bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple Cavitary Lung Lesions in an Adolescent: Case Report of a Rare Presentation of Nodular Lymphocyte Predominant Hodgkin Lymphoma
Authors: Soliman Moaaz , Neemuchwala Fatima , Sankar Amanda , Jasty Rama , Rabah Raja , Popova Antonia P. , Newman Erika A.
Published: August 2018

A 14-year-old male patient presented with a nonproductive cough, weight loss, fatigue, and malaise. A chest radiograph showed large bilateral cavitary lung lesions in both upper and lower lobes that failed to improve with antibiotics and anti-inflammatory medications. Infectious and rheumatologic work-ups were negative. Thoracoscopic lung biopsies were diagnostic for nodular lymphocyte predominant Hodgkin lymphoma (NLPHL). The patient received combination chemotherapy and immunotherapy based on current treatment standards with an excellent clinical response. NLPHL is a rare B-cell lymphoma that typically presents as peripheral lymph nodal disease, clinically distinct from classical Hodgkin lymphoma. The prognosis of NLPHL in children is favorable, although relapse rates are high. This case details several unique features of NLPHL and describes the presentation, diagnosis, and treatment of an adolescent male with a rare pulmonary and cervical NLPHL, the first such case described in a pediatric patient.
Irish Respiratory Clinical Nurse Specialists’ Experiences of Their Role
Authors: Fallon Noreen , Cassidy Irene , Doody Owen
Published: August 2018

Aim and Objectives:

The aim of this study was to explore respiratory clinical nurse specialists’ (CNSs’) experiences of their role.

Background:

Respiratory illnesses are currently 1 of the top 3 causes of mortality resulting in 1 in 5 deaths and are associated with significant human burden. Respiratory CNSs play a vital role in the management of respiratory disease through supporting improvements in quality of life, reduction of exacerbations, and subsequent hospital admission. While published literature exists regarding the CNS role, there is a dearth of published literature on the respiratory CNS role.

Design:

A qualitative descriptive design allowed the researcher to elicit respiratory CNSs’ experiences of their role.

Methods:

Ethical approval was obtained, CNSs were purposively sampled (n = 10), and data were collected by semistructured interviews, transcribed, and analyzed using content thematic analysis.

Results:

Three themes were identified within the findings: “multidimensional role,” “interacting and collaborating,” and “advancing the role.”

Conclusions:

Overall the study highlights that respiratory CNSs are active in the role as clinical experts, advocators, educators, collaborators, consultants, and health promoters. These findings recognize the importance of evaluating and building on the current CNS workforce in respiratory care and evaluating future development of the CNS role in specialized aspects of respiratory care in line with population and service needs.
Use of a Systematic Consultation Process to Facilitate Nursing Research Projects
Authors: Tehan Rebecca I. , Smith Carolyn R. , Draucker Claire B. , Martsolf Donna S.
Published: August 2018

Purpose/Objectives:

The purpose of this article is to describe the use of a well-established, 5-stage consultation process, to advise a research team on planning strategies to engage domestic violence shelters (DVSs) as community partners in their study. The research team is testing a health promotion intervention for teens living in shelters with their parent and needed to enlist shelters as sites to recruit teens and conduct the intervention. Consultation aims were to (a) identify highly promising strategies described in peer-reviewed literature for identifying, recruiting, and collaborating with community organizations in research and (b) identify DVSs that would potentially serve as effective community partners for the study.

Methods:

A clinical nurse specialist and a public health master’s degree student led the consultation. The consultation process included (a) a systematic review of 29 peer-reviewed articles about research or program evaluation studies that engaged community partners and (b) a comprehensive online search of information about DVSs.

Outcomes:

Consultants identified 104 strategies used in studies to engage community partners and 10 specific DVSs most likely to effectively engage in the study.

Conclusion:

Clinical nurse specialists are well situated to provide consultation to research teams and should follow well-established consultation processes and systematic data collection procedures.
Improved Tumor Purity Metrics in Next-generation Sequencing for Clinical Practice: The Integrated Interpretation of Neoplastic Cellularity and Sequencing Results (IINCaSe) Approach
Authors: Patel Nirali M. , Jo Heejoon , Eberhard David A. , Yin Xiaoying , Hayward Michele C. , Stein Matthew K. , Hayes David Neil , Grilley-Olson Juneko E.
Published: August 2018

