bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generating Bona Fide Mammalian Prions with Internal Deletions
Authors: Munoz-Montesino Carola , Sizun Christina , Moudjou Mohammed , Herzog Laetitia , Reine Fabienne , Chapuis Jérôme , Ciric Danica , Igel-Egalon Angelique , Laude Hubert , Béringue Vincent , Rezaei Human , Dron Michel 
Published: May 2016

ABSTRACT

Mammalian prions are PrP proteins with altered structures causing transmissible fatal neurodegenerative diseases. They are self-perpetuating through formation of beta-sheet-rich assemblies that seed conformational change of cellular PrP. Pathological PrP usually forms an insoluble protease-resistant core exhibiting beta-sheet structures but no more alpha-helical content, loosing the three alpha-helices contained in the correctly folded PrP. The lack of a high-resolution prion structure makes it difficult to understand the dynamics of conversion and to identify elements of the protein involved in this process. To determine whether completeness of residues within the protease-resistant domain is required for prions, we performed serial deletions in the helix H2 C terminus of ovine PrP, since this region has previously shown some tolerance to sequence changes without preventing prion replication. Deletions of either four or five residues essentially preserved the overall PrP structure and mutant PrP expressed in RK13 cells were efficiently converted into bona fide prions upon challenge by three different prion strains. Remarkably, deletions in PrP facilitated the replication of two strains that otherwise do not replicate in this cellular context. Prions with internal deletion were self-propagating and
de novo
infectious for naive homologous and wild-type PrP-expressing cells. Moreover, they caused transmissible spongiform encephalopathies in mice, with similar biochemical signatures and neuropathologies other than the original strains. Prion convertibility and transfer of strain-specific information are thus preserved despite shortening of an alpha-helix in PrP and removal of residues within prions. These findings provide new insights into sequence/structure/infectivity relationship for prions.

IMPORTANCE
Prions are misfolded PrP proteins that convert the normal protein into a replicate of their own abnormal form. They are responsible for invariably fatal neurodegenerative disorders. Other aggregation-prone proteins appear to have a prion-like mode of expansion in brains, such as in Alzheimer's or Parkinson's diseases. To date, the resolution of prion structure remains elusive. Thus, to genetically define the landscape of regions critical for prion conversion, we tested the effect of short deletions. We found that, surprisingly, removal of a portion of PrP, the C terminus of alpha-helix H2, did not hamper prion formation but generated infectious agents with an internal deletion that showed characteristics essentially similar to those of original infecting strains. Thus, we demonstrate that completeness of the residues inside prions is not necessary for maintaining infectivity and the main strain-specific information, while reporting one of the few if not the only bona fide prions with an internal deletion.
Viral Evasion and Manipulation of Host RNA Quality Control Pathways
Authors: Hogg J. Robert 
Published: May 2016

ABSTRACT
Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance.
Human Cytomegalovirus pUL93 Links Nucleocapsid Maturation and Nuclear Egress
Authors: DeRussy Bernadette M. , Boland Molly T. , Tandon Ritesh 
Published: May 2016

ABSTRACT
Human cytomegalovirus (HCMV) pUL93 and pUL77 are both essential for virus growth, but their functions in the virus life cycle remain mostly unresolved. Homologs of pUL93 and pUL77 in herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV) are known to interact to form a complex at capsid vertices known as the capsid vertex-specific component (CVSC), which likely stabilizes nucleocapsids during virus maturation and also aids in nuclear egress. In herpesviruses, nucleocapsids assemble and partially mature in nuclear replication compartments and then travel to the inner nuclear membrane (INM) for nuclear egress. The factors governing the recruitment of nucleocapsids to the INM are not known. Kinetic analysis of pUL93 demonstrates that this protein is expressed late during infection and localizes primarily to the nucleus of infected cells. pUL93 associates with both virions and capsids and interacts with the components of the nuclear egress complex (NEC), namely, pUL50, pUL53, and pUL97, during infection. Also, multiple regions in pUL93 can independently interact with pUL77, which has been shown to help retain viral DNA during capsid assembly. These studies, combined with our earlier report of an essential role of pUL93 in viral DNA packaging, indicate that pUL93 serves as an important link between nucleocapsid maturation and nuclear egress.

