bluuebunny/crossref_metadata_2025 huggingface dataset:
Antimicrobial Susceptibility Patterns of Brachyspira Species Isolated from Swine Herds in the United States
Authors: Mirajkar Nandita S. , Davies Peter R. , Gebhart Connie J.
Published: June 2016

Outbreaks of swine dysentery, caused by
Brachyspira hyodysenteriae
and the recently discovered “
Brachyspira hampsonii
,” have reoccurred in North American swine herds since the late 2000s. Additionally, multiple
Brachyspira
species have been increasingly isolated by North American diagnostic laboratories. In Europe, the reliance on antimicrobial therapy for control of swine dysentery has been followed by reports of antimicrobial resistance over time. The objectives of our study were to determine the antimicrobial susceptibility trends of four
Brachyspira
species originating from U.S. swine herds and to investigate their associations with the bacterial species, genotypes, and epidemiological origins of the isolates. We evaluated the susceptibility of
B. hyodysenteriae
,
B. hampsonii
,
Brachyspira pilosicoli
, and
Brachyspira murdochii
to tiamulin, valnemulin, doxycycline, lincomycin, and tylosin by broth microdilution and that to carbadox by agar dilution. In general,
Brachyspira
species showed high susceptibility to tiamulin, valnemulin, and carbadox, heterogeneous susceptibility to doxycycline, and low susceptibility to lincomycin and tylosin. A trend of decreasing antimicrobial susceptibility by species was observed (
B. hampsonii
>
B. hyodysenteriae
>
B. murdochii
>
B. pilosicoli
). In general,
Brachyspira
isolates from the United States were more susceptible to these antimicrobials than were isolates from other countries. Decreased antimicrobial susceptibility was associated with the genotype, stage of production, and production system from which the isolate originated, which highlights the roles of biosecurity and husbandry in disease prevention and control. Finally, this study also highlights the urgent need for Clinical and Laboratory Standards Institute-approved clinical breakpoints for
Brachyspira
species, to facilitate informed therapeutic and control strategies.
Dengue Virus Subverts Host Innate Immunity by Targeting Adaptor Protein MAVS
Authors: He Zhenjian , Zhu Xun , Wen Weitao , Yuan Jie , Hu Yiwen , Chen Jiahui , An Shu , Dong Xinhuai , Lin Cuiji , Yu Jianchen , Wu Jueheng , Yang Yi , Cai Junchao , Li Jun , Li Mengfeng
Published: June 2016

Dengue virus (DENV) is the most common mosquito-borne virus infecting humans and is currently a serious global health challenge. To establish infection in its host cells, DENV must subvert the production and/or antiviral effects of interferon (IFN). The aim of this study was to understand the mechanisms by which DENV suppresses IFN production. We determined that DENV NS4A interacts with mitochondrial antiviral signaling protein (MAVS), which was previously found to activate NF-κB and IFN regulatory factor 3 (IRF3), thus inducing type I IFN in the mitochondrion-associated endoplasmic reticulum membranes (MAMs). We further demonstrated that NS4A is associated with the N-terminal CARD-like (CL) domain and the C-terminal transmembrane (TM) domain of MAVS. This association prevented the binding of MAVS to RIG-I, resulting in the repression of RIG-I-induced IRF3 activation and, consequently, the abrogation of IFN production. Collectively, our findings illustrate a new molecular mechanism by which DENV evades the host immune system and suggest new targets for anti-DENV strategies.

IMPORTANCE
Type I interferon (IFN) constitutes the first line of host defense against invading viruses. To successfully establish infection, dengue virus (DENV) must counteract either the production or the function of IFN. The mechanism by which DENV suppresses IFN production is poorly understood and characterized. In this study, we demonstrate that the DENV NS4A protein plays an important role in suppressing interferon production through binding MAVS and disrupting the RIG-I–MAVS interaction in mitochondrion-associated endoplasmic reticulum membranes (MAMs). Our study reveals that MAVS is a novel host target of NS4A and provides a molecular mechanism for DENV evasion of the host innate immune response. These findings have important implications for understanding the pathogenesis of DENV and may provide new insights into using NS4A as a therapeutic and/or prevention target.
Nonstructural 3 Protein of Hepatitis C Virus Modulates the Tribbles Homolog 3/Akt Signaling Pathway for Persistent Viral Infection
Authors: Tran Si C. , Pham Tu M. , Nguyen Lam N. , Park Eun-Mee , Lim Yun-Sook , Hwang Soon B.
Published: June 2016

Hepatitis C virus (HCV) infection often causes chronic hepatitis, liver cirrhosis, and ultimately hepatocellular carcinoma. However, the mechanisms underlying HCV-induced liver pathogenesis are still not fully understood. By transcriptome sequencing (RNA-Seq) analysis, we recently identified host genes that were significantly differentially expressed in cell culture-grown HCV (HCVcc)-infected cells. Of these, tribbles homolog 3 (TRIB3) was selected for further characterization. TRIB3 was initially identified as a binding partner of protein kinase B (also known as Akt). TRIB3 blocks the phosphorylation of Akt and induces apoptosis under endoplasmic reticulum (ER) stress conditions. HCV has been shown to enhance Akt phosphorylation for its own propagation. In the present study, we demonstrated that both mRNA and protein levels of TRIB3 were increased in the context of HCV replication. We further showed that promoter activity of TRIB3 was increased by HCV-induced ER stress. Silencing of TRIB3 resulted in increased RNA and protein levels of HCV, whereas overexpression of TRIB3 decreased HCV replication. By employing an HCV pseudoparticle entry assay, we further showed that TRIB3 was a negative host factor involved in HCV entry. Both
in vitro
binding and immunoprecipitation assays demonstrated that HCV NS3 specifically interacted with TRIB3. Consequently, the association of TRIB3 and Akt was disrupted by HCV NS3, and thus, TRIB3-Akt signaling was impaired in HCV-infected cells. Moreover, HCV modulated TRIB3 to promote extracellular signal-regulated kinase (ERK) phosphorylation, activator protein 1 (AP-1) activity, and cell migration. Collectively, these data indicate that HCV exploits the TRIB3-Akt signaling pathway to promote persistent viral infection and may contribute to HCV-mediated pathogenesis.