Neoplastic cellularity contributes to the analytic sensitivity of most present technologies for mutation detection, such that they underperform when stroma and inflammatory cells dilute a cancer specimen’s variant fraction. Thus, tumor purity assessment by light microscopy is used to determine sample adequacy before sequencing and to interpret the significance of negative results and mutant allele fraction afterwards. However, pathologist estimates of tumor purity are imprecise and have limited reproducibility. With the advent of massively parallel sequencing, large amounts of molecular data can be analyzed by computational purity algorithms. We retrospectively compared tumor purity of 3 computational algorithms with neoplastic cellularity using hematoxylin and eosin light microscopy to determine which was best for clinical evaluation of molecular profiling. Data were analyzed from 881 cancer patients from a clinical trial cohort, LCCC1108 (UNCseq), whose tumors had targeted massively parallel sequencing. Concordance among algorithms was poor, and the specimens analyzed had high rates of algorithm failure partially due to variable tumor purity. Computational tumor purity estimates did not add value beyond the pathologist’s estimate of neoplastic cellularity microscopy. To improve present methods, we propose a semiquantitative, clinically applicable strategy based on mutant allele fraction and copy number changes present within a given specimen, which when combined with the morphologic tumor purity estimate, guide the interpretation of next-generation sequencing results in cancer patients.
Subcutaneous Mastectomy Improves Satisfaction with Body and Psychosocial Function in Trans Men: Findings of a Cross-Sectional Study Using the BODY-Q Chest Module
Authors: van de Grift Tim C. , Elfering Lian , Greijdanus Marijke , Smit Jan Maerten , Bouman Mark-Bram , Klassen Anne F. , Mullender Margriet G.
Published: August 2018

Background:

The effectiveness of gender-confirming surgery is best evaluated on the basis of patient-reported outcomes. This is the first explorative study using the BODY-Q chest module, administered in trans men before and after mastectomy.

Methods:

Between October of 2016 and May of 2017, trans men were recruited to participate in a cross-sectional study. Data collection included standardized anamnesis and examination, screening questions on depression/anxiety, and seven BODY-Q scales, including new scales measuring satisfaction of the chest and nipples. Mean scores for preoperative and postoperative participants were compared, and regression analyses were conducted to identify factors associated with BODY-Q scores.

Results:

In total, 101 persons participated (89 percent; 50 preoperatively and 51 postoperatively). Postoperative participants reported significantly higher (better) scores on the chest (67), nipple (58), body (58) (t tests, all p < 0.001), and psychological (60) (t test, p = 0.05) scales compared with preoperative patients. Postoperative chest and nipple mean scores did not differ significantly from a gynecomastia comparison, whereas scores were less favorable on the psychosocial domains. Preoperatively, chest scores were not associated with objective breast size. Lower postoperative chest scores were associated with planned revision surgery (β = −0.52) and depressive symptoms (β = −0.59).

Conclusions:

The present findings indicate that chest and nipple satisfaction differences in trans men undergoing mastectomy can be detected using the BODY-Q chest module. Future prospective studies are needed to measure clinical change in satisfaction and how this relates to changes in other aspects of health-related quality of life.
Hybrid Prepectoral Breast Reconstruction: A Surgical Approach that Combines the Benefits of Autologous and Implant-Based Reconstruction
Authors: Momeni Arash , Kanchwala Suhail
Published: August 2018

Background:

The advantages of hybrid breast reconstruction (i.e., the combination of free tissue transfer with simultaneous implant placement) are well known. In an attempt to further minimize morbidity and simplify the procedure, the authors have modified their approach in that a prepectoral approach is now routinely chosen.

Methods:

A retrospective analysis of patients who underwent immediate microsurgical breast reconstruction with simultaneous prepectoral implant placement was performed. Clinical outcomes and postoperative complications were examined.

Results:

A total of 23 patients with a mean age of 46.6 years (range, 26 to 72 years) and mean body mass index of 25.8 kg/m2 (range, 21.4 to 32.1 kg/m2) underwent reconstruction with 46 free flaps with simultaneous prepectoral silicone gel implant placement. The most common implant volume was 210 cc (range, 150 to 255 cc). Postoperative complications included hematoma [n = 1 (4.3 percent)], mastectomy skin flap necrosis [n = 5 (21.7 percent)], fat necrosis [n = 3 (13 percent)], and delayed wound healing at the flap donor site [n = 4 (17.4 percent)]. No case of implant malposition, implant infection, flap loss, or “red breast” syndrome was encountered during a mean follow-up of 8.4 months (range, 2 to 17 months).

Conclusions:

Prepectoral hybrid breast reconstruction is a safe procedure that combines the benefits of autologous and implant-based reconstruction. Although the transfer of well-vascularized soft tissue allows reconstruction of natural breast ptosis, the addition of an implant provides the desired projection, but without being associated with complications such as rippling or animation deformity.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Implementing a Warm Handoff Between Hospital and Skilled Nursing Facility Clinicians
Authors: Campbell Britton Meredith , Hodshon Beth , Chaudhry Sarwat I.
Published: August 2018

Objectives

Care transitions between hospitals and skilled nursing facilities (SNFs) are associated with disruptions in patient care and high risk for adverse events. Communication between hospital-based and SNF-based clinicians is often suboptimal; there have been calls to foster direct, real-time communication between sending and receiving clinicians to enhance patient safety. This article described the implementation of a warm handoff between hospital and SNF physicians and advanced practice providers at the time of hospital discharge.

Methods

Before patient transfer, hospital clinicians called SNF clinicians to provide information relevant to the continuation of safe patient care and offer SNF clinicians the opportunity to ask clarifying questions. The calls were documented in the hospital discharge summary.

