bluuebunny/crossref_metadata_2025 huggingface dataset:
Supply‐Chain Research Opportunities with the Poor as Suppliers or Distributors in Developing Countries
Authors: Sodhi ManMohan S. , Tang Christopher S.
Published: August 2013

Many social enterprises and some companies have developed supply chains with the poor as suppliers or distributors to alleviate poverty and to create revenues for themselves. Such supply chains have created new research opportunities because they raise issues fundamentally different from those examined in the existing operations management literature. We report this phenomenon of supply chains with the poor as suppliers or distributors in developing countries and identify operations management (OM) research opportunities. We also provide some stylized models to serve as potential seeds for modeling‐based research in this area.
Browse‐and‐Switch: Retail‐Online Competition under Value Uncertainty
Authors: Balakrishnan Anantaram , Sundaresan Shankar , Zhang Bo
Published: August 2013

Although online shopping is becoming popular, consumers who are unsure about whether to buy a product may find it advantageous to visit a brick‐and‐mortar retail store to first examine the product before purchasing it. But, after browsing at the store, consumers have the option of switching to an e‐tailer to purchase the item at a cheaper price rather than buying at the store. Recent business press refers to this browse‐and‐switch behavior as “showrooming,” and attributes to it the declining profits of brick‐and‐mortar retailers. To study the effect of the browse‐and‐switch option on retail and online pricing strategies and profits, we analyze a stylized economic model that incorporates uncertainty in consumers' valuation of the product, captures the heterogeneity among consumers in their inclination to purchase online, and permits product returns. We consider various equilibrium scenarios for different combinations of consumer shopping behaviors, characterize the parameter ranges for each scenario, and demonstrate that browse‐and‐switch behavior can indeed occur under equilibrium. Our analysis further shows that the option for consumers to browse‐and‐switch intensifies competition, reducing the profits for both firms.
A stock‐and‐flow simulation model of the US blood supply
Authors: Simonetti Arianna , Forshee Richard A. , Anderson Steven A. , Walderhaug Mark
Published: August 2013

Background

Lack of reporting requirements for the amount of blood stored in blood banks and hospitals poses challenges to effectively monitor the US blood supply. Effective strategies to minimize collection and donation disruptions in the supply require an understanding of the daily amount of blood available in the system.

Study Design and Methods

A stock‐and‐flow simulation model of the US blood supply was developed to obtain estimates of the daily on‐hand availability of blood, with uncertainty and by ABO/Rh type. The model simulated potential impact on supply of using different blood management practices for transfusion: first in‐first out (FIFO), using the oldest stored red blood cell units first; non‐FIFO likely oldest, preferentially selecting older blood; and non‐FIFO likely newest, preferentially selecting younger blood.

Results

Simulation results showed higher estimates of the steady‐state of the blood supply level for FIFO (1,630,000 units, 95% prediction interval [PI] 1,610,000‐1,650,000) than non‐FIFO scenarios (likely oldest, 1,530,000 units, 95% PI 1,500,000‐1,550,000; and likely newest, 1,190,000 units, 95% PI 1,160,000‐1,220,000), either for overall blood or by blood types.

Conclusion

To our knowledge, this model represents a first attempt to evaluate the impact of different blood management practices on daily availability and distribution of blood in the US blood supply. The average storage time before blood is being issued was influenced by blood management practices, for preferences of blood that is younger and also that use specific blood types. The model also suggests which practice could best approximate the current blood management system and may serve as useful tool for blood management.
A comprehensive survey of both RHD and RHCE allele frequencies in sub‐Saharan Africa
Authors: Granier Thomas , Beley Sophie , Chiaroni Jacques , Bailly Pascal , Silvy Monique
Published: August 2013

Background

The RH system is one of the most polymorphic blood group systems with numerous allele variants affecting Rh polypeptides expression. This complexity is at the origin of difficulties for transfusion of African patients especially sickle cell disease patients requiring chronic transfusion therapy with high risk of immunization. As a complete survey of RH variants is lacking in African populations, we performed red blood cell genotyping to determine the type and frequency of RHD and RHCE alleles in sub‐Saharan African populations.