IMPORTANCE
TRIB3 is a pseudokinase protein that acts as an adaptor in signaling pathways for important cellular processes. So far, the functional involvement of TRIB3 in virus-infected cells has not yet been demonstrated. We showed that both mRNA and protein expression levels of TRIB3 were increased in the context of HCV RNA replication. Gene silencing of TRIB3 increased HCV RNA and protein levels, and thus, overexpression of TRIB3 decreased HCV replication. TRIB3 is known to promote apoptosis by negatively regulating the Akt signaling pathway under ER stress conditions. Most importantly, we demonstrated that the TRIB3-Akt signaling pathway was disrupted by NS3 in HCV-infected cells. These data provide evidence that HCV modulates the TRIB3-Akt signaling pathway to establish persistent viral infection.
Ebola Virus Does Not Induce Stress Granule Formation during Infection and Sequesters Stress Granule Proteins within Viral Inclusions
Authors: Nelson Emily V. , Schmidt Kristina M. , Deflubé Laure R. , Doğanay Sultan , Banadyga Logan , Olejnik Judith , Hume Adam J. , Ryabchikova Elena , Ebihara Hideki , Kedersha Nancy , Ha Taekjip , Mühlberger Elke
Published: June 2016

A hallmark of Ebola virus (EBOV) infection is the formation of viral inclusions in the cytoplasm of infected cells. These viral inclusions contain the EBOV nucleocapsids and are sites of viral replication and nucleocapsid maturation. Although there is growing evidence that viral inclusions create a protected environment that fosters EBOV replication, little is known about their role in the host response to infection. The cellular stress response is an effective antiviral strategy that leads to stress granule (SG) formation and translational arrest mediated by the phosphorylation of a translation initiation factor, the α subunit of eukaryotic initiation factor 2 (eIF2α). Here, we show that selected SG proteins are sequestered within EBOV inclusions, where they form distinct granules that colocalize with viral RNA. These inclusion-bound (IB) granules are functionally and structurally different from canonical SGs. Formation of IB granules does not indicate translational arrest in the infected cells. We further show that EBOV does not induce formation of canonical SGs or eIF2α phosphorylation at any time postinfection but is unable to fully inhibit SG formation induced by different exogenous stressors, including sodium arsenite, heat, and hippuristanol. Despite the sequestration of SG marker proteins into IB granules, canonical SGs are unable to form within inclusions, which we propose might be mediated by a novel function of VP35, which disrupts SG formation. This function is independent of VP35's RNA binding activity. Further studies aim to reveal the mechanism for SG protein sequestration and precise function within inclusions.

IMPORTANCE
Although progress has been made developing antiviral therapeutics and vaccines against the highly pathogenic Ebola virus (EBOV), the cellular mechanisms involved in EBOV infection are still largely unknown. To better understand these intracellular events, we investigated the cellular stress response, an antiviral pathway manipulated by many viruses. We show that EBOV does not induce formation of stress granules (SGs) in infected cells and is therefore unrestricted by their concomitant translational arrest. We identified SG proteins sequestered within viral inclusions, which did not impair protein translation. We further show that EBOV is unable to block SG formation triggered by exogenous stress early in infection. These findings provide insight into potential targets of therapeutic intervention. Additionally, we identified a novel function of the interferon antagonist VP35, which is able to disrupt SG formation.
Mutants at the 2-Fold Interface of Adeno-associated Virus Type 2 (AAV2) Structural Proteins Suggest a Role in Viral Transcription for AAV Capsids
Authors: Aydemir Fikret , Salganik Maxim , Resztak Justyna , Singh Jasbir , Bennett Antonette , Agbandje-McKenna Mavis , Muzyczka Nicholas
Published: June 2016

We previously reported that an amino acid substitution, Y704A, near the 2-fold interface of adeno-associated virus (AAV) was defective for transcription of the packaged genome (M. Salganik, F. Aydemir, H. J. Nam, R. McKenna, M. Agbandje-McKenna, and N. Muzyczka, J Virol 88:1071–1079, 2013, doi:
http://dx.doi.org/10.1128/JVI.02093-13
). In this report, we have characterized the defect in 6 additional capsid mutants located in a region ∼30 Å in diameter on the surface of the AAV type 2 (AAV2) capsid near the 2-fold interface. These mutants, which are highly conserved among primate serotypes, displayed a severe defect (3 to 6 logs) in infectivity. All of the mutants accumulated significant levels of uncoated DNA in the nucleus, but none of the mutants were able to accumulate significant amounts of genomic mRNA postinfection. In addition, wild-type (wt) capsids that were bound to the conformational antibody A20, which is known to bind the capsid surface in the region of the mutants, were also defective for transcription. In all cases, the mutant virus particles, as well as the antibody-bound wild-type capsids, were able to enter the cell, travel to the nucleus, uncoat, and synthesize a second strand but were unable to transcribe their genomes. Taken together, the phenotype of these mutants provides compelling evidence that the AAV capsid plays a role in the transcription of its genome, and the mutants map this functional region on the surface of the capsid near the 2-fold interface. This appears to be the first example of a viral structural protein that is also involved in the transcription of the viral genome that it delivers to the nucleus.