Results

A total of 2417 patient discharges were eligible for inclusion. Warm handoffs were documented at an increasing rate throughout implementation of the intervention, beginning with 15.78% (n = 3) in stage 1, then 20.27% (n = 75) in stage 2, and finally 46.89% (n = 951) in stage 3. The overall average rate of documentation was 42.57%. Participant feedback indicated that clinicians were most concerned about understanding the purpose of the warm handoff, managing their workload, and improving the efficiency of the process.

Conclusions

Use of a warm handoff showed promise in improving communication during hospital-SNF patient transfers. However, the implementation also highlighted specific barriers to the handoff related to organizational structures and clinician workload. Addressing these underlying issues will be critical in ensuring continued participation and support for efforts that foster direct communication among clinicians from different healthcare institutions.
Efficacy and Safety of a Tofacitinib-based Immunosuppressive Regimen After Kidney Transplantation: Results From a Long-term Extension Trial
Authors: Busque Stephan , Vincenti Flavio G. , Tedesco Silva Helio , O’Connell Philip J. , Yoshida Atsushi , Friedewald John J. , Steinberg Steven M. , Budde Klemens , Broeders Emine N. , Kim Yon Su , Hahn Carolyn M. , Li Huihua , Chan Gary
Published: August 2018

Background

Tofacitinib is an oral Janus kinase inhibitor. This open-label, long-term extension (LTE) study (NCT00658359) evaluated long-term tofacitinib treatment in stable kidney transplant recipients (n = 178) posttransplant.

Methods

Patients who completed 12 months of cyclosporine (CsA) or tofacitinib treatment in the phase IIb parent study (NCT00483756) were enrolled into this LTE study, evaluating long-term tofacitinib treatment over months 12 to 72 posttransplant. Patients were analyzed by tofacitinib less-intensive (LI) or more-intensive (MI) regimens received in the parent study. For both groups, tofacitinib dose was reduced from 10 to 5 mg twice daily by 6 months into the LTE. Patients were followed up through month 72 posttransplant, with a focus on month 36 results.

Results

Tofacitinib demonstrated similar 36-month patient and graft survival rates to CsA. Biopsy-proven acute rejection rates at month 36 were 11.2% for CsA, versus 10.0% and 7.4% (both P > 0.05) for tofacitinib LI and MI, respectively. Least squares mean estimated glomerular filtration rates were 9 to 15 mL/min per 1.73 m2 higher for tofacitinib versus CsA at month 36. The proportions of patients with grade 2/3 interstitial fibrosis and tubular atrophy in month 36 protocol biopsies were 20.0% for LI and 18.2% for MI (both P > 0.05) versus 33.3% for CsA. Kaplan-Meier cumulative serious infection rates at month 36 were numerically higher for tofacitinib LI (43.9%; P = 0.45) and significantly higher for MI (55.9%; P < 0.05) versus CsA (37.1%).

Conclusions

Long-term tofacitinib continued to be effective in preventing renal allograft acute rejection and preserving renal function. However, long-term tofacitinib and mycophenolic acid product combination was associated with persistent serious infection risk.
Rare Elizabethkingia anophelis meningitis case in a Danish male
Authors: Nielsen Hans Linde , Tarpgaard Irene Harder , Fuglsang-Damgaard David , Thomsen Philip Kjettinge , Brisse Sylvain , Dalager-Pedersen Michael
Published: August 2018

Introduction.
Elizabethkingia anophelis is a Gram-negative, aerobic, non-motile rod belonging to the family Flavobacteriaceae. Over the last 5 years, it has emerged as an opportunistic human pathogen involved in neonatal meningitis and sepsis, as well as nosocomial outbreaks. It has been isolated from the midgut of the Anopheles gambiae mosquito, but there is no evidence for a role of the mosquito in human infections, and very little is known regarding the routes of transmission to humans. Recent studies, primarily from South-East Asia, suggest that E. anophelis, and not Elizabethkingia meningoseptica, is the predominant human pathogen of this genus. However, identification to the species level has been difficult due to the limitations of the current MALDI-TOF MS (matrix-associated laser desorption ionization-time of flight MS) systems for correct species identification.

Case presentation. Here, we present a rare case of E. anophelis meningitis in a Danish male, who had a travel exposure to Malaysia 7 weeks before hospitalization. A multidrug-resistant Elizabethkingia species was isolated from blood and cerebrospinal fluid, and genomic sequencing was used to characterize the phylogenetic position of the isolate, which was determined as associated with previously described sublineage 11. The patient was successfully treated with intravenous moxifloxacin and rifampicin for 2 weeks with no major sequelae, but we did not find the source of transmission.

Conclusion. All clinical microbiologists should be aware of the present limitations of the MALDI-TOF MS systems for correct species identification, and therefore we recommend the use of genome sequencing for the correct identification at the species and sublineage level.
The Landscape of Enteric Pathogen Exposure of Young Children in Public Domains of Low-Income, Urban Kenya: The Influence of Exposure Pathway and Spatial Range of Play on Multi-Pathogen Exposure Risks
Authors: Medgyesi Danielle , Sewell Daniel , Senesac Reid , Cumming Oliver , Mumma Jane , Baker Kelly K.
Published: August 2018

Background

Young children are infected by a diverse variety of enteric pathogens in low-income, high-burden countries. Little is known about which conditions pose the greatest risk for enteric pathogen exposure and infection. Young children frequently play in residential public areas around their household, including areas contaminated by human and animal feces, suggesting these exposures are particularly hazardous.