IMPORTANCE
HCMV causes life-threatening disease and disability in immunocompromised patients and congenitally infected newborns. In this study, we investigated the functions of HCMV essential tegument protein pUL93 and determined that it interacts with the components of the nuclear egress complex, namely, pUL50, pUL53, and pUL97. We also found that pUL93 specifically interacts with pUL77, which helps retain viral DNA during capsid assembly. Together, our data point toward an important role of pUL93 in linking virus maturation to nuclear egress. In addition to expanding our knowledge of the process of HCMV maturation, information from these studies will also be utilized to develop new antiviral therapies.
Release of Infectious Hepatitis C Virus from Huh7 Cells Occurs via a
trans
-Golgi Network-to-Endosome Pathway Independent of Very-Low-Density Lipoprotein Secretion
Authors: Mankouri Jamel , Walter Cheryl , Stewart Hazel , Bentham Matthew , Park Wei Sun , Heo Won Do , Fukuda Mitsunori , Griffin Stephen , Harris Mark 
Published: May 2016

ABSTRACT

The release of infectious hepatitis C virus (HCV) particles from infected cells remains poorly characterized. We previously demonstrated that virus release is dependent on the endosomal sorting complex required for transport (ESCRT). Here, we show a critical role of
trans
-Golgi network (TGN)-endosome trafficking during the assembly, but principally the secretion, of infectious virus. This was demonstrated by both small interfering RNA (siRNA)-mediated silencing of TGN-associated adaptor proteins and a panel of dominant negative (DN) Rab GTPases involved in TGN-endosome trafficking steps. Importantly, interfering with factors critical for HCV release did not have a concomitant effect on secretion of triglycerides, ApoB, or ApoE, indicating that particles are likely released from Huh7 cells via pathways distinct from that of very-low-density lipoprotein (VLDL). Finally, we show that HCV NS2 perturbs TGN architecture, redistributing TGN membranes to closely associate with HCV core protein residing on lipid droplets. These findings support the notion that HCV hijacks TGN-endosome trafficking to facilitate particle assembly and release. Moreover, although essential for assembly and infectivity, the trafficking of mature virions is seemingly independent of host lipoproteins.

IMPORTANCE
The mechanisms by which infectious hepatitis C virus particles are assembled and released from the cell are poorly understood. We show that the virus subverts host cell trafficking pathways to effect the release of virus particles and disrupts the structure of the Golgi apparatus, a key cellular organelle involved in secretion. In addition, we demonstrate that the mechanisms used by the virus to exit the cell are distinct from those used by the cell to release lipoproteins, suggesting that the virus effects a unique modification to cellular trafficking pathways.
Tegument Protein ORF45 Plays an Essential Role in Virion Morphogenesis of Murine Gammaherpesvirus 68
Authors: Jia Xing , Shen Sheng , Lv Ying , Zhang Ziwei , Guo Haitao , Deng Hongyu 
Published: May 2016

ABSTRACT
Tegument proteins play critical roles in herpesvirus morphogenesis. ORF45 is a conserved tegument protein of gammaherpesviruses; however, its role in virion morphogenesis is largely unknown. In this work, we determined the ultrastructural localization of murine gammaherpesvirus 68 (MHV-68) ORF45 and found that this protein was incorporated into virions around the site of host-derived vesicles. Notably, the absence of ORF45 inhibited nucleocapsid egress and blocked cytoplasmic virion maturation, demonstrating that ORF45 is essential for MHV-68 virion morphogenesis.
Stathmin is a highly sensitive and specific biomarker for vulvar high-grade squamous intraepithelial lesions
Authors: Nooij Linda S , Dreef Enno J , Smit Vincent T H B M , van Poelgeest Mariëtte I E , Bosse Tjalling 
Published: May 2016

