bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continental‐level population differentiation and environmental adaptation in the mushroom Suillus brevipes
Authors: Branco Sara , Bi Ke , Liao Hui‐Ling , Gladieux Pierre , Badouin Hélène , Ellison Christopher E. , Nguyen Nhu H. , Vilgalys Rytas , Peay Kabir G. , Taylor John W. , Bruns Thomas D. 
Published: October 2016

AbstractRecent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large‐scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation.
In vitro cell culture system optimization of keratinocytes from oral lichen planus (OLP) patients
Authors: Cao T , Zhang H , Zhou L , Wang Y , Du G , Yao H , Wang Y , Luo Q , Chen F , Wang W , Tang G 
Published: October 2016

ObjectivesThe aim of this study was to optimize the culture system of keratinocytes obtained from patients with oral lichen planus (OLP) and verify whether this model could simulate the local inflammatory environment of OLP.Materials and methodsKeratinocytes were isolated from 48 patients with OLP and cultured in vitro. The ultrastructure of OLP keratinocytes was observed via electron microscopy. The expression of pancytokeratin and vimentin was determined by immunohistochemistry, and the proliferation of OLP keratinocytes was measured by CCK‐8 assay. Immunofluorescence staining was used to detect TLR4 and NF‐κB p65 expression, and the levels of IL‐1β, IL‐6, and TNF‐α in the supernatant were measured by ELISA.ResultsWhen seeded in plates precoated with recombinant human type‐1 collagen, keratinocytes isolated from patients who received systemic antifungal treatment and were younger than 40 years were more successful to be cultured in vitro. Characteristic pancytokeratin was expressed in almost all OLP keratinocytes. Compared with normal oral keratinocytes, OLP keratinocytes demonstrated higher levels of TLR4/NF‐κB p65 and inflammatory cytokines, including IL‐1β, IL‐6, and TNF‐α.ConclusionsWe successfully optimized the culture system of OLP keratinocytes,which mimicked the local inflammatory environment of OLP and may be used as a cell model of OLP.
Parturition effects on reproductive health in the gilt and sow
Authors: Peltoniemi OAT , Björkman S , Oliviero C 
Published: October 2016

ContentsIn this review, we address significant characteristics of parturition in the pig and their connection to post‐partum reproductive health and fertility. We discuss the normal physiology and behaviour around parturition and the effect of the second phase (expulsion of foetuses) on the third phase of parturition (expulsion of foetal membranes). In addition, we intend to cover retained placenta, and the connection to post‐partum uterine health and fertility in the contemporary prolific sow. We also explore factors that support successful parturition or can cause potential problems. Successful parturition in the pig includes the possibility to express adequate maternal behaviour, rapid expulsion of the piglets, complete expulsion of the placenta, neonatal activity and colostrum intake. Abnormal incidents during any phase of parturition can cause subsequent problems. Duration of the expulsion phase of foetuses can be used as a simple measure of whether parturition is considered successful. Prolonged parturition can impair health of the sow and piglet and fertility after weaning. New insights, such as adding more fibre to sow diets during pregnancy, and especially during the period prior to farrowing, may prevent constipation, increase water intake of the sow around parturition and increase milk intake and performance of piglets. Maternal characteristics, including maternal behaviour, ease of parturition, colostrum production and piglet quality parameters, may be utilized to improve success rate of reproductive management during farrowing and early lactation. Additionally, we share some of the recent developments in methods, including ultrasonography in evaluation of post‐partum uterine health. In conclusion, successful farrowing is of the greatest importance for reproductive health of the sow and survival of the piglets. We suggest connections exist among prolonged farrowing and yield of colostrum, retained placenta, development of PDS, and impaired involution of the uterus and reduced subsequent fertility.
Heritage in New Town Extensions: Recent Dutch Experiences in the use of Heritage in Large New Building EstatesThis paper is an elaboration of one part of the author's inaugural lecture, that was published as a Dutch‐language brochure (Renes ).
Authors: Renes J. 
Published: October 2016