Study Design and Methods

A total of 347 blood samples were collected from individuals of six nonpygmoid and three pygmoid populations. RH typing was performed using two single‐tube multiplex polymerase chain reaction amplifications (BioArray Solutions, Immucor).

Results

All six sub‐Saharan nonpygmoid populations exhibited constant variety in both type and frequency of aberrant RHD and RHCE alleles. Predicted partial RH1 (1.8%) and RH5 (0.9%) phenotypes were less than expected. Conversely, predicted partial phenotype RH2 (5.5%) was frequent. Data confirmed the high frequency of samples positive for the non–clinically significant RH10/RH20 antigens (39.5%) and revealed a high frequency of RH54 (DAK, 8.1%). The pygmoid groups showed higher percentages of predicted partial RH antigens and greater heterogeneity reflecting wide genetic differentiation.

Conclusion

Our data show that frequencies of aberrant RHD and RHCE alleles were similar, irrespective of location and ethnicity. In view of the predicted frequencies and relative clinical significance of both private antigens and high‐prevalence antigens absent, the most relevant assays for individuals of African descent in a transfusion setting are for 1) partial RH2 in the patient and 2) RH54 (DAK) in the donor.
The Motion Constants of Linear Autonomous Dynamical Systems
Authors: Sinclair Andrew J. , Hurtado John E.
Published: August 2013

The time-independent integrals, here referred to as motion constants, for general nth-order linear autonomous systems are developed. Although it is commonly believed that this topic has been fully addressed, close inspection of the literature reveals that a comprehensive development is missing. This paper provides a complete tutorial treatment of the calculation of these motion constants. The process involves a state transformation to a canonical form of uncoupled real subsystems. Following this, motion constants that are internal to each subsystem are found, after which motion constants that connect the subsystems to each other are computed. Complete sets of n − 1 real single-valued motion constants can be formed for all linear autonomous systems with a single exception. The exception is systems composed of undamped oscillators whose frequency ratio is irrational. Such systems are known to exhibit ergodic behavior and lack a number of analytic motion constants.
Thermal barrier coating deposition by rarefied gas jet assisted processes: Simulations of deposition on a stationary airfoil
Authors: Rodgers Theron M. , Zhao Hengbei , Wadley Haydn N. G.
Published: August 2013

The uniform coating of a complex shaped substrate, such as a gas turbine airfoil, by collisionless physical vapor deposition processes requires rotation/translation of the substrate or sources and is inconceivable for regions on the substrate that are never in the line-of-sight of the vapor source. Recently developed directed vapor deposition processes use electron beam evaporation and inert gas jets to entrain, transport, and deposit metal oxide vapor in an environment where many vapor atom collisions occur prior to deposition. Direct simulation Monte Carlo simulations and experimental depositions of a rare earth modified thermal barrier coating are used to investigate fundamental aspects of the deposition process, including coating thickness and column orientation, over the surface of a nonrotated model airfoil substrate with substantial non-line-of-sight regions. The coating thickness uniformity was found to depend on the deposition chamber pressure and the pressure ratio between the low-pressure deposition chamber and high-pressure reservoir upstream of the gas jet forming nozzle. Under slow flow conditions, significant coating of the non-line-of-sight regions was possible. The growth column orientation is found to also vary over the substrate surface due to changes in the local incidence angle distribution of depositing vapor atoms. The variation in growth column orientation is not predictable by the Tangent rule widely used for predicting columnar growth orientation in physical vapor deposition processes.
Strain induced microstructural and ordering behaviors of epitaxial Fe38.5Pd61.5 films grown by pulsed laser deposition
Authors: Steiner Matthew A. , Comes Ryan B. , Floro Jerrold A. , Soffa William A. , Fitz-Gerald James M. , Smentkowski Vincent S.
Published: August 2013