AimsDifferentiating between human papilloma virus-dependent vulvar low-grade and high-grade squamous intraepithelial lesions (LSILs and HSILs) remains difficult in selected cases. Stathmin, a protein involved in cell cycle progression, might be a useful additional marker for this differentiation. The aim of this study was to investigate the additional diagnostic value of stathmin expression in vulvar intraepithelial neoplastic (VIN) lesions.MethodsImmunohistochemical analysis was used to evaluate stathmin, P16 and Ki67 expression in 91 samples, including LSILs (n=16), HSILs (n=50), differentiated VIN (dVIN; n=10), lichen sclerosis (LS; n=10) and normal vulvar tissue (n=5).ResultsStathmin was expressed in more than one-third of the epithelium in all HSILs and in 20% of LSILs. P16 and Ki67 were expressed in more than one-third of the epithelium in 94% of HSILs and in 13% and 40% of LSILs, respectively. Stathmin was expressed in more than one-third of the epithelium in 10% of the dVIN and in none of the LS or normal lesions. P16 and Ki67 expression was not present in more than one-third of the epithelium in any of these lesions. The sensitivity of stathmin for differentiating between LSILs and HSILs was 100% compared with a sensitivity of 94% for both p16 and Ki67. The specificity of stathmin, p16 and Ki67 was 80%, 87% and 60%, respectively.ConclusionsStathmin is a highly sensitive and specific biomarker for the diagnosis of vulvar HSIL. In addition to the more commonly used immunohistochemical markers p16 and Ki67, stathmin can be a useful diagnostic tool for identifying HSILs, especially in cases in which differentiating between LSIL and HSIL is difficult.
Effects on cigarette consumption of a work–family supportive organisational intervention: 6-month results from the work, family and health network study
Authors: Hurtado David A , Okechukwu Cassandra A , Buxton Orfeu M , Hammer Leslie , Hanson Ginger C , Moen Phyllis , Klein Laura C , Berkman Lisa F 
Published: May 2016

BackgroundObservational studies have linked work–family issues with cigarette consumption. This study examined the 6-month effects on cigarette consumption of a work–family supportive organisational intervention among nursing home workers.MethodsGroup randomised controlled trial where 30 nursing homes across New England states were randomly assigned to either usual practice or to a 4-month intervention aimed at reducing work–family conflict via increased schedule control and family supportive supervisory behaviours (FSSB). Cigarette consumption was based on self-reported number of cigarettes per week, measured at the individual level.ResultsA total of 1524 direct-care workers were enrolled in the trial. Cigarette consumption was prevalent in 30% of the sample, consuming an average of 77 cigarettes/week. Smokers at intervention sites reduced cigarette consumption by 7.12 cigarettes, while no reduction was observed among smokers at usual practice sites (b=−7.12, 95% CI −13.83 to −0.40, p<0.05) (d=−0.15). The majority of smokers were US-born White nursing assistants, and among this subgroup, the reduction in cigarette consumption was stronger (b=−12.77, 95% CI −22.31 to −3.22, p<0.05) (d=−0.27). Although the intervention prevented a decline in FSSB (d=0.08), effects on cigarette consumption were not mediated by FSSB.ConclusionsCigarette consumption was reduced among smokers at organisations where a work–family supportive intervention was implemented. This effect, however, was not explained by specific targets of the intervention, but other psychosocial pathways related to the work–family interface.Trial registration numberNCT02050204; results.
Optimal planting date, row width, and critical weed-free period for grain amaranth and quinoa grown in Ontario, Canada
Authors: Nurse Robert E. , Obeid Kristen , Page Eric R. 
Published: May 2016

The popularity of grain amaranth and quinoa is growing in Ontario, increasing the interest in their cultivation. Two experiments were conducted in southern Ontario in 2013 and 2014 to evaluate optimal planting date (every two weeks from early May to late July), row width (38 or 75 cm), and critical weed-free period (the component of the critical period of weed control that defines the number of days that the crop must remain weed-free to prevent yield loss) in each crop. Grain amaranth and quinoa both reached physiological maturity and produced yields when planting dates ranged from mid-May to late-June. When either crop was seeded in July, yields decreased by more than 50% and the crop did not always reach maturity before the first frost. While row width did not have an impact on yield, it is advisable to grow the crops in wider rows (75 cm) to facilitate weed control early in the growing season (up to 30 d after emergence (DAE)). The critical weed-free period was 24 and 16 DAE for grain amaranth and quinoa, respectively, after which yields were maintained at 95% of the weed-free control. Based on these data, both crops could easily be integrated into the normal cropping rotations found in southern Ontario.
Therapeutic Benefit of Selective Inhibition of p110α PI3-Kinase in Pancreatic Neuroendocrine Tumors
Authors: Soler Adriana , Figueiredo Ana M. , Castel Pau , Martin Laura , Monelli Erika , Angulo-Urarte Ana , Milà-Guasch Maria , Viñals Francesc , Baselga Jose , Casanovas Oriol , Graupera Mariona 
Published: May 2016