ABSTRACTHeritage has become a major theme in Dutch spatial planning. A number of recent Dutch urban extension projects offer interesting case studies on the integration of heritage into planning. The projects were part of a large housing programme, known as the Vinex programme, which was initiated by the Dutch national government but executed by local authorities. They therefore provide interesting cases for comparison. This paper presents a number of these projects, focusing on the use of heritage, which allows us to classify different ways of incorporating heritage into plans: integration, embeddedness and isolation. Another classification involves different views and interpretations about heritage, and describes diminishing degrees of authenticity entailed in preservation, transformation and inspiration. Combining both types of classification may offer a framework for further research on the relationship between heritage and planning.
Assessment of tear film osmolarity using the TearLab™ osmometer in normal dogs and dogs with keratoconjunctivitis sicca
Authors: Sebbag Lionel , Park Shin Ae , Kass Philip H. , Maggs David J. , Attar Mayssa , Murphy Christopher J. 
Published: October 2016

AbstractObjectiveTo evaluate repeatability and reproducibility of tear osmolarity measured using the TearLab™ osmometer in normal dogs and to assess its diagnostic potential in dogs with keratoconjunctivitis sicca (KCS).Animals studiedBeagle dogs; six normal and five with KCS.ProceduresTear osmolarity and Schirmer tear test‐1 (STT‐1) values were obtained at various times. Normal dogs were assessed for diurnal variation and repeatability and reproducibility of measurements. Dogs with KCS were evaluated before and after 5 months’ topical twice‐daily therapy with 2% cyclosporine.ResultsMean ± SD tear osmolarity (mOsm/L) was significantly higher in normal dogs (337.4 ± 16.2) than in dogs with KCS before therapy (306.2 ± 18.0; P < 0.0001), but not following therapy with 2% cyclosporine (330.5 ± 13.7; P = 1.00). Osmolarity readings lower than 325.5 mOsm/L were suggestive of KCS (84.8% sensitivity and 87.1% specificity). In normal dogs, tear osmolarity readings were stable during the daytime (P = 0.99). Repeated measurements revealed high variability and typically poor‐to‐moderate repeatability and reproducibility, although this was improved by taking three successive measurements at each session. Considering combined data from all dogs, a positive correlation existed between STT‐1 and tear osmolarity measurements (Pearson's correlation test, P = 0.04, r = 0.62).ConclusionsCanine tear osmolarity as determined by TearLab™ osmometer was variable, required multiple readings to be informative, and differed from values reported for humans. Dogs with KCS had a lower tear osmolarity than did normal dogs, and this increased following cyclosporine therapy.
Clinical Laboratory Testing in the Era of Directly Acting Antiviral Therapies for Hepatitis C
Authors: Wilson Eleanor M. , Rosenthal Elana S. , Kattakuzhy Sarah , Tang Lydia , Kottilil Shyam 
Published: October 2016

SUMMARY
Directly acting antiviral (DAA) combination therapies for chronic hepatitis C virus (HCV) infection are highly effective, but treatment decisions remain complex. Laboratory testing is important to evaluate a range of viral, host, and pharmacological factors when considering HCV treatment, and patients must be monitored during and after therapy for safety and to assess the viral response. In this review, we discuss the laboratory tests relevant for the treatment of HCV infection in the era of DAA therapy, grouped according to viral and host factors.
Cost Analysis of Implementing Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Plus Real-Time Antimicrobial Stewardship Intervention for Bloodstream Infections
Authors: Patel Twisha S. , Kaakeh Rola , Nagel Jerod L. , Newton Duane W. , Stevenson James G. 
Published: October 2016