IMPORTANCE
Many viruses package enzymes within their capsids that assist in expressing their genomes postinfection, e.g., retroviruses. A number of nonenveloped viruses, including AAV, carry proteases that are needed for capsid maturation or for capsid modification during infection. We describe here what appears to be the first example of a nonenveloped viral capsid that appears to have a role in promoting transcription. A total of six mutants at the AAV capsid 2-fold interface were shown to have a severe defect in expressing their genomes, and the defect was at the level of mRNA accumulation. This suggests that AAV capsids have a novel role in promoting the transcription of the genomes that they have packaged. Since wt virions could not complement the mutant viruses, and the mutant viruses did not effectively inhibit wt gene expression, our results suggest that the capsid exerts its effect on transcription in
cis
.
Human T-Lymphotropic Virus Type 1-Induced Overexpression of Activated Leukocyte Cell Adhesion Molecule (ALCAM) Facilitates Trafficking of Infected Lymphocytes through the Blood-Brain Barrier
Authors: Curis Céline , Percher Florent , Jeannin Patricia , Montange Thomas , Chevalier Sébastien A. , Seilhean Danielle , Cartier Luis , Couraud Pierre-Olivier , Gout Olivier , Gessain Antoine , Ceccaldi Pierre-Emmanuel , Afonso Philippe V.
Published: June 2016

Human T-lymphotropic virus type 1 (HTLV-1) is the etiological agent of a slowly progressive neurodegenerative disease, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). This disease develops upon infiltration of HTLV-1-infected lymphocytes into the central nervous system, mostly the thoracic spinal cord. The central nervous system is normally protected by a physiological structure called the blood-brain barrier (BBB), which consists primarily of a continuous endothelium with tight junctions. In this study, we investigated the role of activated leukocyte cell adhesion molecule (ALCAM/CD166), a member of the immunoglobulin superfamily, in the crossing of the BBB by HTLV-1-infected lymphocytes. We demonstrated that ALCAM is overexpressed on the surface of HTLV-1-infected lymphocytes, both in chronically infected cell lines and in primary infected CD4
+
T lymphocytes. ALCAM overexpression results from the activation of the canonical NF-κB pathway by the viral transactivator Tax. In contrast, staining of spinal cord sections of HAM/TSP patients showed that ALCAM expression is not altered on the BBB endothelium in the context of HTLV-1 infection. ALCAM blockade or downregulation of ALCAM levels significantly reduced the migration of HTLV-1-infected lymphocytes across a monolayer of human BBB endothelial cells. This study suggests a potential role for ALCAM in HAM/TSP pathogenesis.

IMPORTANCE
Human T-lymphotropic virus type 1 (HTLV-1) is the etiological agent of a slowly progressive neurodegenerative disease, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). This disease is the consequence of the infiltration of HTLV-1-infected lymphocytes into the central nervous system (CNS), mostly the thoracic spinal cord. The CNS is normally protected by a physiological structure called the blood-brain barrier (BBB), which consists primarily of a continuous endothelium with tight junctions. The mechanism of migration of lymphocytes into the CNS is unclear. Here, we show that the viral transactivator Tax increases activated leukocyte cell adhesion molecule (ALCAM/CD166) expression. This molecule facilitates the migration of lymphocytes across the BBB endothelium. Targeting this molecule could be of interest in preventing or reducing the development of HAM/TSP.
Two Polypyrimidine Tracts in Intron 4 of the Major Immediate Early Gene Are Critical for Gene Expression Switching from IE1 to IE2 and for Replication of Human Cytomegalovirus
Authors: Hou Wangheng , Torres Lilith , Cruz-Cosme Ruth , Arroyo Fernando , Irizarry Luis , Luciano Dalia , Márquez Arturo , Rivera Leslie L. , Sala Antonio L. , Luo Min-hua , Tang Qiyi
Published: June 2016

The human cytomegalovirus (HCMV) major immediate early (MIE) gene is essential for viral replication. The most abundant products encoded by the MIE gene include IE1 and IE2. Genes of IE1 and IE2 share the MIE promoter (MIEP), the first 3 exons, and the first 2 introns. IE1 is expressed earlier than IE2 after CMV infection or MIE gene transfection. In this study, we identified 2 polypyrimidine (Py) tracts in intron 4 (between exons 4 and 5) that are responsible for transcriptional switching from IE1 to IE2. The first Py is important and the second one is essential for the splicing and expression of IE2. In searching for the mechanisms of MIE gene switching from IE1 to IE2, we found that the second Py was required for the IE2's fourth intron to bind to a splicing factor such as U2AF65, as determined by an RNA electrophoretic mobility shift assay and a chromatin immunoprecipitation (ChIP) assay, while the first Py enhanced the binding of U2AF65 with the intron. An HCMV BACmid with the second Py mutated failed to produce any virus, while the HCMV with the first Py mutated replicated with a defective phenotype. Furthermore, we designed a small RNA (scRNAPy) that is complementary to the intron RNA covering the two Pys. The scRNAPy interfered with the interaction of U2AF65 with the intron and repressed the IE2 expression. Therefore, our studies implied that IE2 gene splicing might be an anti-CMV target.