Abstract
Purpose: Mutations in the PI3K pathway occur in 16% of patients with pancreatic neuroendocrine tumors (PanNETs), which suggests that these tumors are an exciting setting for PI3K/AKT/mTOR pharmacologic intervention. Everolimus, an mTOR inhibitor, is being used to treat patients with advanced PanNETs. However, resistance to mTOR-targeted therapy is emerging partially due to the loss of mTOR-dependent feedback inhibition of AKT. In contrast, the response to PI3K inhibitors in PanNETs is unknown.
Experimental Design: In the current study, we assessed the frequency of PI3K pathway activation in human PanNETs and in RIP1-Tag2 mice, a preclinical tumor model of PanNETs, and we investigated the therapeutic efficacy of inhibiting PI3K in RIP1-Tag2 mice using a combination of pan (GDC-0941) and p110α-selective (GDC-0326) inhibitors and isoform-specific PI3K kinase-dead–mutant mice.
Results: Human and mouse PanNETs showed enhanced pAKT, pPRAS40, and pS6 positivity compared with normal tissue. Although treatment of RIP1-Tag2 mice with GDC-0941 led to reduced tumor growth with no impact on tumor vessels, the selective inactivation of the p110α PI3K isoform, either genetically or pharmacologically, reduced tumor growth as well as vascular area. Furthermore, GDC-0326 reduced the incidence of liver and lymph node metastasis compared with vehicle-treated mice. We also demonstrated that tumor and stromal cells are implicated in the antitumor activity of GDC-0326 in RIP1-Tag2 tumors.
Conclusions: Our data provide a rationale for p110α-selective intervention in PanNETs and unravel a new function of this kinase in cancer biology through its role in promoting metastasis. Clin Cancer Res; 22(23); 5805–17. ©2016 AACR.
Initial Experience With High-Risk Patients Excluded From Clinical Trials
Authors: Barakat Amr F. , Hussein Ayman A. , Saliba Walid I. , Bassiouny Mohammed , Tarakji Khaldoun , Kanj Mohamed , Jaber Wael , Rodriguez L. Leonardo , Grimm Richard , Hussain M. Shazam , Russman Andrew , Uchino Ken , Wisco Dolora , Rasmussen Peter , Bain Mark , Vargo John , Zuccaro Gregory , Gottesman David , Lindsay Bruce D. , Wazni Oussama M. 
Published: May 2016

Background—
The implantation of left atrial appendage closure device (WATCHMAN, Boston Scientific, Natick, MA) is an alternative option to oral anticoagulation (OAC) for stroke prevention in atrial fibrillation. Patients require short-term OAC after implantation to avoid device thrombosis. The 2 clinical trials that assessed this device excluded patients thought not to be candidates for OAC. As such, little is known about the safety of this strategy in patients with previous major bleeding events.

Methods and Results—

All 20 consecutive patients with history of spontaneous major bleeding while on OAC who had subsequently undergone WATCHMAN device implantation at our institution were included. A newly conceived multidisciplinary Atrial Fibrillation Stroke Prevention Center evaluated patients for candidacy for device implantation and subsequent antithrombotic therapy. The primary outcome was spontaneous major bleeding while receiving short-term postprocedural OAC. Median CHA
2
DS
2
-VASc and HAS-BLED scores were 5 (quartiles 5–6) and 5 (quartiles 4–5), respectively. Previous major bleeding events were major gastrointestinal bleeding, intracranial bleeding, spontaneous hemopericardium with cardiac tamponade, and hemarthrosis in 11, 7, 1, and 1 patients, respectively. None of the patients had spontaneous major bleeding during the course of OAC after device implantation. In 1 patient, OAC was discontinued after 40 days because of mechanical fall with head trauma resulting in subdural hematoma with no associated neurological deficits; this was managed conservatively.

Conclusions—
With careful multidisciplinary evaluation, a short course of OAC after WATCHMAN device implantation in patients with previous spontaneous major bleeding events is associated with low risk of recurrent spontaneous major bleeding.
Relationship Between Femoral Vascular Closure Devices and Short-Term Mortality From 271 845 Percutaneous Coronary Intervention Procedures Performed in the United Kingdom Between 2006 and 2011
Authors: Farooq Vasim , Goedhart Dick , Ludman Peter , de Belder Mark A. , Harcombe Alun , El-Omar Magdi 
Published: May 2016

Background—
The impact of vascular closure devices (VCDs) via the femoral arterial access site on short-term mortality in patients undergoing percutaneous coronary intervention is currently unknown.