Objectives

The objective of this study was to examine how the dose of six types of common enteric pathogens, and the probability of exposure to one or multiple enteric pathogens for young children playing at public play areas in Kisumu, Kenya is influenced by the type and frequency of child play behaviors that result in ingestion of soil or surface water, as well as by spatial variability in the number of public areas children are exposed to in their neighborhood.

Methods

A Bayesian framework was employed to obtain the posterior distribution of pathogen doses for a certain number of contacts. First, a multivariate random effects tobit model was used to obtain the posterior distribution of pathogen concentrations, and their interdependencies, in soil and surface water, based upon empirical data of enteric pathogen contamination in three neighborhoods of Kisumu. Then, exposure doses were estimated using behavioral contact parameters from previous studies, and contrasted under different exposure conditions.

Results

Multi-pathogen exposure of children at public play areas was common. Pathogen doses and the probability of multi-pathogen ingestion increased with: higher frequency of environmental contact, especially for surface water; larger volume of soil or water ingested; and with play at multiple sites in the neighborhood versus single site play.

Discussion

Child contact with surface water and soil at public play areas in their neighborhood is an important cause of exposure to enteric pathogens in Kisumu, and behavioral, environmental, and spatial conditions are determinants of exposure.
Allele frequency dynamics in a pedigreed natural population
Authors: Chen Nancy , Juric Ivan , Cosgrove Elissa J. , Bowman Reed , Fitzpatrick John W. , Schoech Stephan J. , Clark Andrew G. , Coop Graham
Published: August 2018

A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes - variation in individual survival, reproductive success, and movement - are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.
Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis
Authors: Maniatis Silas , Äijö Tarmo , Vickovic Sanja , Braine Catherine , Kang Kristy , Mollbrink Annelie , Fagegaltier Delphine , Andrusivová Žaneta , Saarenpää Sami , Saiz-Castro Gonzalo , Cuevas Miguel , Watters Aaron , Lundeberg Joakim , Bonneau Richard , Phatnani Hemali
Published: August 2018

Paralysis occurring in amyotrophic lateral sclerosis (ALS) results from denervation of skeletal muscle as a consequence of motor neuron degeneration. Interactions between motor neurons and glia contribute to motor neuron loss, but the spatiotemporal ordering of molecular events that drive these processes in intact spinal tissue remains poorly understood. Here, we use spatial transcriptomics to obtain gene expression measurements of mouse spinal cords over the course of disease, as well as of postmortem tissue from ALS patients, to characterize the underlying molecular mechanisms in ALS. We identify novel pathway dynamics, regional differences between microglia and astrocyte populations at early time-points, and discern perturbations in several transcriptional pathways shared between murine models of ALS and human postmortem spinal cords.

One Sentence Summary

Analysis of the ALS spinal cord using Spatial Transcriptomics reveals spatiotemporal dynamics of disease driven gene regulation.
One read per cell per gene is optimal for single-cell RNA-Seq
Authors: Zhang M. J. , Ntranos V. , Tse D.
Published: August 2018

An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells? A mathematical framework reveals that, for estimating many important gene properties, the optimal allocation is to sequence at the depth of one read per cell per gene. Interestingly, the corresponding optimal estimator is not the widely-used plugin estimator but one developed via empirical Bayes.
Rapid and efficient C-terminal labeling of nanobodies for DNA-PAINT
Authors: Fabricius Valentin , Lefèbre Jonathan , Geertsema Hylkje , Marino Stephen F. , Ewers Helge
Published: August 2018

Single molecule localization-based approaches to superresolution microscopy (SMLM) create images that resolve features smaller than the diffraction limit of light by rendering them from the sequentially measured positions of thousands of individual molecules. New SMLM approaches based on the transient binding of very bright dyes via DNA-DNA interaction (DNA-PAINT) allow the resolution of dyes only a few nanometers apartin vitro. This imaging of cellular structures requires the specific association of dyes to their targets, which results in an additional “linkage error”. This error can be minimized by using extremely small, single-domain antibody-based binders such as nanobodies, but the DNA-oligomers used in DNA-PAINT are of significant size in comparison to nanobodies and may interfere with binding. We have here developed an optimized procedure based on enzymatic labeling and click-chemistry for the coupling of DNA oligomers to the nanobody C-terminus, which is located on the opposite side of the epitope-binding domain. Our approach allows for straightforward labeling, purification and DNA-PAINT imaging. We performed high efficiency labeling of two different nanobodies and show dual color multiplexed SMLM to demonstrate the general applicability of our labeling scheme.
Software tools for automated transmission electron dmicroscopy
Authors: Schorb Martin , Haberbosch Isabella , Hagen Wim JH , Schwab Yannick , Mastronarde David N
Published: August 2018