IMPORTANCE
CMV is a ubiquitous herpesvirus and a significant cause of disease and death in the immunocompromised and elderly. Insights into its gene regulation will provide clues in designing anti-CMV strategies. The MIE gene is one of the earliest genes of CMV and is essential for CMV replication. It is known that the MIE gene needs to be spliced to produce more than two proteins; however, how MIE gene splicing is regulated remains elusive. In the present studies, we identified two Pys in intron 4 and found that the first Py is important and the second is required for the splicing and expression of IE2. We further investigated the mechanisms of gene switching from IE1 to IE2 and found that the two Pys are responsible for U2AF65's binding with intron 4. Therefore, the Pys in intron 4 are the
cis
elements that determine the fate of IE2 splicing. Furthermore, we found that a small RNA that is complementary to intron 4 repressed IE2 expression. Hence, we provide the first piece of evidence for a unique mechanism of MIE gene regulation at the splicing level.
Herpes Simplex Virus Capsid Localization to ESCRT-VPS4 Complexes in the Presence and Absence of the Large Tegument Protein UL36p
Authors: Kharkwal Himanshu , Smith Caitlin G. , Wilson Duncan W.
Published: June 2016

UL36p (VP1/2) is the largest protein encoded by herpes simplex virus 1 (HSV-1) and resides in the innermost layer of tegument, the complex protein layer between the capsid and envelope. UL36p performs multiple functions in the HSV life cycle, including a critical but unknown role in capsid cytoplasmic envelopment. We tested whether UL36p is essential for envelopment because it is required to engage capsids with the cellular ESCRT/Vps4 apparatus. A green fluorescent protein (GFP)-fused form of the dominant negative ATPase Vps4-EQ was used to irreversibly tag ESCRT envelopment sites during infection by UL36p-expressing and UL36-null HSV strains. Using fluorescence microscopy and scanning electron microscopy, we quantitated capsid/Vps4-EQ colocalization and examined the ultrastructure of the corresponding viral assembly intermediates. We found that loss of UL36p resulted in a two-thirds reduction in the efficiency of capsid/Vps4-EQ association but that the remaining UL36p-null capsids were still able to engage the ESCRT envelopment apparatus. It appears that although UL36p helps to couple HSV capsids to the ESCRT pathway, this is likely not the sole reason for its absolute requirement for envelopment.

IMPORTANCE
Envelopment of the HSV capsid is essential for the assembly of an infectious virion and requires the complex interplay of a large number of viral and cellular proteins. Critical to envelope assembly is the virally encoded protein UL36p, whose function is unknown. Here we test the hypothesis that UL36p is essential for the recruitment of cellular ESCRT complexes, which are also known to be required for envelopment.
The Epigenetic Pathways to Ribosomal DNA Silencing
Authors: Srivastava Rakesh , Srivastava Rashmi , Ahn Seong Hoon
Published: June 2016

Heterochromatin is the transcriptionally repressed portion of eukaryotic chromatin that maintains a condensed appearance throughout the cell cycle. At sites of ribosomal DNA (rDNA) heterochromatin, epigenetic states contribute to gene silencing and genome stability, which are required for proper chromosome segregation and a normal life span. Here, we focus on recent advances in the epigenetic regulation of rDNA silencing in
Saccharomyces cerevisiae
and in mammals, including regulation by several histone modifications and several protein components associated with the inner nuclear membrane within the nucleolus. Finally, we discuss the perturbations of rDNA epigenetic pathways in regulating cellular aging and in causing various types of diseases.
Genetically Engineered Phages: a Review of Advances over the Last Decade
Authors: Pires Diana P. , Cleto Sara , Sillankorva Sanna , Azeredo Joana , Lu Timothy K.
Published: June 2016

Soon after their discovery in the early 20th century, bacteriophages were recognized to have great potential as antimicrobial agents, a potential that has yet to be fully realized. The nascent field of phage therapy was adversely affected by inadequately controlled trials and the discovery of antibiotics. Although the study of phages as anti-infective agents slowed, phages played an important role in the development of molecular biology. In recent years, the increase in multidrug-resistant bacteria has renewed interest in the use of phages as antimicrobial agents. With the wide array of possibilities offered by genetic engineering, these bacterial viruses are being modified to precisely control and detect bacteria and to serve as new sources of antibacterials. In applications that go beyond their antimicrobial activity, phages are also being developed as vehicles for drug delivery and vaccines, as well as for the assembly of new materials. This review highlights advances in techniques used to engineer phages for all of these purposes and discusses existing challenges and opportunities for future work.
Mediterranean outflow pump: An alternative mechanism for the Lago-mare and the end of the Messinian Salinity Crisis
Authors: Marzocchi Alice , Flecker Rachel , van Baak Christiaan G.C. , Lunt Daniel J. , Krijgsman Wout
Published: June 2016