ABSTRACT

Studies evaluating rapid diagnostic testing plus stewardship intervention have consistently demonstrated improved clinical outcomes for patients with bloodstream infections. However, the cost of implementing new rapid diagnostic testing can be significant, and such testing usually does not generate additional revenue. There are minimal data evaluating the impact of adding matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for rapid organism identification and dedicating pharmacy stewardship personnel time on the total hospital costs. A cost analysis was performed utilizing patient data generated from the hospital cost accounting system and included additional costs of MALDI-TOF equipment, supplies and personnel, and dedicated pharmacist time for blood culture review and of making interventions to antimicrobial therapy. The cost analysis was performed from a hospital perspective for 3-month blocks before and after implementation of MALDI-TOF plus stewardship intervention. A total of 480 patients with bloodstream infections were included in the analysis: 247 in the preintervention group and 233 in the intervention group. Thirty-day mortality was significantly improved in the intervention group (12% versus 21%,
P
< 0.01), and the mean length of stay was reduced, although the difference was not statistically significant (13.0 ± 16.5 days versus 14.2 ± 16.7 days,
P
= 0.44). The total hospital cost per bloodstream infection was lower in the intervention group ($42,580 versus $45,019). Intensive care unit cost per bloodstream infection accounted for the largest share of the total costs in each group and was also lower in the intervention group ($10,833 versus $13,727). Implementing MALDI-TOF plus stewardship review and intervention decreased mortality for patients with bloodstream infections. Despite the additional costs of implementing MALDI-TOF and of dedicating pharmacy stewardship personnel time to interventions, the total hospital costs decreased by $2,439 per bloodstream infection, for an approximate annual cost savings of $2.34 million.
Prospective Biomarker Screening for Diagnosis of Invasive Aspergillosis in High-Risk Pediatric Patients
Authors: Loeffler Juergen , Hafner Julia , Mengoli Carlo , Wirth Clemens , Heussel Claus Peter , Löffler Claudia , White P. Lewis , Ullmann Andrew J. , Michel Denise , Wiegering Verena , Wölfl Matthias , Schlegel Paul Gerhardt , Einsele Hermann , Springer Jan , Eyrich Matthias 
Published: October 2016

ABSTRACT

Combined biomarker screening is increasingly used to diagnose invasive aspergillosis (IA) in high-risk patients. In adults, the combination of galactomannan (GM) and fungal DNA detection has proven to be beneficial in the diagnosis of IA. Data in purely pediatric cohorts are scarce. Here, we monitored 39 children shortly before and after allogeneic stem cell transplantation twice weekly by use of a commercial GM enzyme-linked immunosorbent assay (ELISA) and a PCR assay based on amplification of the pan-
Aspergillus
ITS1/5.8S ribosomal operon. In addition, clinical data were recorded and classification of IA was performed according to the European Organization for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) criteria. Among the 39 high-risk children, we identified 4 patients (10.3%) with probable and 2 (5.1%) with possible IA. All patients with probable IA were repeatedly positive for both tests (means of 9.5 and 6.8 positive GM and PCR samples, respectively), whereas both possible IA cases were detected by PCR. The sensitivity and specificity were, respectively, 67% and 89% for GM and 100% and 63% for PCR. Positive and negative predictive values were, respectively, 50% and 100% for GM and 27% and 100% for PCR. For the combined testing approach, both values were 100%. The number of positive samples seemed to be lower in patients undergoing antifungal therapy. Sporadically positive tests occurred in 12% (GM) and 42% (PCR) of unclassified patients. In summary, our data show that combined monitoring for GM and fungal DNA also results in a high diagnostic accuracy in pediatric patients. Future studies have to determine whether combined testing is suitable for early detection of subclinical disease and how antifungal prophylaxis impacts assay performance.
Influenza A Viruses of Swine (IAV-S) in Vietnam from 2010 to 2015: Multiple Introductions of A(H1N1)pdm09 Viruses into the Pig Population and Diversifying Genetic Constellations of Enzootic IAV-S
Authors: Takemae Nobuhiro , Harada Michiyo , Nguyen Phuong Thanh , Nguyen Tung , Nguyen Tien Ngoc , To Thanh Long , Nguyen Tho Dang , Pham Vu Phong , Le Vu Tri , Do Hoa Thi , Vo Hung Van , Le Quang Vinh Tin , Tran Tan Minh , Nguyen Thanh Duy , Thai Phuong Duy , Nguyen Dang Hoang , Le Anh Quynh Thi , Nguyen Diep Thi , Uchida Yuko , Saito Takehiko 
Published: October 2016