In the recent years, electron microscopy in the life sciences has witnessed increasing demand for high-throughput data collection in both structural and cellular biology. We present a combination of software tools that enable automated acquisition guided by image analysis for a wide variety of Transmission Electron Microscopy applications. Using these tools, we demonstrate dose-reduction in single particle cryo-EM experiments, fully automated acquisition of every single cell in a plastic section and automated targeting of features on serial sections for 3D volume imaging even across multiple grids.
The Nonsense-Mediated mRNA Decay pathway degrades dendritically-targeted mRNAs to regulate long-term potentiation and cognitive function
Authors: Notaras Michael , Allen Megan , Longo Francesco , Volk Nicole , Toth Miklos , Li Jeon Noo , Klann Eric , Colak Dilek
Published: August 2018

Synaptic plasticity relies on new protein synthesis in dendrites that involves the selective translation of specific mRNAs. This requires a tight control of mRNA levels in dendrites. Consistently, RNA translation and degradation pathways have been recently linked to neurodevelopmental and neuropsychiatric diseases, suggesting a role for RNA regulation in synaptic plasticity and cognition. Despite being the only RNA regulatory pathway that is associated with multiple mental illnesses, the Nonsense-Mediated mRNA Decay (NMD) pathway presents an unexplored regulatory mechanism for synaptic function and plasticity. NMD is a highly conserved and selective RNA degradation pathway that exerts its function in a cell- and spatiotemporally-specific manner. Here, we show that neuron-specific disruption of NMD in adulthood attenuates learning, memory, hippocampal LTP, and potentiates perseverative/repetitive behavior. While it is known that local translation of specific mRNAs in dendrites enables synaptic plasticity, the tightly-controlled mechanisms that regulate local quantity of specific mRNAs remains poorly understood. We report that the NMD pathway operates within dendrites to regulate GluR1 surface levels. Specifically, NMD modulates the internalization of GluR1 and promotes its local synthesis in dendrites. We identified AMPK as a mechanistic substrate for NMD that contributes to the NMD-mediated regulation of GluR1 by limiting total GluR1 levels. These data establish that NMD regulates synaptic plasticity, cognition, and local protein synthesis in dendrites, providing fundamental insight into the neuron-specific function of NMD within the brain.
Atomic-level characterization of conformational transition and substrate binding of xCT transporter
Authors: Sharma M. , Rohithaswa A. C.
Published: August 2018

xCT is a component of heterodimeric amino acids transporter system Xc- that has been known to work at the cross-roads of maintaining neurological processes and regulating antioxidant defense. xCT is a sodium-independent amino acid antiporter, that imports L- cystine and exports L-glutamate in a 1:1 ratio. The transporter has 12 transmembrane domains with intracellular N- and C-termini, which can undergo various conformational changes while switching the ligand accessibilities from intracellular to extracellular site. In the present study, we generated two homology models of human xCT in two distinct conformations: inward facing occluded state and outward facing open state. We investigated the conformational transitions within these two states by employing series of targeted molecular dynamics simulations. Our results indicated the substrate translocation channel composed of transmembrane helices TMs 1, 3, 6, 8, and 10. Further, we analyzed the ligand binding within the intermediate conformations obtained from the transition simulations. We docked anionic L-cystine and L-glutamate within the cavities alone or in combination to assess the two distinct binding scenarios for xCT as antiporter. We also assessed the interactions between the ligand and xCT and observed that ligands bind to similar residues within the channel, and these residues are essential for substrate binding/permeation. In addition, we analyzed the correlations between ligand binding and conformational transition and observed conformations that are representatives for intermediate ligand bound states. The results presented in the study provide insights into the interplay of conformational transition and ligand binding as xCT goes from one probable conformation to another while transporting the ligand. And the data thus adds to the existing evidence of alternating access mechanism pertaining to the functioning of transporters.
Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes and Neighboring Endogenous Genes
Authors: Laboulaye Mallory A. , Duan Xin , Qiao Mu , Whitney Irene E. , Sanes Joshua R.
Published: August 2018

Transgenic mouse lines are routinely employed to label and manipulate distinct cell types. The transgene generally comprises cell-type specific regulatory elements linked to a cDNA encoding a reporter or other proteins. However, off-target expression seemingly unrelated to the regulatory elements in the transgene is often observed, and sometimes suspected to reflect influences related to the site of transgene integration in the genome. To test this hypothesis, we used a proximity ligation-based method, Targeted Locus Amplification (TLA), to map the insertion sites of three well-characterized transgenes that appeared to exhibit insertion site-dependent expression in retina. The nearest endogenous genes to transgenes HB9-GFP, Mito-P, and TYW3 are Cdh6, Fat4 and Khdrbs2, respectively. For two lines, we demonstrate that expression reflects that of the closest endogenous gene (Fat4 and Cdh6), even though the distance between transgene and endogenous gene is 550 and 680 kb, respectively. In all three lines, the transgenes decrease expression of the neighboring endogenous genes. In each case, the affected endogenous gene was expressed in at least some of the cell types that the transgenic line has been used to mark and study. These results provide insights into the effects of transgenes and endogenous genes on each other’s expression, demonstrate that mapping insertion site is valuable for interpreting results obtained with transgenic lines, and indicate that TLA is a reliable method for integration site discovery.
Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida
Authors: Joo Sunjoo , Wang Ming Hsiu , Lui Gary , Lee Jenny , Barnas Andrew , Kim Eunsoo , Sudek Sebastian , Worden Alexandra Z. , Lee Jae-Hyeok
Published: August 2018

