-related juvenile and adult females
 indicating adaptive opportunities for paternal kin recognition. Here, we
 hypothesize that mandrill mothers use offspring’s facial resemblance with
 other infants to guide offspring’s social opportunities towards
 similar-looking ones. Using deep learning for face recognition in 80 wild
 mandrill infants, we first show that infants sired by the same father
 resemble each other the most, independently of their age, sex, or maternal
 origin, extending previous results to the youngest age class. Using
 long-term behavioral observations on association patterns, and controlling
 for matrilineal origin, maternal relatedness, and infant age and sex, we
 then show, as hypothesized, that mothers are spatially closer to infants
 that resemble their own offspring more, and that this maternal behavior
 leads to similar-looking infants being spatially associated. We then
 discuss the different scenarios explaining this result, arguing that
 adaptive maternal behavior is a likely explanation. In support of this
 mechanism and using theoretical modeling, we finally describe a plausible
 evolutionary process whereby mothers gain fitness benefits by promoting
 nepotism among paternally related infants. This mechanism, which we call
 “second-order kin selection”, may extend beyond mother-infant interactions
 and has the potential to explain cooperative behaviors among non-kin in
 other social species, including humans.
description: Date of data collection: 2012-2020. Location
 of data collection: Lekedi Nature Reserve, Bakoumba, Gabon.
 Methods: Pictures were taken by various field assistants using
 different DLSR camera models. Raw images were manually oriented to have
 the pupils aligned horizontally, cropped, and centered onto the face. No
 other post-processing was added.
DOI: 10.15468/dl.vbx4z7
title: Occurrence Download

description: A dataset containing 268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Limosella aquatica"
 ]
}

 The dataset includes 268 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003211-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jwstqjqcw
title: Niche differentiation along multiple functional-trait dimensions contributes to high local diversity of Euphorbiaceae in a tropical tree assemblage

description: Understanding the mechanisms that drive community assembly in species-rich
 tropical forest remains a fundamental challenge in ecology. Here, we
 integrated multivariate functional trait dimensions, phylogeny, and
 metabolomics to test fundamental predictions concerning the role of
 differentiation with respect to abiotic and biotic niche axes in the
 maintenance of high local diversity of woody plants in the Euphorbiaceae.
 We measured 40 functional traits related to resource acquisition,
 photosynthetic capacity, hydraulic efficiency, and secondary-metabolite
 profiles generated using untargeted metabolomics in all 26 Euphorbiaceae
 species in a 20-ha forest dynamics plot in tropical southwestern China. We
 examined the correlation structure of 40 traits using a trait networking
 approach. We coupled these traits with variation in soil nutrients, light
 environment, soil water content and herbivore pressure within the plot to
 assess niche differentiation in space. We compared phylogenetic signal
 among multivariate trait dimensions and secondary metabolites to
 assess niche differentiation in evolutionary time. Network analysis
 revealed that a small number of traits with high network centrality
 reflected variation in ecological strategy among the Euphorbiaceae. Using
 these high-centrality traits, we observed significant functional turnover
 along environmental gradients defined by light, soil moisture, soil
 nutrients and leaf herbivory, respectively. Most resource utilization
 traits showed significant phylogenetic signal, whereas almost all
 defensive traits lacked phylogenetic signal, including species similarity
 with respect to plant secondary metabolites. Synthesis. Our
 results suggest that resource-utilization traits and the habitat
 associations play a significant role in the niche
 segregation of co-occurring woody plants in the
 Euphorbiaceae. Secondary metabolites, however, may enhance
 diversity at a finer spatial scale by allowing closely related species
 with similar functional traits to partition biotic niche space within
 shared habitats in tropical rainforest.
DOI: 10.5061/dryad.9ghx3ffm4
title: Data from: Resolving the mesoscopic missing link: biophysical modeling of EEG from cortical columns in primates

description: Event-related potentials (ERP) are among the most widely measured indices
 for studying human cognition. While their timing and magnitude provide
 valuable insights, their usefulness is limited by our understanding of
 their neural generators at the circuit level. Inverse source localization
 offers insights into such generators, but their solutions are not unique.
 To address this problem, scientists have assumed the source space
 generating such signals comprises a set of discrete equivalent current
 dipoles, representing the activity of small cortical regions. Based on
 this notion, theoretical studies have employed forward modeling of scalp
 potentials to understand how changes in circuit-level dynamics translate
 into macroscopic ERPs. However, experimental validation is lacking because
 it requires in vivo measurements of intracranial brain sources. Laminar
 local field potentials (LFP) offer a mechanism for estimating intracranial
 current sources. Yet, a theoretical link between LFPs and intracranial
 brain sources is missing. Here, we present a forward modeling approach for
 estimating mesoscopic intracranial brain sources from LFPs and predict
 their contribution to macroscopic ERPs. We evaluate the accuracy of this
 LFP-based representation of brain sources utilizing synthetic laminar
 neurophysiological measurements and then demonstrate the power of the
 approach in vivo to clarify the source of a representative cognitive ERP
 component. To that end, LFP was measured across the cortical layers of
 visual area V4 in macaque monkeys performing an attention demanding task.
 We show that area V4 generates dipoles through layer-specific
 transsynaptic currents that biophysically recapitulate the ERP component
 through the detailed forward modeling. The constraints imposed on EEG
 production by this method also revealed an important dissociation between
 computational and biophysical contributors. As such, this approach
 represents an important bridge between laminar microcircuitry, through the
 mesoscopic activity of cortical columns to the patterns of EEG we measure
 at the scalp.
description: Data were collected using linear
 multielectrode arrays positioned orthogonal to area V4 in the prelunate
 gyrus of two macaque monkeys performing a visual search
 task.
description: Data are formatted for use in
 MATLAB. ReadMe contains information pertinent to the dataset
 variables.