RaMALDI: Enabling simultaneous Raman and MALDI imaging of the same tissue section.

Multimodal tissue imaging techniques that integrate two complementary modalities are powerful discovery tools for unraveling biological processes and identifying biomarkers of disease. Combining Raman spectroscopic imaging (RSI) and matrix-assisted laser-desorption/ionization (MALDI) mass spectrometry imaging (MSI) to obtain fused images with the advantages of both modalities has the potential of providing spatially resolved, sensitive, specific biomolecular information, but has so far involved two separate sample preparations, or even consecutive tissue sections for RSI and MALDI MSI, resulting in images with inherent disparities. We have developed RaMALDI, a streamlined, integrated, multimodal imaging workflow of RSI and MALDI MSI, performed on a single tissue section with one sample preparation protocol.

Association between prenatal antimicrobial use and offspring attention deficit hyperactivity disorder.

Background: Gut-brain cross-talk may play an important role in modulating neurodevelopment. Few studies have examined the association between antimicrobials that influence infant gut microbiota assemblage and attention deficit hyperactivity disorder (ADHD).

Objective: To examine the association between maternal prenatal antimicrobial use and ADHD in offspring at 10 years of age.

Outcomes Following Anterior Cruciate Ligament Reconstruction with Patellar Tendon vs Hamstring Autografts: A Systematic Review of Randomized Controlled Trials with a Mean Follow-up of 15 Years.

Background: The two most common surgical treatment modalities for anterior cruciate ligament reconstruction (ACL), patellar tendon (PT) and hamstring tendon (HS) autografts, have been shown to have outcomes that are both similar and favorable; however, many of these are short or intermediate-term. The objective of this systematic review is to evaluate randomized controlled trials (RCTs) with a minimum 10-year follow-up data to compare the long-term outcomes of ACL reconstructions performed using PT and HS autografts.

Methods: This systematic review followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines.

Infant gut bacterial community composition and food-related manifestation of atopy in early childhood.

Background: Immunoglobulin E-mediated food allergy (IgE-FA) has emerged as a global public health concern. Immune dysregulation is an underlying mechanism for IgE-FA, caused by "dysbiosis" of the early intestinal microbiota. We investigated the association between infant gut bacterial composition and food-related atopy at age 3-5 years using a well-characterized birth cohort.

Trends and Characteristics of Clinical Trials Participation for Inflammatory Bowel Disease in the United States: A Report From IBD Partners.

Background And Aims: There are currently several recruitment challenges in randomized controlled trials (RCTs) for inflammatory bowel disease (IBD), which prolong the drug approval process and affect the generalizability of study results. The purpose of this study is to characterize individuals who participate in IBD RCTs and identify factors that could influence future recruitment strategies.

Methods: We performed a cross-sectional study within the IBD Partners cohort comparing patients with current or prior participation in an RCT of medical therapy for IBD to those without any RCT participation.

Therapeutic trials of biologics in primary biliary cholangitis: An open label study of abatacept and review of the literature.

Primary biliary cholangitis (PBC) is a classic autoimmune disease in which humoral, cytotoxic, and innate immune responses have been implicated with the specific targeting of a mitochondrial antigen. The mainstay of treatment remains the bile acid ursodeoxycholic acid (UDCA). Corticosteroids may have some benefits, but to date, clinical trials of biologics targeting B cells and IL-12/23 have not shown any efficacy.

Family Practitioner-Directed Hepatitis C Therapy With Direct-Acting Antivirals Achieves High-Sustained Virologic Response in Prison Population.

The burden of hepatitis C virus (HCV) infection is disproportionately high in U.S. federal and state prisons.

Monte Carlo explicitly correlated many-body Green's function theory.

A highly scalable stochastic algorithm is proposed and implemented for computing the basis-set-incompleteness correction to the diagonal, frequency-independent self-energy of the second-order many-body Green's function (GF2) theory within the explicitly correlated (F12) formalism. The 6-, 9-, 12-, and 15-dimensional integrals comprising the F12 correction are directly evaluated by the Monte Carlo method using appropriate weight functions for importance sampling. The method is naturally and easily parallelized, involves minimal memory space and no disk I/O, and can use virtually any mathematical form of a correlation factor.

Monte Carlo explicitly correlated second-order many-body perturbation theory.

A stochastic algorithm is proposed and implemented that computes a basis-set-incompleteness (F12) correction to an ab initio second-order many-body perturbation energy as a short sum of 6- to 15-dimensional integrals of Gaussian-type orbitals, an explicit function of the electron-electron distance (geminal), and its associated excitation amplitudes held fixed at the values suggested by Ten-no. The integrals are directly evaluated (without a resolution-of-the-identity approximation or an auxiliary basis set) by the Metropolis Monte Carlo method. Applications of this method to 17 molecular correlation energies and 12 gas-phase reaction energies reveal that both the nonvariational and variational formulas for the correction give reliable correlation energies (98% or higher) and reaction energies (within 2 kJ mol with a smaller statistical uncertainty) near the complete-basis-set limits by using just the aug-cc-pVDZ basis set.

The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii.

Background: Drosophila suzukii differs from other melanogaster group members in their proclivity for laying eggs in fresh fruit rather than in fermenting fruits. Olfaction and gustation play a critical role during insect niche formation, and these senses are largely mediated by two important receptor families: olfactory and gustatory receptors (Ors and Grs). Earlier work from our laboratory has revealed how the olfactory landscape of D.

Pooled segregant sequencing reveals genetic determinants of yeast pseudohyphal growth.