The final stage of the Messinian salinity crisis (MSC) was characterized by brackish-water “Lago-mare” conditions in the intermediate and marginal basins of the Mediterranean Sea. The presence of Paratethyan (former Black Sea) fauna in these deposits has fueled long-lasting controversies over the connectivity between the Mediterranean and Paratethys and contemporary sea-level drops in both basins. Here, we use the results of sub-precessional climate simulations to calculate the freshwater budget of the Mediterranean and Paratethys in the Messinian. We show that, during the MSC, the freshwater budget of Paratethys was positive, while the Mediterranean was negative. Using these numerical constraints, we propose a Mediterranean outflow pump as an alternative scenario for the two most dramatic hydrological changes in the MSC: (1) the Halite–Lago-mare transition and (2) the Pliocene reestablishment of marine conditions. Following the maximum MSC lowstand during halite formation, progressive Mediterranean sea-level rise resulting from African river runoff and overspill from both the Atlantic and Paratethys eventually reached the level of the Paratethys sill. A density contrast at this gateway caused dense Mediterranean waters to flow into the Paratethys, driving a compensatory return flow. This “pump” mechanism significantly enhanced Paratethyan inflow to the Mediterranean, creating suitable conditions for the Lago-mare fauna to migrate and thrive. When the Mediterranean sea level finally reached the height of the Gibraltar sill, Mediterranean outflow restarted there and enhanced exchange with the Atlantic Ocean. During this reorganization of the circulation, brackish and hypersaline waters were pumped out of the Mediterranean, and open-marine conditions were reestablished without major flooding of the basin at the Miocene-Pliocene boundary.
Hydrothermal alteration of seafloor peridotites does not influence oxygen fugacity recorded by spinel oxybarometry
Authors: Birner Suzanne K. , Warren Jessica M. , Cottrell Elizabeth , Davis Fred A.
Published: June 2016

Olivine, orthopyroxene, and spinel compositions within seafloor peridotites yield important information about the nature of Earth’s mantle. Major element compositions of these minerals can be used to calculate oxygen fugacity, a thermodynamic property critical to understanding phase equilibria in the upper mantle. This study examines how hydrothermal alteration at the seafloor influences peridotite chemistry. The Tonga Trench (South Pacific Ocean) exposes lithospheric forearc peridotites that range from highly altered to completely unaltered and provides an ideal sample suite for investigating the effect of alteration on spinel peridotite major element chemistry and calculated oxygen fugacity. Using the Tonga peridotites, we develop a qualitative alteration scale rooted in traditional point-counting methodology. We show that high degrees of serpentinization do not affect mineral parameters such as forsterite number in olivine, iron site occupancy in orthopyroxene, and Fe3+/ΣFe ratio in spinel. Additionally, while serpentinization is a redox reaction that leaves behind an oxidized residue, the oxygen fugacity recorded by mantle minerals is unaffected by nearby low-temperature serpentinization. As a result, oxygen fugacity measured by spinel oxybarometry in seafloor peridotites is representative of mantle processes, rather than an artifact of late-stage seafloor alteration.
Management of a patient with pericardial decompression syndrome and HOCM
Authors: Fozing Thierry , Zouri Nayef , Adam Oliver , Oezbek Cem
Published: June 2016

A 44-year-old man, with a history of arterial hypertension, was referred with increasing shortness of breath due to a large pericardial effusion and imminent tamponade. Emergency ultrasound-guided pericardiocentesis resulted in the rapid withdrawal of 2760 cc of serous fluid. 3 hours later, the patient developed acute pulmonary oedema, which was successfully treated. Hypertrophic obstructive cardiomyopathy was later diagnosed and malignancy was excluded as a cause of the effusion. Clinicians performing pericardiocentesis need to be aware of pericardial decompression syndrome (PDS), a rare but serious complication. Although the underlying mechanisms causing PDS are not fully understood, patients with high left ventricular (LV) filling pressures are at particular risk. In other words: diastolic dysfunction of the LV is a risk factor for the occurrence of PDS.
Complete response and long-term survival of leptomeningeal carcinomatosis from breast cancer with maintenance endocrine therapy
Authors: Almajed Muneera Majed , Esfahani Khashayar , Pelmus Manuela , Panasci Lawrence
Published: June 2016

Leptomeningeal carcinomatosis carries a poor prognosis in breast cancer. Treatment modalities are geared towards tumour molecular characteristics, as well as symptoms and patient performance status. It has previously been postulated that endocrine treatments used for the treatment of metastatic breast cancer do cross the blood–brain barrier and can achieve antineoplastic effects in the central nervous system. We report a case of metastatic breast cancer in a 65-year-old woman who developed leptomeningeal carcinomatosis. She was initially treated with intrathecal methotrexate, which was stopped due to toxicity, followed by maintenance endocrine therapy. She achieved a sustained complete radiological and cerebrospinal fluid cytological response for over 9 years. She eventually passed away of ischaemic bowel unrelated to her cancer.
Lethargy and vision loss: successful management of rhinocerebral mucormycosis
Authors: Mulki Ramzi , Masab Muhammad , Eiger Glenn , Perloff Sarah
Published: June 2016

Rhinocerebral mucormycosis (RCM) is an angioinvasive fungal infection most often caused byRhizopus oryzae. It is usually associated with an underlying risk factor and is associated with a poor prognosis. There are no consensus guidelines on the optimal management of this aggressive disease; most management decisions are based on case reports and expert opinion. We report a successfully managed case of RCM in an insulin-dependent diabetic, initially presenting with a change in mental status, rapidly progressing to complete right eye blindness and ophthalmoplegia and complicated by multiple cerebral infarctions and abscesses. We describe the diagnostic approach and various therapeutic interventions undertaken to successfully manage our patient.
Unusual case of acute neck pain: acute calcific longus colli tendinitis
Authors: Joshi Gunjan S , Fomin Daren A , Joshi Gargi S , Serano Richard D
Published: June 2016