Homeobox transcription factors (TFs) in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, representing remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. To delineate the ancestry of TALE-TALE heterodimerization, we analyzed TALE endowment in the algal radiations of Archaeplastida, ancestral to land plants. Homeodomain phylogeny and bioinformatics analysis partitioned TALEs into two broad groups, KNOX and non-KNOX. Each group shares previously defined heterodimerization domains, plant KNOX-homology in the KNOX group and animal PBC-homology in the non-KNOX group, indicating their deep ancestry. Protein-protein interaction experiments showed that the TALEs in the two groups all participated in heterodimerization. These results indicate that the TF dyads consisting of KNOX/MEIS and PBC-containing TALEs must have evolved early in eukaryotic evolution, a likely function being to accurately execute the haploid-to-diploid transitions during sexual development.

Author summary

Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Highly conserved TALE-superclass homeobox TF networks in major eukaryotic lineages suggest deep ancestry of developmental mechanisms. Our results support the hypothesis that in early eukaryotes, the TALE heterodimeric configuration provided transcription-on switches via dimerization-dependent subcellular localization, ensuring execution of the haploid-to-diploid transition only when the gamete fusion is correctly executed between appropriate partner gametes, a system that then diversified in the several lineages that engage in complex multicellular organization.
Killing from the inside: Intracellular role of T3SS in the fate ofPseudomonas aeruginosawithin macrophages revealed bymgtCandoprFmutants
Authors: Garai Preeti , Berry Laurence , Moussouni Malika , Bleves Sophie , Blanc-Potard Anne-Béatrice
Published: August 2018

While considered solely an extracellular pathogen, increasing evidence indicates thatPseudomonas aeruginosaencounters intracellular environment in diverse mammalian cell types, including macrophages. In the present study, we have deciphered the intramacrophage fate of wild-typeP. aeruginosaPAO1 strain by live and electron microscopy.P. aeruginosafirst resided in phagosomal vacuoles and subsequently could be detected in the cytoplasm, indicating phagosomal escape of the pathogen, a finding also supported by vacuolar rupture assay. The intracellular bacteria could eventually induce cell lysis. Two bacterial factors, MgtC and OprF, recently identified to be important for survival ofP. aeruginosain macrophages, were found to be involved in bacterial escape from the phagosome as well as cell lysis caused by intracellular bacteria. Strikingly, type III secretion system (T3SS) genes ofP. aeruginosawere down-regulated within macrophages in bothmgtCandoprFmutants. Concordantly, cyclic di-GMP (c-di-GMP) level was increased in both mutants, providing a clue for negative regulation of T3SS inside macrophages. Consistent with the phenotypes and gene expression pattern ofmgtCandoprFmutants, a T3SS mutant(ΔpscN)exhibited defect in phagosomal escape and macrophage lysis driven by internalized bacteria. Importantly, these effects appeared to be largely dependent on the ExoS effector, in contrast with the known T3SS-dependent, but ExoS independent, cytotoxicity caused by extracellularP. aeruginosatowards macrophages. Hence, our work highlights T3SS and ExoS, whose expression is modulated by MgtC and OprF, as key players in the intramacrophage life ofP. aeruginosa, allowing internalized bacteria to evade macrophages.

Author summary

The ability of professional phagocytes to ingest and kill microorganisms is central to host defense andPseudomonas aeruginosahas developed mechanisms to avoid being killed by phagocytes. While considered an extracellular pathogen,P. aeruginosahas been reported to be engulfed by macrophages in animal models. Here, we visualized the fate ofP. aeruginosawithin cultured macrophages, revealing macrophage lysis driven by intracellularP. aeruginosa. Two bacterial factors, MgtC and OprF, recently discovered to be involved in the intramacrophage survival ofP. aeruginosa, appeared to play role in this cytotoxicity caused by intracellular bacteria. We provided evidence that type III secretion system (T3SS) gene expression is lowered intracellularly inmgtCandoprFmutants. We further showed that intramacrophageP. aeruginosauses its T3SS, specifically the ExoS effector, to promote phagosomal escape and cell lysis. We thus describe a transient intramacrophage stage ofP. aeruginosathat could contribute to bacterial dissemination.
Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
Authors: McDowell Ian C. , Barrera Alejandro , D'Ippolito Anthony M. , Vockley Christopher M. , Hong Linda K. , Leichter Sarah M. , Bartelt Luke C. , Majoros William H. , Song Lingyun , Safi Alexias , Koçak D. Dewran , Gersbach Charles A. , Hartemink Alexander J. , Crawford Gregory E. , Engelhardt Barbara E. , Reddy Timothy E.
Published: August 2018