Epitaxialfilms of Fe38.5Pd61.5 at the L10-L12 eutectoid composition have been grown on MgO(001) oriented substrates by pulsed laser deposition. The effect of deposition temperature on the magnetic,microstructural, and crystallographic natures of these films are discussed. The films in this study exhibit atomic ordering with increasing deposition temperature, transitioning from the disordered face centered cubic (FCC)phase to an L12 ordered phase, which is tetragonally distorted due to epitaxial strain. This distortion leads to a perturbation in the Fe occupancy of the Pd superlattice sites at nonstoichiometric compositions. Additionally,Fe38.5Pd61.5filmsgrown at 550 °C have been found in an unique two-phase microstructure of prismatic, Fe60Pd40disordered FCC secondary phases with 10–100 nm facets oriented along the ⟨110⟩ substrate directions,embedded within a nearly stoichiometric ordered L12-Fe27Pd73matrix. These secondary phase precipitates exhibit single domain magnetic axis rotation, while the ordered L12 matrix has a magnetic easy axis aligned in-plane.
Social Learning of Migratory Performance
Authors: Mueller Thomas , O’Hara Robert B. , Converse Sarah J. , Urbanek Richard P. , Fagan William F.
Published: August 2013

Follow the Leader

How birds migrate between wintering and breeding grounds, often over thousands of kilometers through difficult conditions, remains mysterious. The recovery of North American Whooping Cranes by release of captive-reared birds trained to migrate by following aircraft provided an opportunity for

Mueller
et al.

(p.
999
; see the cover) to analyze 8 years of data for individual birds. The presence of older birds within a group of migrating cranes significantly decreased the deviations the flock took from a straight line migration path. The lack of evidence for a genetic component indicates that social learning dominates any innate capacity in developing migratory behavior.
Paleofluvial Mega-Canyon Beneath the Central Greenland Ice Sheet
Authors: Bamber Jonathan L. , Siegert Martin J. , Griggs Jennifer A. , Marshall Shawn J. , Spada Giorgio
Published: August 2013

Ice Lubricant

The Greenland and Antarctic ice sheets both possess hydrological systems that allow water accumulating from the melting of surface ice to be transported to the base of the ice sheet. If that water, when it reaches the ice-bedrock interface, is distributed over large areas, it will lubricate rapid ice sheet flow toward the sea.

Bamber
et al.

(p.
997
) report the existence of a large, 750-km-long subglacial canyon in northern Greenland, which may act as a channel for the transport of basal meltwater to the margin of the ice sheet and thus influence overall ice sheet dynamics.
Reaction of O
2
with Subsurface Oxygen Vacancies on TiO
2
Anatase (101)
Authors: Setvín Martin , Aschauer Ulrich , Scheiber Philipp , Li Ye-Fei , Hou Weiyi , Schmid Michael , Selloni Annabella , Diebold Ulrike
Published: August 2013

Oxide Chemistry Below the Surface

Although metal oxides, such as titanium dioxide (TiO
2
), are used for catalytic oxidation reactions and photocatalysis, the O
2
does not react directly with substrates. Vacancies in the surface region of the TiO
2
rutile phase can transfer a negative charge to adsorbed O
2
to create more reactive species. By contrast, in anatase—the phase associated with nanoscale TiO
2
particles—subsurface vacancies form.

Setvin
et al.

(p.
988
) used a scanning tunneling microscopy tip to pull these vacancies to the surface in a niobiumdoped anatase crystal and followed the transformation of adsorbed O
2
−
into a peroxo species and a bridging O
2
dimer.
βCaMKII in Lateral Habenula Mediates Core Symptoms of Depression
Authors: Li Kun , Zhou Tao , Liao Lujian , Yang Zhongfei , Wong Catherine , Henn Fritz , Malinow Roberto , Yates John R. , Hu Hailan
Published: August 2013

Depression and the Habenula

The lateral habenula (LHb) appears to have a role in depression. However, the underlying mechanisms are poorly understood, and by using multiple rodent models of depression,

Li
et al.

(p.
1016
) identified a signaling pathway and associated neuronal adaptations in which the enzyme βCaMKII was selectively up-regulated in the LHb. Manipulations that enhanced βCaMKII levels increased depression-related phenotypes, and RNA interference of CaMKIIb blunted depression. Enhanced βCaMKII levels in the habenula promoted excitatory synaptic transmission on these neurons and increased action potential firing mediated by an up-regulation of a specific subtype of glutamate receptors.
Molecular Basis of Tubulin Transport Within the Cilium by IFT74 and IFT81
Authors: Bhogaraju Sagar , Cajanek Lukas , Fort Cécile , Blisnick Thierry , Weber Kristina , Taschner Michael , Mizuno Naoko , Lamla Stefan , Bastin Philippe , Nigg Erich A. , Lorentzen Esben
Published: August 2013

Cilium Conundrum

The cilium has emerged as the antenna of eukaryotic cells, having numerous functions in sensory reception and developmental signaling. Several disorders, such as polycystic kidney disease, are the result of compromised cilia structure.