Acute calcific longus colli tendinitis (ACLCT), a very rare cause of severe neck pain, dysphagia and odynophagia, is often mistaken for other common causes of neck pain. However, prompt recognition of this uncommon presentation is important to prevent unnecessary medical and surgical intervention. A 46-year-old Caucasian man presented with a 1-day history of severe neck pain, headache and odynophagia. The patient was afebrile with stable vital signs, however, the laboratory data showed mildly elevated C reactive protein and erythrocyte sedimentation rate. The physical examination was remarkable for markedly reduced cervical range of motion. MRI revealed the pathognomonic findings of paravertebral oedema and calcification. The definitive diagnosis of ACLCT was made and the patient was successfully managed with a short course of oral steroid, benzodiazepine and aural acupuncture, with complete resolution of the condition within a week.
Identification of responders to inhaled corticosteroids in a chronic obstructive pulmonary disease population using cluster analysis
Authors: Hinds David R , DiSantostefano Rachael L , Le Hoa V , Pascoe Steven
Published: June 2016

Objectives

To identify clusters of patients who may benefit from treatment with an inhaled corticosteroid (ICS)/long-acting β2agonist (LABA) versus LABA alone, in terms of exacerbation reduction, and to validate previously identified clusters of patients with chronic obstructive pulmonary disease (COPD) (based on diuretic use and reversibility).

Design

Post hoc supervised cluster analysis using a modified recursive partitioning algorithm of two 1-year randomised, controlled trials of fluticasone furoate (FF)/vilanterol (VI) versus VI alone, with the primary end points of the annual rate of moderate-to-severe exacerbations.

Setting

Global.

Participants

3255 patients with COPD (intent-to-treat populations) with a history of exacerbations in the past year.

Interventions

FF/VI 50/25 µg, 100/25 µg or 200/25 µg, or VI 25 µg; all one time per day.

Outcome measures

Mean annual COPD exacerbation rate to identify clusters of patients who benefit from adding an ICS (FF) to VI bronchodilator therapy.

Results

Three clusters were identified, including two groups that benefit from FF/VI versus VI: patients with blood eosinophils >2.4% (RR=0.68, 95% CI 0.58 to 0.79), or blood eosinophils ≤2.4% and smoking history ≤46 pack-years, experienced a reduced rate of exacerbations with FF/VI versus VI (RR=0.78, 95% CI 0.63 to 0.96), whereas those with blood eosinophils ≤2.4% and smoking history >46 pack-years were identified as non-responders (RR=1.22, 95% CI 0.94 to 1.58). Clusters of patients previously identified in the fluticasone propionate/salmeterol (SAL) versus SAL trials of similar design were not validated; all clusters of patients tended to benefit from FF/VI versus VI alone irrespective of diuretic use and reversibility.

Conclusions

In patients with COPD with a history of exacerbations, those with greater blood eosinophils or a lower smoking history may benefit more from ICS/LABA versus LABA alone as measured by a reduced rate of exacerbations. In terms of eosinophils, this finding is consistent with findings from other studies; however, the validity of the 2.4% cut-off and the impact of smoking history require further investigation.

Trial registration numbers

NCT01009463;NCT01017952; Post-results.
Conflict of interest between professional medical societies and industry: a cross-sectional study of Italian medical societies’ websites
Authors: Fabbri Alice , Gregoraci Giorgia , Tedesco Dario , Ferretti Filippo , Gilardi Francesco , Iemmi Diego , Lisi Cosima , Lorusso Angelo , Natali Francesca , Shahi Edit , Rinaldi Alessandro
Published: June 2016

Objective

To describe how Italian medical societies interact with pharmaceutical and medical device industries through an analysis of the information available on their websites.

Design

Cross sectional study.

Setting

Italy.

Participants

154 medical societies registered with the Italian Federation of Medical-Scientific Societies.

Main outcome measures

Indicators of industry sponsorship (presence of industry sponsorship in the programme of the last medical societies’ annual conference; presence of manufacturers’ logos on the homepage; presence of industry sponsorship of satellite symposia during the last annual conference).

Results

131 Italian medical societies were considered. Of these, 4.6% had an ethical code covering relationships with industry on their websites, while 45.6% had a statute that mentioned the issue of conflict of interest and 6.1% published the annual financial report. With regard to industry sponsorship, 64.9% received private sponsorship for their last conference, 29.0% had manufacturers’ logos on their webpage, while 35.9% had industry-sponsored satellite symposia at their last conference. The presence of an ethical code on the societies’ websites was associated with both an increased risk of industry sponsorship of the last conference (relative risk (RR) 1.22, 95% CIs 1.01 to 1.48 after adjustment) and of conferences and/or satellite symposia (RR 1.22, 95% CIs 1.02 to 1.48 after adjustment) but not with the presence of manufacturers’ logos on the websites (RR 1.79, 95% CIs 0.66 to 4.82 after adjustment). No association was observed with the other indicators of governance and transparency.