Glucocorticoids are potent steroid hormones that regulate immunity and metabolism by activating the transcription factor (TF) activity of glucocorticoid receptor (GR). Previous models have proposed that DNA binding motifs and sites of chromatin accessibility predetermine GR binding and activity. However, there are vast excesses of both features relative to the number of GR binding sites. Thus, these features alone are unlikely to account for the specificity of GR binding and activity. To identify genomic and epigenetic contributions to GR binding specificity and the downstream changes resultant from GR binding, we performed hundreds of genome-wide measurements of TF binding, epigenetic state, and gene expression across a 12-h time course of glucocorticoid exposure. We found that glucocorticoid treatment induces GR to bind to nearly all pre-established enhancers within minutes. However, GR binds to only a small fraction of the set of accessible sites that lack enhancer marks. Once GR is bound to enhancers, a combination of enhancer motif composition and interactions between enhancers then determines the strength and persistence of GR binding, which consequently correlates with dramatic shifts in enhancer activation. Over the course of several hours, highly coordinated changes in TF binding and histone modification occupancy occur specifically within enhancers, and these changes correlate with changes in the expression of nearby genes. Following GR binding, changes in the binding of other TFs precede changes in chromatin accessibility, suggesting that other TFs are also sensitive to genomic features beyond that of accessibility.
4-(4-Acetyl-5-methyl-1H-1,2,3-triazol-1-yl)benzonitrile: crystal structure and Hirshfeld surface analysis
Authors: Zukerman-Schpector Julio , Dias Cássio da S. , Schwab Ricardo S. , Jotani Mukesh M. , Tiekink Edward R. T.
Published: August 2018

The title compound, C12H10N4O, comprises a central 1,2,3-triazole ring (r.m.s. deviation = 0.0030 Å) flanked by N-bound 4-cyanophenyl and C-bound acetyl groups, which make dihedral angles of 54.64 (5) and 6.8 (3)° with the five-membered ring, indicating a twisted molecule. In the crystal, the three-dimensional architecture is sustained by carbonyl-C=O...π(triazoyl), cyano-C[triple-bond]N...π(triazoyl) (these interactions are shown to be attractive based on non-covalent interaction plots) and π–π stacking interactions [intercentroid separation = 3.9242 (9) Å]. An analysis of the Hirshfeld surface shows the important contributions made by H...H (35.9%) and N...H (26.2%) contacts to the overall surface, as well as notable contributions by O...H (9.9%), C...H (8.7%), C...C (7.3%) and C...N (7.2%) contacts.
Crystal structure and luminescent properties of bis[2,6-dimethyl-3-(pyridin-2-yl-κN)pyridin-4-yl-κC
4](2,2,6,6-tetramethylheptane-3,5-dionato-κ2
O,O′)iridium(III) ethyl acetate monosolvate
Authors: Park Ki-Min , Moon Suk-Hee , Kang Youngjin
Published: August 2018

In the solvated title compound, [Ir(C12H11N2)2(C11H19O2)]·CH3CO2C2H5, the IrIII ion adopts a distorted octahedral coordination environment resulting from its coordination by two C,N-chelating 2,6-dimethyl-3-(pyridin-2-yl)pyridin-4-yl ligands and one O,O′-chelating 2,2,6,6-tetramethylheptane-3,5-dionate ligand. The C,N-chelating ligands are perpendicular to each other [dihedral angle between the least-squares planes = 87.86 (5)°] and are arranged in a cis-C,C′ and trans-N,N′ fashion. In the crystal, pairwise C—H...π interactions between inversion-related IrIII complexes are present, forming a dimeric structure. The title complex shows bright bluish–green emission with good quantum efficiency in solution at room temperature.
Redetermination of ammonium metavanadate
Authors: Pérez-Benítez Aarón , Bernès Sylvain
Published: August 2018

The crystal structure of ammonium metavanadate, NH4VO3, a compound widely used as a starting material for the synthesis of vanadium and polyoxidovanadate compounds, had been determined twice using single-crystal X-ray data [Syneček & Hanic (1954). Czech. J. Phys. 4, 120–129 (Weissenberg data); Hawthorne & Calvo (1977). J. Solid State Chem. 22, 157–170 (four-circle diffractometer data)]. Its structure is now redetermined at higher resolution using Ag Kα radiation, and the result is compared with the former refinements. Structural data for the polymeric [VO3]∞ chain remain unchanged, while more accurate parameters are obtained for the ammonium cation, improving the description of hydrogen-bonding interactions in the crystal structure.
The impact of sociocultural context on strategic renewal
Authors: Au Kevin , Han Stone , Chung Hsi-Mei
Published: August 2018

Purpose

The purpose of this paper is to contribute a multilevel, cross-national analysis of the role that sociocultural context may play to enrich the understanding of strategic renewal in family firms. The authors conceptualize sociocultural context as consisting of firm-level social contexts and national culture, and propose that: heterogeneous social contexts in family firm management, i.e. family CEO and multigenerational involvement, give rise to mindsets that have differential effects on renewal efforts and that the proposed effects are subject to variation due to the moderation of national cultural dimensions of uncertainty avoidance and power distance.