ABSTRACT
Active surveillance of influenza A viruses of swine (IAV-S) involving 262 farms and 10 slaughterhouses in seven provinces in northern and southern Vietnam from 2010 to 2015 yielded 388 isolates from 32 farms; these viruses were classified into H1N1, H1N2, and H3N2 subtypes. Whole-genome sequencing followed by phylogenetic analysis revealed that the isolates represented 15 genotypes, according to the genetic constellation of the eight segments. All of the H1N1 viruses were entirely A(H1N1)pdm09 viruses, whereas all of the H1N2 and H3N2 viruses were reassortants among 5 distinct ancestral viruses: H1 and H3 triple-reassortant (TR) IAV-S that originated from North American pre-2009 human seasonal H1, human seasonal H3N2, and A(H1N1)pdm09 viruses. Notably, 93% of the reassortant IAV-S retained M genes that were derived from A(H1N1)pdm09, suggesting some advantage in terms of their host adaptation. Bayesian Markov chain Monte Carlo analysis revealed that multiple introductions of A(H1N1)pdm09 and TR IAV-S into the Vietnamese pig population have driven the genetic diversity of currently circulating Vietnamese IAV-S. In addition, our results indicate that a reassortant IAV-S with human-like H3 and N2 genes and an A(H1N1)pdm09 origin M gene likely caused a human case in Ho Chi Minh City in 2010. Our current findings indicate that human-to-pig transmission as well as cocirculation of different IAV-S have contributed to diversifying the gene constellations of IAV-S in Vietnam.

IMPORTANCE
This comprehensive genetic characterization of 388 influenza A viruses of swine (IAV-S) isolated through active surveillance of Vietnamese pig farms from 2010 through 2015 provides molecular epidemiological insight into the genetic diversification of IAV-S in Vietnam after the emergence of A(H1N1)pdm09 viruses. Multiple reassortments among A(H1N1)pdm09 viruses and enzootic IAV-S yielded 14 genotypes, 9 of which carried novel gene combinations. The reassortants that carried M genes derived from A(H1N1)pdm09 viruses became predominant, replacing those of the IAV-S that had been endemic in Vietnam since 2011. Notably, one of the novel reassortants likely caused a human case in Vietnam. Given that Vietnam is the second-largest pig-producing country in Asia, continued monitoring of IAV-S is highly important from the viewpoints of both the swine industry and human public health.
An
In Vitro
RNA Synthesis Assay for Rabies Virus Defines Ribonucleoprotein Interactions Critical for Polymerase Activity
Authors: Morin Benjamin , Liang Bo , Gardner Erica , Ross Robin A. , Whelan Sean P. J. 
Published: October 2016

ABSTRACT

We report an
in vitro
RNA synthesis assay for the RNA-dependent RNA polymerase (RdRP) of rabies virus (RABV). We expressed RABV large polymerase protein (L) in insect cells from a recombinant baculovirus vector and the phosphoprotein cofactor (P) in
Escherichia coli
and purified the resulting proteins by affinity and size exclusion chromatography. Using chemically synthesized short RNA corresponding to the first 19 nucleotides (nt) of the rabies virus genome, we demonstrate that L alone initiates synthesis on naked RNA and that P serves to enhance the initiation and processivity of the RdRP. The L-P complex lacks full processivity, which we interpret to reflect the lack of the viral nucleocapsid protein (N) on the template. Using this assay, we define the requirements in P for stimulation of RdRP activity as residues 11 to 50 of P and formally demonstrate that ribavirin triphosphate (RTP) inhibits the RdRP. By comparing the properties of RABV RdRP with those of the related rhabdovirus, vesicular stomatitis virus (VSV), we demonstrate that both polymerases can copy the heterologous promoter sequence. The requirements for engagement of the N-RNA template of VSV by its polymerase are provided by the C-terminal domain (CTD) of P. A chimeric RABV P protein in which the oligomerization domain (OD) and the CTD were replaced by those of VSV P stimulated RABV RdRP activity on naked RNA but was insufficient to permit initiation on the VSV N-RNA template. This result implies that interactions between L and the template N are also required for initiation of RNA synthesis, extending our knowledge of ribonucleoprotein interactions that are critical for gene expression.