The pseudohyphal growth response is a dramatic morphological transition and presumed foraging mechanism wherein yeast cells form invasive and surface-spread multicellular filaments. Pseudohyphal growth has been studied extensively as a model of conserved signaling pathways controlling stress responses, cell morphogenesis, and fungal virulence in pathogenic fungi. The genetic contribution to pseudohyphal growth is extensive, with at least 500 genes required for filamentation; as such, pseudohyphal growth is a complex trait, and linkage analysis is a classical means to dissect the genetic basis of a complex phenotype.

The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response.

The yeast Saccharomyces cerevisiae undergoes a dramatic growth transition from its unicellular form to a filamentous state, marked by the formation of pseudohyphal filaments of elongated and connected cells. Yeast pseudohyphal growth is regulated by signaling pathways responsive to reductions in the availability of nitrogen and glucose, but the molecular link between pseudohyphal filamentation and glucose signaling is not fully understood. Here, we identify the glucose-responsive Sks1p kinase as a signaling protein required for pseudohyphal growth induced by nitrogen limitation and coupled nitrogen/glucose limitation.

TEAK: topology enrichment analysis framework for detecting activated biological subpathways.

To mine gene expression data sets effectively, analysis frameworks need to incorporate methods that identify intergenic relationships within enriched biologically relevant subpathways. For this purpose, we developed the Topology Enrichment Analysis frameworK (TEAK). TEAK employs a novel in-house algorithm and a tailor-made Clique Percolation Method to extract linear and nonlinear KEGG subpathways, respectively.

A large-scale complex haploinsufficiency-based genetic interaction screen in Candida albicans: analysis of the RAM network during morphogenesis.

The morphogenetic transition between yeast and filamentous forms of the human fungal pathogen Candida albicans is regulated by a variety of signaling pathways. How these pathways interact to orchestrate morphogenesis, however, has not been as well characterized. To address this question and to identify genes that interact with the Regulation of Ace2 and Morphogenesis (RAM) pathway during filamentation, we report the first large-scale genetic interaction screen in C.

Engagement and retention: measuring breadth and depth of participant use of an online intervention.

Background: The Internet provides us with tools (user metrics or paradata) to evaluate how users interact with online interventions. Analysis of these paradata can lead to design improvements.

Objective: The objective was to explore the qualities of online participant engagement in an online intervention.

Conditionally controlling nuclear trafficking in yeast by chemical-induced protein dimerization.

We present here a protocol to conditionally control the nuclear trafficking of target proteins in yeast. In this system, rapamycin is used to heterodimerize two chimeric proteins. One chimera consists of a FK506-binding protein (FKBP12) fused to a cellular 'address' (nuclear localization signal or nuclear export sequence).

Within-woman change in regulatory T cells from pregnancy to the postpartum period.

Regulatory T cells (Treg cells) are an important area of investigation in human health and disease. In this study, the trajectory of percentage of Treg cells (defined as CD4+CD25+Foxp3+CD127--lymphocytes) was measured in the blood of 208 women during pregnancy and up to three additional times in the postpartum period (1, 6 and 12 months postpartum). Whether the trajectory was affected by gravidity, parity, neonatal sex, pet exposure, maternal atopic and asthma status, smoking, maternal race or other pregnancy factors was examined.

Independent sets of DNA oligonucleotides for nanotechnology applications.

Independent sets of DNA oligonucleotides, which only bind with their Watson-Crick complements, have potential use in self-assembly of nanostructures, since they minimize errors and inefficiency from unwanted binding. A software tool implemented a thermodynamic model for DNA duplex formation and was used to generate large independent sets of DNA oligonucleotides. The principle of the approach was experimentally verified on a sample set of oligonucleotides.

Effects of false-positive prostate cancer screening results on subsequent prostate cancer screening behavior.

Objectives: Little is known about screening behavior following a false-positive prostate cancer screening result, which we have defined as a screening result with "abnormal/suspicious" labeling that did not result in a prostate cancer diagnosis within 14 months. The purpose of this analysis was to examine whether age, race, education, or previous false-positive prostate cancer screening results via prostate-specific antigen or digital rectal exam predict decision to obtain subsequent prostate cancer screening.

Methods: Data were drawn from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial.

Family history, dust mite exposure in early childhood, and risk for pediatric atopy and asthma.

Background: Dust mite allergen exposure is considered a major determinant of sensitization to these allergens during childhood and a risk factor for pediatric asthma.

Objective: By using a birth cohort in a setting with a substantial burden of dust mite allergen, we evaluated exposure and risk for outcomes related to allergy and asthma.

Methods: We collected dust from the bedrooms of 428 children born from 1987 to 1989 and measured Der f 1 and Der p 1 (microg/g dust, combined).

Sociodemographic differences in the receipt of colorectal cancer surveillance care following treatment with curative intent.

Background: Despite limited evidence of its effectiveness, most guidelines recommend colorectal cancer survivors undergo posttreatment surveillance care. This article describes the posttreatment use of colon examinations, carcinoembryonic antigen (CEA) testing, and metastatic disease testing among a managed care population.

Methods: Two hundred fifty-one patients with colorectal cancer enrolled in a managed care organization at diagnosis (1/1/90-12/31/95) and treated with curative intent.

Occupational metal exposures and the risk of Parkinson's disease.

Occupational exposure to specific metals (manganese, copper, lead, iron, mercury, zinc, aluminum and others) appears to be a risk factor for Parkinson's disease (PD) in some, but not all, case-control studies. These epidemiological studies are reviewed. Several methodological issues that may account for the lack of unanimity of findings are discussed, and suggestions for improved case-control methodology are offered.