Design/methodology/approach

The authors use unique date set consisting of 959 family firms from 26 countries drawn from a cross-national, quantitative study of family firms.

Findings

The authors found that family CEO is negatively related to renewal across cultures, and this relationship is attenuated by uncertainty avoidance and power distance. In addition, multigenerational involvement is positively related to renewal, and this relationship is enhanced by the two cultural dimensions.

Practical implications

The authors suggest that decision makers examine how different contexts, practices and cognition contribute to overall dominant logics that exist in firm. In doing so, they can evaluate how logics as a whole affect renewal, and also how different parts of the logics play a role. This overall evaluation will afford managers a holistic picture of renewal forces that operate in family firm and allow managers to make precise changes to enhance strategic renewal.

Originality/value

The findings support the contention that there is cultural-dependent countervailing effects on strategic renewal within family firms.
Design and optimization of a slot antenna for microwave heating of agglomerates
Authors: Kinoshita Takahiro , Sugihashi Atsushi
Published: August 2018

Purpose

The microwave heating technique can be used in the production of iron for productivity improvement when the consumption of low-quality iron ore increases. Iron-containing dust agglomerates are an important source of iron; however, the crushing strength of raw agglomerates is low, which decreases the yield owing to breaking. Therefore, they need to be dried using a “band dryer” to reduce the amount of excess water and improve their crushing strength. This paper aims to present the structure of an antenna that efficiently provides microwave energy to the agglomerate layer inside the band dryer.

Design/methodology/approach

Electromagnetic field analysis and experiments that simulate inside the band dryer were performed to evaluate the radiation efficiency of the slot antenna for microwave heating of the agglomerate layer in the presence of a metal conveyor.

Findings

The results show that slot height should be larger than the antenna position from the metal conveyor and smaller than the sum of the antenna position and quarter of the guide wavelength, to maximize the radiation efficiency of the antenna. By satisfying this condition, the radiation efficiency was higher than 75 per cent in the experiments.

Originality/value

This paper presents for the first time the optimum relation between slot height and antenna position to apply the microwave heating technique to iron-containing agglomerates in a band dryer.
L’Aquila, central Italy, and the “disaster cycle”, 2009-2017
Authors: Alexander David E.
Published: August 2018

Purpose

The purpose of this paper is to offer a critical examination of the aftermath of the L’Aquila earthquake of 6 April 2009. It considers the elements of the recovery process that are unique or exceptional and endeavours to explain them.

Design/methodology/approach

The analysis is based on a survey and synthesis of the abundant literature on the disaster, coupled with observations from the author’s many visits to L’Aquila and personal involvement in the debates on the questions raised during the aftermath.

Findings

Several aspects of the disaster are unique. These include the use of large, well-appointed buildings as temporary accommodation and the efforts to use legal processes to obtain justice for alleged mismanagement of both the early emergency situation and faults in the recovery process.

Research limitations/implications

Politics, history, economics and geography have conspired to make the L’Aquila disaster and its aftermath a multi-layered event that poses considerable challenges of interpretation.

Practical implications

The L’Aquila case teaches first that moderate seismic events can entail a long and difficult process of recovery if the initial vulnerability is high. Second, for processes of recovery to be rational, they need to be safeguarded against the effects of political expediency and bureaucratic delay.

Social implications

Many survivors of the L’Aquila disaster have been hostages to fortune, victims as much of broader political and socio-economic forces than of the earthquake itself.

Originality/value

Although there are now many published analyses of the L’Aquila disaster, as the better part of a decade has elapsed since the event, there is value in taking stock and making a critical assessment of developments. The context of this disaster is dynamic and extraordinarily sophisticated, and it provides the key to interpretation of developments that otherwise would probably seem illogical.
Gathering places in the aftermath of Hurricane Harvey
Authors: Nelan Mary M. , Schumann III Ronald L.
Published: August 2018

Purpose

The purpose of this paper is to introduce the concept of gathering places in disaster recovery, and describe types of active gathering places where residents and aid workers in Southern Texas, USA, came seeking resources, information and emotional support one month after Hurricane Harvey.

Design/methodology/approach

Semi-structured interviews in the field with 81 residents and 44 aid workers identified active gathering places and their functions. Researchers utilized a snowball sample design to identify and visit further gathering places until saturation. Field observations and a regional damage survey conducted by car add further context to interview data.

Findings

In total, 22 distinct types of gathering places were identified from the 123 unique gathering places documented. Overall, the displacement of residents created an obstacle to their recovery and access to resources and gathering places; residents characterized a lack of formalized emotional support centers – primarily relying on informal gatherings with friends and neighbors to meet their needs; and gathering places were limited in their ability to foster a communal recovery among the residents.

Originality/value

This study addresses a gap in the research, focusing on where and how individuals access resources, information and emotional support in the short-term recovery following a disaster event. This research combines two traditions, hazards geography and disaster sociology, to investigate what gathering places exist one month after a major disaster, where those places are located, and what purpose they serve.