IMPORTANCE
The current understanding of the structural and functional significance of the components of the rabies virus replication machinery is incomplete. Although structures are available for the nucleocapsid protein in complex with RNA, and also for portions of P, information on both the structure and function of the L protein is lacking. This study reports the expression and purification of the full-length L protein of RABV and the characterization of its RdRP activity
in vitro
. The study provides a new assay that has utility for screening inhibitors and understanding their mechanisms of action, as well as defining new interactions that are required for RdRP activity.
Pivotal Role of Receptor-Interacting Protein Kinase 1 and Mixed Lineage Kinase Domain-Like in Neuronal Cell Death Induced by the Human Neuroinvasive Coronavirus OC43
Authors: Meessen-Pinard Mathieu , Le Coupanec Alain , Desforges Marc , Talbot Pierre J. 
Published: October 2016

ABSTRACT

Human coronaviruses (HCoV) are respiratory pathogens with neuroinvasive, neurotropic, and neurovirulent properties, highlighting the importance of studying the potential implication of these viruses in neurological diseases. The OC43 strain (HCoV-OC43) was reported to induce neuronal cell death, which may participate in neuropathogenesis. Here, we show that HCoV-OC43 harboring two point mutations in the spike glycoprotein (rOC/U
s183–241
) was more neurovirulent than the wild-type HCoV-OC43 (rOC/ATCC) in mice and induced more cell death in murine and human neuronal cells. To evaluate the role of regulated cell death (RCD) in HCoV-OC43-mediated neural pathogenesis, we determined if knockdown of Bax, a key regulator of apoptosis, or RIP1, a key regulator of necroptosis, altered the percentage of neuronal cell death following HCoV-OC43 infection. We found that Bax-dependent apoptosis did not play a significant role in RCD following infection, as inhibition of Bax expression mediated by RNA interference did not confer cellular protection against the cell death process. On the other hand, we demonstrated that RIP1 and MLKL were involved in neuronal cell death, as RIP1 knockdown and chemical inhibition of MLKL significantly increased cell survival after infection. Taken together, these results indicate that RIP1 and MLKL contribute to necroptotic cell death after HCoV-OC43 infection to limit viral replication. However, this RCD could lead to neuronal loss in the mouse CNS and accentuate the neuroinflammation process, reflecting the severity of neuropathogenesis.

IMPORTANCE
Because they are naturally neuroinvasive and neurotropic, human coronaviruses are suspected to participate in the development of neurological diseases. Given that the strain OC43 is neurovirulent in mice and induces neuronal cell death, we explored the neuronal response to infection by characterizing the activation of RCD. Our results revealed that classical apoptosis associated with the Bax protein does not play a significant role in HCoV-OC43-induced neuronal cell death and that RIP1 and MLKL, two cellular proteins usually associated with necroptosis (an RCD back-up system when apoptosis is not adequately induced), both play a pivotal role in the process. As necroptosis disrupts cellular membranes and allows the release of damage-associated molecular patterns (DAMP) and possibly induces the production of proinflammatory cytokines, it may represent a proinflammatory cell death mechanism that contributes to excessive neuroinflammation and neurodegeneration and eventually to neurological disorders after a coronavirus infection.
The Long and Complicated Relationship between Epstein-Barr Virus and Epithelial Cells
Authors: Hutt-Fletcher Lindsey M. 
Published: October 2016

ABSTRACT
The roles of epithelial cells in infection and persistence of the Epstein-Barr virus (EBV) have long been difficult to resolve. However, recent developments have reinforced the conclusion that these cells are a major site of virus replication and raised the possibility that, like papillomaviruses, EBV has evolved to take advantage of epithelial differentiation to ensure survival, persistence, and spread.