Methods and Results—

The association between femoral arterial vascular access site management (manual pressure [including external clamp] versus VCD) and 30-day mortality was examined in a national real-world registry of 271 845 patients undergoing percutaneous coronary intervention for elective, non–ST-segment–elevation myocardial infarction and ST-segment–elevation myocardial infarction indications in the United Kingdom between 2006 and 2011. Crude and propensity score–corrected analyses were performed using Cox regression, with additional analyses undertaken in clinically relevant subgroups; 40.1% (n=109 001) of subjects were treated with manual pressure and 59.9% (n=162 844) with VCD. Subjects treated with VCD had fewer comorbidities and were less likely to present with ST-segment–elevation myocardial infarction and cardiogenic shock (
P
<0.001). Crude 30-day mortality was lower in the group treated with VCD compared with manual pressure (hazard ratio [HR], 0.58; 95% confidence interval [CI], 0.54–0.61; 1.4% versus 2.4%, log rank
P
<0.0001), findings that were substantially reduced but persisted after propensity score correction (HR, 0.91; 95% CI, 0.86–0.97; 1.8% versus 2.0% versus
P
<0.001). A more pronounced association of VCD with a reduction in 30-day mortality was evident in females (HR, 0.85; 95% CI, 0.77–0.94;
P
interaction
=0.037), presentation with acute coronary syndrome (HR, 0.88; 95% CI, 0.83–0.94;
P
interaction
=0.0027), or recent lysis (HR, 0.63; 95% CI, 0.40–1.01;
P
interaction
=0.0001).

Conclusions—
When compared with manual pressure, VCD was associated with a minor short-term (30-day) prognostic benefit after propensity score correction in the global population and clinically relevant subgroups. The potential for residual confounding factors impacting on short-term mortality cannot be excluded, despite the study having measured and balanced all recorded confounder factors.
A Diagram is a Trivial Machine
Authors: Asef Mario 
Published: May 2016

Abstract
I generate diagrams with the purpose of understanding the narratives, form, and aesthetics of sociocultural and political structures. This leaves room for the production of artistic works that can be introduced into the machinery of everyday life. The idea of the diagram emerged almost at the same time as the idea of the machine, although we cannot really tell which existed first. However, it seems clear that both are intrinsically connected. Machines and diagrams can be seen as a representation of a narrative system that leads the process of the creation of knowledge. What they share is essentially narrative: we create machines using diagrammatic narratives, and with those same narratives, we create knowledge. Narratives are the real machines.
Reconstructing the development of the aspect marker te ‘to acquire’ in Southwestern Yuè: a missing link between Yuè and Hakka
Authors: Kwok Bit-Chee 
Published: May 2016

This paper provides a synchronic description and reconstructs the developmental pathway of the aspect marker te in four Southwestern Yuè dialects of Chinese, located in far western Guǎngdōng. Synchronically, te functions as a perfective aspect marker and a perfect aspect marker (similar to Mandarin Chinese le but different from Cantonese zo). Diachronically, te is believed to have been transferred from the neighboring Hakka dialects through substratum influence. We argue that te is grammaticalized from the verb dé 得 ‘to acquire,’ of the Hakka dialects. This study reveals that the aspectual use of te is an essential part of a missing link between Yuè and Hakka. Cet article offre des descriptions synchroniques et reconstruit la voie de développement du marqueur aspectuel te dans quatre dialectes chinois de Yuè du sud-ouest, qui se trouvent à l’extrême-ouest de la province de Guǎngdōng. Synchroniquement, te fonctionne à la fois comme un marquer aspectuel du perfectif et du parfait (comparable à le en chinois mandarin mais différent du zo en cantonais). Diachroniquement, nous pensons que te a été emprunté des dialectes voisins de Hakka, et ainsi subi d’une influence de substrat. Nous argumentons en faveur de l’origine Hakka de te : il est grammaticalisé du verbe dé 得 qui signifie ‘acquérir’ dans les dialectes Hakka. Cette étude révèle que l'usage aspectuel de te joue un rôle essentiel du lien manquant entre les groupes dialectaux de Yuè et Hakka.