The Effect of Antidepressants on Withdrawal in Patients with Alcohol Dependence: A Retrospective Study.

The use of electronic health records has expanded in the past decades, with healthcare entities storing terabytes of patient health data. In this study, we investigated how these databases can be utilized to generate clinically relevant information. We used the Office of Addiction Services and Supports Client Data Systems data merged with the NYS Medicaid Data Warehouse to study the relationship of certain antidepressants on alcohol withdrawal (AW) rates in patients with alcohol dependence (AD).

Allopolyploid origin and diversification of the Hawaiian endemic mints.

Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification.

High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species.

With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered.

Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska.

During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U.

Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation.

Collective cell behavior contributes to all stages of cancer progression. Understanding how collective behavior emerges through cell-cell interactions and decision-making will advance our understanding of cancer biology and provide new therapeutic approaches. Here, we summarize an interdisciplinary discussion on multicellular behavior in cancer, draw lessons from other scientific disciplines, and identify future directions.

Navigation between initial and desired community states using shortcuts.

Ecological management problems often involve navigating from an initial to a desired community state. We ask whether navigation without brute-force additions and deletions of species is possible via: adding/deleting a small number of individuals of a species, changing the environment, and waiting. Navigation can yield direct paths (single sequence of actions) or shortcut paths (multiple sequences of actions with lower cost than a direct path).

The spatial propagation and increasing dominance of Gilbertiodendron dewevrei (Fabaceae) in the eastern Congo basin.

Though substantial research has been conducted on possible historical, physiological, and symbiotic mechanisms that permit monodominance to occur within tropical lowland rainforests, less is known about the successional rates at which monodominance exerts itself on surrounding forest structures. Here we extend efforts to evaluate the longitudinal dynamics of Gilbertiodendron dewevrei-dominated forest in Central Africa by considering this species' spatial dynamics. Using three 10-ha censused field plots measured across three time periods, we present the first quantitative estimates of the spatial propagation of Gilbertiodendron into adjacent mixed species forest.

Holistic Wellness Coaching for Older Adults: Preliminary Evidence for a Novel Wellness Intervention in Senior Living Communities.

Although resident wellness is increasingly a priority in senior living communities, there are few programs that promote holistic wellness in later life. A total of 79 residents (ages 71 to 97; = 84.27, = 6.

Genomic insights into rapid speciation within the world's largest tree genus Syzygium.

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide.

Insights into bear evolution from a Pleistocene polar bear genome.

The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos).

Efficient Dynamics Estimation with Adaptive Model Sets.

Robotic systems frequently operate under changing dynamics, such as driving across varying terrain, encountering sensing and actuation faults, or navigating around humans with uncertain and changing intent. In order to operate effectively in these situations, robots must be capable of efficiently estimating these changes in order to adapt at the decision-making, planning, and control levels. Typical estimation approaches maintain a fixed set of candidate models at each time step; however, this can be computationally expensive if the number of models is large.

An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas.

The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP.

Education and Outreach in Physical Sciences in Oncology.

Physical sciences are often overlooked in the field of cancer research. The Physical Sciences in Oncology Initiative was launched to integrate physics, mathematics, chemistry, and engineering with cancer research and clinical oncology through education, outreach, and collaboration. Here, we provide a framework for education and outreach in emerging transdisciplinary fields.

Correction: Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer.

[This corrects the article DOI: 10.1371/journal.pcbi.

Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer.

Drug resistance in breast cancer cell populations has been shown to arise through phenotypic transition of cancer cells to a drug-tolerant state, for example through epithelial-to-mesenchymal transition or transition to a cancer stem cell state. However, many breast tumors are a heterogeneous mixture of cell types with numerous epigenetic states in addition to stem-like and mesenchymal phenotypes, and the dynamic behavior of this heterogeneous mixture in response to drug treatment is not well-understood. Recently, we showed that plasticity between differentiation states, as identified with intracellular markers such as cytokeratins, is linked to resistance to specific targeted therapeutics.