Conclusions

This survey shows that industry sponsorship of Italian medical societies’ conferences is common, while the presence of a structured regulatory system is not. Disclosure of the amount of industry funding to medical societies is scarce. The level of transparency therefore needs to be improved and the whole relationship between medical societies and industry should be further disciplined in order to avoid any potential for conflict of interest.
Validation of chronic obstructive pulmonary disease (COPD) diagnoses in healthcare databases: a systematic review protocol
Authors: Rimland Joseph M , Abraha Iosief , Luchetta Maria Laura , Cozzolino Francesco , Orso Massimiliano , Cherubini Antonio , Dell'Aquila Giuseppina , Chiatti Carlos , Ambrosio Giuseppe , Montedori Alessandro
Published: June 2016

Introduction

Healthcare databases are useful sources to investigate the epidemiology of chronic obstructive pulmonary disease (COPD), to assess longitudinal outcomes in patients with COPD, and to develop disease management strategies. However, in order to constitute a reliable source for research, healthcare databases need to be validated. The aim of this protocol is to perform the first systematic review of studies reporting the validation of codes related to COPD diagnoses in healthcare databases.

Methods and analysis

MEDLINE, EMBASE, Web of Science and the Cochrane Library databases will be searched using appropriate search strategies. Studies that evaluated the validity of COPD codes (such as the International Classification of Diseases 9th Revision and 10th Revision system; the Real codes system or the International Classification of Primary Care) in healthcare databases will be included. Inclusion criteria will be: (1) the presence of a reference standard case definition for COPD; (2) the presence of at least one test measure (eg, sensitivity, positive predictive values, etc); and (3) the use of a healthcare database (including administrative claims databases, electronic healthcare databases or COPD registries) as a data source. Pairs of reviewers will independently abstract data using standardised forms and will assess quality using a checklist based on the Standards for Reporting of Diagnostic accuracy (STARD) criteria. This systematic review protocol has been produced in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) 2015 statement.

Ethics and dissemination

Ethics approval is not required. Results of this study will be submitted to a peer-reviewed journal for publication. The results from this systematic review will be used for outcome research on COPD and will serve as a guide to identify appropriate case definitions of COPD, and reference standards, for researchers involved in validating healthcare databases.

Trial registration number

CRD42015029204.
The impact of changing economic conditions on overweight risk among children in California from 2008 to 2012
Authors: Oddo Vanessa M , Nicholas Lauren Hersch , Bleich Sara N , Jones-Smith Jessica C
Published: June 2016

Background

The recent economic recession represents an opportunity to test whether decreases in economic resources may have deleterious consequences on childhood overweight/obesity risk.

Methods

We investigated the association between indicators of changing macroeconomic conditions from 2008 to 2012 and overweight/obesity risk among school-aged children in California (n=1 741 712) using longitudinal anthropometric measurements. Multivariate regression, with individual and county fixed effects, was used to examine the effects of annual county-level unemployment and foreclosure rates on risk of child overweight/obesity, overall and among subgroups (race/ethnicity, sex, county-level median household income and county-level urban/rural status).

Results

From 2008 to 2012, ∼38% of children were overweight/obese and unemployment and foreclosure rates averaged 11% and 6.9%, respectively. A 1-percentage point (pp) increase in unemployment was associated with a 1.4 pp (95% CI 1.3 to 1.5) increase in overweight/obesity risk. Therefore, a child of average weight could expect a 14% increase in their body mass index z-score in association with a 1 pp increase in unemployment during the study period. We found some differences in the magnitude of the effects for unemployment among demographic subgroups, with the largest effects observed for unemployment among American Indians and Pacific Islanders.

Conclusions

Comparing children to themselves over time, we provide evidence that increases in county-level unemployment are associated with increased overweight/obesity risk. Given that overweight among children with lower economic resources remains a challenge for public health, these findings highlight the importance of policy-level approaches, which aim to mitigate the impact of decreased resources as economic conditions change.
Republished: Intraventricular thrombolysis after endovascular treatment of a ruptured arteriovenous malformation
Authors: Wang Arthur , Ray Abhishek , Hu Yin C
Published: June 2016

Intraventricular haemorrhage (IVH) secondary to arteriovenous malformation (AVM) rupture carries significant morbidity and mortality. External ventricular drainage of IVH is frequently complicated by thrombus formation within the ventricular catheter and therefore often unsuccessful at treating hydrocephalus in this setting. Intraventricular administration of recombinant tissue-type plasminogen activator (rtPA) has proved successful in the treatment of spontaneous panventricular haemorrhage. However, usage of rtPA is contraindicated in the setting of a ruptured AVM or aneurysm in which the bleeding source has not been secured. There are only a few reports of intraventricular thrombolysis in the treatment of IVH from AVM rupture. We present the case of successful application of rtPA to treat IVH after endovascularly securing the haemorrhage site of the AVM. Intraventricular thrombolysis remains an option for the treatment of IVH in the setting of AVM rupture and should be considered on a case-by-case basis.
Footprintless disruption of prosurvival genes in aneuploid cancer cells using CRISPR/Cas9 technology
Authors: Krachulec Justyna M. , Sedlmeier Georg , Thiele Wilko , Sleeman Jonathan P.
Published: June 2016

