Killing and Impairing Fetuses.

Could it be that if a fetus is not a person abortion is still immoral? One affirmative answer comes in the form of 'The Impairment Argument', which utilizes 'The Impairment Principle' to argue that abortion is immoral even if fetuses lack personhood. I argue 'The Impairment Argument' fails. It is not adequately defended from objections, and abortion is, in fact, a counterexample to the impairment principle.

The long and the short of it: Mechanisms of synchronous and compensatory dynamics across temporal scales.

Synchronous dynamics (fluctuations that occur in unison) are universal phenomena with widespread implications for ecological stability. Synchronous dynamics can amplify the destabilizing effect of environmental variability on ecosystem functions such as productivity, whereas the inverse, compensatory dynamics, can stabilize function. Here we combine simulation and empirical analyses to elucidate mechanisms that underlie patterns of synchronous versus compensatory dynamics.

Liberating host-virus knowledge from biological dark data.

Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis.

Stomatal development in the cycad family Zamiaceae.

Background And Aims: The gymnosperm order Cycadales is pivotal to our understanding of seed-plant phylogeny because of its phylogenetic placement close to the root node of extant spermatophytes and its combination of both derived and plesiomorphic character states. Although widely considered a 'living fossil' group, extant cycads display a high degree of morphological and anatomical variation. We investigate stomatal development in Zamiaceae to evaluate variation within the order and homologies between cycads and other seed plants.

Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms.

Domestic and captive animals and cultivated plants should be recognised as integral components in contemporary ecosystems. They interact with wild organisms through such mechanisms as hybridization, predation, herbivory, competition and disease transmission and, in many cases, define ecosystem properties. Nevertheless, it is widespread practice for data on domestic, captive and cultivated organisms to be excluded from biodiversity repositories, such as natural history collections.

E-Mentoring Female Underrepresented Public Health Student Researchers: Supporting a More Diverse Postpandemic Workforce.

Within higher education, underrepresented students continue to face inequalities and discrimination, with unique challenges surfacing during the COVID-19 pandemic. Mentoring through formal or informal channels is one way to offer assistance to such students. During COVID-19 lockdowns, as classes and work moved online, mentoring also transitioned online.

Evaluating the success of treatments that slow spread of an invasive insect pest.

Background: Treatments for the suppression and eradication of insect populations undergo substantial testing to ascertain their efficacy and safety, but the generally limited spatial and temporal scope of such studies limit knowledge of how contextual factors encountered in operational contexts shape the relative success of pest management treatments. These contextual factors potentially include ecological characteristics of the treated area, or the timing of treatments relative to pest phenology and weather events. We used an extensive database on over 1000 treatments of nascent populations of Lymantria dispar (L.

The IDIP framework for assessing protein function and its application to the prion protein.

The quest to determine the function of a protein can represent a profound challenge. Although this task is the mandate of countless research groups, a general framework for how it can be approached is conspicuously lacking. Moreover, even expectations for when the function of a protein can be considered to be 'known' are not well defined.

FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II.

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J.

Community Approaches for Integrating Environmental Exposures into Human Models of Disease.

Background: A critical challenge in genomic medicine is identifying the genetic and environmental risk factors for disease. Currently, the available data links a majority of known coding human genes to phenotypes, but the environmental component of human disease is extremely underrepresented in these linked data sets. Without environmental exposure information, our ability to realize precision health is limited, even with the promise of modern genomics.

Inference for Convolutionally Observed Diffusion Processes.

We propose a new statistical observation scheme of diffusion processes named convolutional observation, where it is possible to deal with smoother observation than ordinary diffusion processes by considering convolution of diffusion processes and some kernel functions with respect to time parameter. We discuss the estimation and test theories for the parameter determining the smoothness of the observation, as well as the least-square-type estimation for the parameters in the diffusion coefficient and the drift one of the latent diffusion process. In addition to the theoretical discussion, we also examine the performance of the estimation and the test with computational simulation, and show an example of real data analysis for one EEG data whose observation can be regarded as smoother one than ordinary diffusion processes with statistical significance.

Transforming the study of organisms: Phenomic data models and knowledge bases.

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology.

COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein.

The spike glycoprotein of the SARS-CoV-2 virus, which causes COVID-19, has attracted attention for its vaccine potential and binding capacity to host cell surface receptors. Much of this research focus has centered on the ectodomain of the spike protein. The ectodomain is anchored to a transmembrane region, followed by a cytoplasmic tail.

Gold Standard for macromolecular crystallography diffraction data.

Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules. Over the last few decades, most MX data have been collected at synchrotron beamlines using a large number of different detectors produced by various manufacturers and taking advantage of various protocols and goniometries. These data came in their own formats: sometimes proprietary, sometimes open.

A novel curation system to facilitate data integration across regional citizen science survey programs.

Integrative modeling methods can now enable macrosystem-level understandings of biodiversity patterns, such as range changes resulting from shifts in climate or land use, by aggregating species-level data across multiple monitoring sources. This requires ensuring that taxon interpretations match up across different sources. While encouraging checklist standardization is certainly an option, coercing programs to change species lists they have used consistently for decades is rarely successful.

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.

Background: Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype.

Results: We used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments.

Flux-based hierarchical organization of Escherichia coli's metabolic network.

Biological networks across scales exhibit hierarchical organization that may constrain network function. Yet, understanding how these hierarchies arise due to the operational constraint of the networks and whether they impose limits to molecular phenotypes remains elusive. Here we show that metabolic networks include a hierarchy of reactions based on a natural flux ordering that holds for every steady state.

Best practices for high data-rate macromolecular crystallography (HDRMX).

In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata.

Fetuses, newborns, & parental responsibility.

I defend a relational account of difference in the moral status between fetuses and newborns. The difference in moral status between a fetus and a newborn is that the newborn baby is the proper object of 'parental responsibility' whereas the fetus is not. 'Parental responsibilities' are a moral dimension of a 'parent-child relation', a relation which newborn babies stand in, but fetuses do not.

Integrating Subjective and Objective Dimensions of Resilience in Fire-Prone Landscapes.

Resilience has become a common goal for science-based natural resource management, particularly in the context of changing climate and disturbance regimes. Integrating varying perspectives and definitions of resilience is a complex and often unrecognized challenge to applying resilience concepts to social-ecological systems (SESs) management. Using wildfire as an example, we develop a framework to expose and separate two important dimensions of resilience: the inherent properties that maintain structure, function, or states of an SES and the human perceptions of desirable or valued components of an SES.

20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration.

Biodiversity information is made available through numerous databases that each have their own data models, web services, and data types. Combining data across databases leads to new insights, but is not easy because each database uses its own system of identifiers. In the absence of stable and interoperable identifiers, databases are often linked using taxonomic names.