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.

Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted therapies. We show here that cell-state heterogeneity, defined by differentiation-state marker expression, is high in triple-negative and basal-like breast cancer subtypes, and that drug tolerant persister (DTP) cell populations with altered marker expression emerge during treatment with a wide range of pathway-targeted therapeutic compounds. We show that MEK and PI3K/mTOR inhibitor-driven DTP states arise through distinct cell-state transitions rather than by Darwinian selection of preexisting subpopulations, and that these transitions involve dynamic remodeling of open chromatin architecture.

Correction: Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.

[This corrects the article DOI: 10.1371/journal.pone.

Reconstruction of Gene Regulatory Networks based on Repairing Sparse Low-rank Matrices.

With the growth of high-throughput proteomic data, in particular time series gene expression data from various perturbations, a general question that has arisen is how to organize inherently heterogenous data into meaningful structures. Since biological systems such as breast cancer tumors respond differently to various treatments, little is known about exactly how these gene regulatory networks (GRNs) operate under different stimuli. Challenges due to the lack of knowledge not only occur in modeling the dynamics of a GRN but also cause bias or uncertainties in identifying parameters or inferring the GRN structure.

HIV Pharmacist's Impact on Inpatient Antiretroviral Errors.

Objectives: Transitions in care between out-patient and in-patient settings provide ample opportunity for medication errors to occur in HIV-infected patients. The purpose of this study was to examine the effectiveness of an HIV pharmacist monitoring service in decreasing antiretroviral medication errors in a large south central teaching hospital in the USA.

Methods: A retrospective, observational study was conducted to examine the frequency of antiretroviral medication errors in HIV-seropositive patients with hospital admissions between 1 September 2011 and 30 September 2013 at a single tertiary care centre in Oklahoma.

Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.

We report here on experimental and theoretical efforts to determine how best to combine drugs that inhibit HER2 and AKT in HER2(+) breast cancers. We accomplished this by measuring cellular and molecular responses to lapatinib and the AKT inhibitors (AKTi) GSK690693 and GSK2141795 in a panel of 22 HER2(+) breast cancer cell lines carrying wild type or mutant PIK3CA. We observed that combinations of lapatinib plus AKTi were synergistic in HER2(+)/PIK3CA(mut) cell lines but not in HER2(+)/PIK3CA(wt) cell lines.

Accelerating Submovement Decomposition With Search-Space Reduction Heuristics.

Objective: Movements made by healthy individuals can be characterized as superpositions of smooth bell-shaped velocity curves. Decomposing complex movements into these simpler "submovement" building blocks is useful for studying the neural control of movement as well as measuring motor impairment due to neurological injury.

Approach: One prevalent strategy to submovement decomposition is to formulate it as an optimization problem.

Disentangling multidimensional spatio-temporal data into their common and aberrant responses.

With the advent of high-throughput measurement techniques, scientists and engineers are starting to grapple with massive data sets and encountering challenges with how to organize, process and extract information into meaningful structures. Multidimensional spatio-temporal biological data sets such as time series gene expression with various perturbations over different cell lines, or neural spike trains across many experimental trials, have the potential to acquire insight about the dynamic behavior of the system. For this potential to be realized, we need a suitable representation to understand the data.

Lifestyle and youthful looks.

Background: Lifestyle has been proven to have a dramatic effect on the risk of age-related diseases. The association of lifestyle and facial ageing has been less well studied.

Objectives: To identify lifestyle factors that associate with perceived facial age in white north European men and women.

Exact reconstruction of gene regulatory networks using compressive sensing.

Background: We consider the problem of reconstructing a gene regulatory network structure from limited time series gene expression data, without any a priori knowledge of connectivity. We assume that the network is sparse, meaning the connectivity among genes is much less than full connectivity. We develop a method for network reconstruction based on compressive sensing, which takes advantage of the network's sparseness.