CRISPR/Cas9 has emerged as a powerful methodology for the targeted editing of genomic DNA sequences. Nevertheless, the intrinsic inefficiency of transfection methods required to use this technique with cultured cells requires the selection and isolation of successfully modified cells, which invariably subjects the cells to stress. Here we report a workflow that allows the isolation of genomically modified cells, even where loss of functional alleles constitutes a selective disadvantage owing to impaired ability to survive stress. Using targeted disruption of the Id1 and Id3 genes in murine B16-F10 and Ret melanoma cell lines as an example, we show that the method allows for the footprintless isolation of CRISPR/Cas9-modified aneuploid cancer cells. We also provide evidence that serial CRISPR/Cas9 modifications can occur, for example when initial homologous recombination events introduce cryptic PAM sequences, and demonstrate that multiple alleles can be successfully targeted in aneuploid cancer cells. By sequencing individual alleles we also found evidence for CRISPR/Cas9-induced transposable element insertion, albeit at a low frequency. This workflow should have broad application in the functional analysis of prosurvival gene function in cultured cells.
Permeability anisotropy and resistivity anisotropy of mechanically compressed mudrocks
Authors: Adams Amy L. , Nordquist Taylor J. , Germaine John T. , Flemings Peter B.
Published: June 2016

Permeability anisotropy (the ratio of the horizontal to vertical permeability) develops in mudrocks at the macroscale due to heterogeneities such as layering and at the element scale (i.e., within a single homogeneous layer or unit) due to decreasing porosity and increasing platy particle alignment. This work describes new experimental methods and results from a laboratory program using cubic specimens to investigate the evolution of mudrock permeability and resistivity at the element scale. A systematic study analyzes the evolution of the permeability anisotropy and electrical resistivity anisotropy using resedimented Boston blue clay (RBBC) over a stress range of 0.4–40 MPa; additional measurements are presented for three other mudrocks within varying clay fraction and clay mineralogy within the stress range 1.2–10 MPa. The permeability anisotropy and the conductivity anisotropy (inverse of the resistivity anisotropy) of all four mudrocks studied ranges from 1 to 2.2 over the porosity range 0.55–0.30. A nearly 1:1 correlation between the electrical conductivity anisotropy and the permeability anisotropy is observed to be independent of clay fraction or clay mineralogy.
Theoretical investigation of methoxide ion reaction on the 7-methyl-4,6-dinitrobenzofuroxan
Authors: Boughdiri Mohamed Ali , Boubaker Taoufik , Tangour Bahoueddine
Published: June 2016

Reaction of the methoxide ion on the 7-methyl-4,6-dinitrobenzofuroxan (DNBF) 1 has been studied theoretically by means of DFT/B3LYP technique to interpret the kinetic–thermodynamic competition between the three possible compounds that are carbanion DNBF− 4 and the two complexed forms (2, 3) of the methoxide group in positions 5 and 7, respectively. Optimized geometry, nbo atomic charge distribution, thermodynamic/kinetic parameters (ΔrH°T, ΔrS°T, ΔrG°T, ΔH*, ΔS*, and ΔG*) and IRC path have been calculated for possible products and their transitional states using water as solvent. All obtained ΔrG°T are negative, ranging from −19.16 to −42.87 kcal mol−1 (1 cal = 4.184 J), indicating the possible observation of all products, but the experimenters only detected the anionic form DNBF−. Fukui indices, which were calculated by means of NBO atomic charge distribution, confirm the electrophilicity of the sites C5 and C7. Transition states barriers, ΔG*, are 14.97, 15.16, and 21.94 kcal mol−1 for the three possible products 2, 3, and 4, respectively, in water. As expected, the most stable compound is carbanion, but it also exhibits the highest activation barrier. If this situation formally engenders a double kinetic–thermodynamic competition, the very weak activation energy of the two complexes in C5 and C7 makes improbable the simultaneous detection of the three expected compounds.
Freshwater molluscan fauna from the Florissant Formation, Colorado: paleohydrologic reconstruction of a latest Eocene lake
Authors: Buskirk Bret L. , Bourgeois Joanne , Meyer Herbert W. , Nesbitt Elizabeth A.
Published: June 2016

The freshwater molluscan assemblage from the uppermost Eocene Florissant Formation (34.07 ± 0.10 Ma), Colorado, USA, provides a reliable proxy in reconstructing past ecology and environmental characteristics of ancient Lake Florissant. In particular, stable-isotope analyses of aragonitic shell material contribute to our understanding of the paleohydrologic history of this ancient lake. Re-examination of molluscan taxonomy in the middle shale and caprock conglomerate (informal) units produces three sphaeriid bivalves (family Sphaeriidae, genus Sphaerium) and two pulmonate gastropod genera (family Planorbidae, genus Gyraulus; and family Lymnaeidae, genus Lymnaea). The middle-shale assemblage, representing quiet-lake deposition, is dominated by pulmonate gastropods; the shell material in all specimens in this unit has been replaced by silica. The caprock conglomerate assemblage, representing redeposition by a debris flow, is dominated by bivalves; specimens within the caprock conglomerate unit are aragonite, interpreted to be biogenic (original). Carbon and oxygen isotope analyses of the aragonite show a strong covariance (all molluscan data: r = 0.83; sphaeriids: r = 0.76) with consistent grouping (δ13C: 0‰ to −5.5‰, δ18O: +2‰ to −5‰) from all families. This result indicates that ancient Lake Florissant was “closed” and that evaporation had a stronger effect on isotopic values than precipitation, for the duration of the sampled interval. This finding is in agreement with our current understanding of how the sediments of the Florissant Formation were deposited within a lake that formed because of a paleoriver being dammed by debris flows.