Forest degradation drives widespread avian habitat and population declines

In many regions of the world, forest management has reduced old forest and simplified forest structure and composition. We hypothesized that such forest degradation has resulted in long-term habitat loss for forest-associated bird species of eastern Canada (130,017 km2) which, in turn, has caused bird-population declines. Despite little change in overall forest cover, we found substantial reductions in old forest as a result of frequent clear-cutting and a broad-scale transformation to intensified forestry. Back-cast species distribution models revealed that breeding habitat loss occurred for 66% of the 54 most common species from 1985 to 2020 and was strongly associated with reduction in old age classes. Using a long-term, independent dataset, we found that habitat amount predicted population size for 94% of species, and habitat loss was associated with population declines for old-forest species. Forest degradation may therefore be a primary cause of biodiversity decline in managed forest landscapes

Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy

Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). First, we describe a simple, general method to map out the spatial and temporal distributions of binding geometries constituting the Cc-CcP encounter state. We show that the spatiotemporal mapping provides a reliable estimate of the experimental coverage and, at higher coverage levels, allows to delineate the conformational space sampled by the minor species. To further refine the encounter state, we performed PRE-based ensemble simulations. The generated solutions reproduce well the experimental data and lie within the allowed regions of the encounter maps, confirming the validity of the mapping approach. The refined encounter ensembles are distributed predominantly in a region encompassing the dominant form of the complex, providing experimental proof for the results of classical theoretical simulations

Lysine demethylases KDM6A and UTY: the X and Y of histone demethylation

Histone demethylases remove transcriptional repressive marks from histones in the nucleus. KDM6A (also known as UTX) is a lysine demethylase which acts on the trimethylated lysine at position 27 in histone 3. The KDM6A gene is located on the X chromosome but escapes X inactivation even though it is not located in the pseudoautosomal region. There is a homologue of KDM6A on the Y chromosome, known as UTY. UTY was thought to have lost its demethylase activity and to represent a non-functional remnant of the ancestral KDM6A gene. However, results with knockout mice suggest that the gene is expressed and the protein performs some function within the cell. Female mice with homozygous deletion of Kdm6a do not survive, but hemizygous males are viable, attributed to the presence of the Uty gene. KDM6A is mutated in the human condition Kabuki syndrome type 2 (OMIM 300867) and in many cases of cancer. The amino acid sequence of KDM6A has been conserved across animal phyla, although it is only found on the X chromosome in eutherian mammals. In this review, we reanalyse existing data from various sources (protein sequence comparison, evolutionary genetics, transcription factor binding and gene expression analysis) to determine the function, expression and evolution of KDM6A and UTY and show that UTY has a functional role similar to KDM6A in metabolism and development

Theory of semiconductor devices : lectures give at Summer Electronics Symposium August 7 to August 18, 1950

http://deepblue.lib.umich.edu/bitstream/2027.42/3509/5/bab2579.0001.001.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/3509/4/bab2579.0001.001.tx

Enhancement of Diffusion-Controlled Reaction Rates by Surface-Induced Orientational Restriction

We explore the means by which immobilization of a substrate on a surface can increase the rate of a diffusion-controlled enzymatic reaction. A quasichemical approach is developed and compared with Brownian dynamics simulations. We use these methods to show that restricting only the orientation of the enzyme by long-range interactions with the surface is sufficient for enhancing catalysis

Does a simplified algorithm and integrated HCV care model improve linkage to care, retention, and cure among people who inject drugs? A pragmatic quality improvement randomized controlled trial protocol.

BACKGROUND: As many as 2.4 million Americans are affected by chronic Hepatitis C Virus (HCV) in the United States.In 2018, the estimated number of adults with a history of HCV infection in San Diego County was 55,354 (95% CI: 25,411-93,329). This corresponded to a seroprevalence of 2.1% (95% CI: 2.1-3.4%). One-third of infections were among PWID. Published research has demonstrated that direct-acting antivirals (DAAs) have high efficacy and can now be used by primary care providers to treat HCV. In addition, limited evidence exists to support the effectiveness of simplified algorithms in clinical trial and real-world settings. Even with expanded access to HCV treatment in primary care settings, there are still groups, especially people who inject drugs (PWID) and people experiencing homelessness, who experience treatment disparities due to access and treatment barriers. The current study extends the simplified algorithm with a streetside one-stop-shop approach with integrated care (including the offer of buprenorphine prescriptions and abscess care) using a mobile clinic situated adjacent to a syringe service program serving many homeless populations. Rates of HCV treatment initiation and retention will be compared between patients offered HCV care in a mobile clinic adjacent to a syringe services program (SSP) and homeless encampment versus those who are linked to a community clinics current practice of usual care, which includes comprehensive patient navigation. METHODS: A quasi-experimental, prospective, interventional, comparative effectiveness trial with allocation of approximately 200 patients who inject drugs and have chronic HCV to the simplified care pathway (intervention group) or the usual care pathway (control group). Block randomization will be performed with a 1:1 randomization. DISCUSSION: Previous research has demonstrated acceptable outcomes for patients treated using simplified algorithms for DAAs and point-of-care testing in mobile medical clinics; however, there are opportunities to explore how these new, innovative systems of care impact treatment initiation rates or other HCV care cascade outcomes among PWID. TRIAL REGISTRATION: We have registered our study with ClinicalTrials.gov, a resource of the United States National Library of Medicine. This database contains research studies from United States and other countries around the world. Our study has not been previously published. The ClinicalTrials.gov registration identifier is NCT04741750

Linking animal movement and remote sensing - mapping resource suitability from a remote sensing perspective

Optical remote sensing is an important tool in the study of animal behavior providing ecologists with the means to understand species–environment interactions in combination with animal movement data. However, differences in spatial and temporal resolution between movement and remote sensing data limit their direct assimilation. In this context, we built a data-driven framework to map resource suitability that addresses these differences as well as the limitations of satellite imagery. It combines seasonal composites of multiyear surface reflectances and optimized presence and absence samples acquired with animal movement data within a cross-validation modeling scheme. Moreover, it responds to dynamic, site-specific environmental conditions making it applicable to contrasting landscapes. We tested this framework using five populations of White Storks (Ciconia ciconia) to model resource suitability related to foraging achieving accuracies from 0.40 to 0.94 for presences and 0.66 to 0.93 for absences. These results were influenced by the temporal composition of the seasonal reflectances indicated by the lower accuracies associated with higher day differences in relation to the target dates. Additionally, population differences in resource selection influenced our results marked by the negative relationship between the model accuracies and the variability of the surface reflectances associated with the presence samples. Our modeling approach spatially splits presences between training and validation. As a result, when these represent different and unique resources, we face a negative bias during validation. Despite these inaccuracies, our framework offers an important basis to analyze species–environment interactions. As it standardizes site-dependent behavioral and environmental characteristics, it can be used in the comparison of intra- and interspecies environmental requirements and improves the analysis of resource selection along migratory paths. Moreover, due to its sensitivity to differences in resource selection, our approach can contribute toward a better understanding of species requirements