Bhogaraju
et al.

(p.
1009
) elucidate how the intraflagellar transport machinery recognizes tubulin, a ciliary cargo that is integral to cilium maintenance and formation and is constantly turned over at the cilium tip.
Strength Under Tension
Authors: Bainer Russell , Weaver Valerie
Published: August 2013

Mechanical tension on a cell from its environment alters the expression of a protein that changes the physical properties of the nucleus.

[Also see Research Article by

Swift
et al.

]
NIH Effort Gambles on Mysterious Extracellular RNAs
Authors: Leslie Mitch
Published: August 2013

A $17 million research program, announced this month by the U.S. National Institutes of Health, aims to determine whether RNA molecules are deliberately released by cells as hormonelike signals—and whether such extracellular RNAs can be harnessed for diagnosis and treatment of human diseases.
A Teacher's Quest
Authors: Mervis Jeffrey
Published: August 2013

Biologist Steve Robinson is leaving a high-level White House post for a high school in New York City in a career-long quest to understand the secret behind great teaching.
Regulators Grapple With an Unorthodox Therapy
Authors: de Vrieze Jop
Published: August 2013

As fecal transplants are becoming popular, governments wonder how to respond.
Antimicrobial Nodule-Specific Cysteine-Rich Peptides Induce Membrane Depolarization-Associated Changes in the Transcriptome of Sinorhizobium meliloti
Authors: Tiricz Hilda , Szűcs Attila , Farkas Attila , Pap Bernadett , Lima Rui M. , Maróti Gergely , Kondorosi Éva , Kereszt Attila
Published: August 2013

Leguminous plants establish symbiosis with nitrogen-fixing alpha- and betaproteobacteria, collectively called rhizobia, which provide combined nitrogen to support plant growth. Members of the inverted repeat-lacking clade of legumes impose terminal differentiation on their endosymbiotic bacterium partners with the help of the nodule-specific cysteine-rich (NCR) peptide family composed of close to 600 members. Among the few tested NCR peptides, cationic ones had antirhizobial activity measured by reduction or elimination of the CFU and uptake of the membrane-impermeable dye propidium iodide. Here, the antimicrobial spectrum of two of these peptides, NCR247 and NCR335, was investigated, and their effect on the transcriptome of the natural target
Sinorhizobium meliloti
was characterized. Both peptides were able to kill quickly a wide range of Gram-negative and Gram-positive bacteria; however, their spectra were only partially overlapping, and differences were found also in their efficacy on given strains, indicating that the actions of NCR247 and NCR335 might be similar though not identical. Treatment of
S. meliloti
cultures with either peptide resulted in a quick downregulation of genes involved in basic cellular functions, such as transcription-translation and energy production, as well as upregulation of genes involved in stress and oxidative stress responses and membrane transport. Similar changes provoked mainly in Gram-positive bacteria by antimicrobial agents were coupled with the destruction of membrane potential, indicating that it might also be a common step in the bactericidal actions of NCR247 and NCR335.
Global Study of IS
6110
in a Successful Mycobacterium tuberculosis Strain: Clues for Deciphering Its Behavior and for Its Rapid Detection
Authors: Millán-Lou Maria Isabel , López-Calleja Ana Isabel , Colmenarejo Cristina , Lezcano Maria Antonia , Vitoria Maria Asunción , del Portillo Patricia , Otal Isabel , Martín Carlos , Samper Sofía
Published: August 2013

The
Mycobacterium tuberculosis
insertion sequence IS
6110
, besides being a very useful tool in molecular epidemiology, seems to have an impact on the biology of bacilli. In the present work, we mapped the 12 points of insertion of IS
6110
in the genome of a successful strain named
M. tuberculosis
Zaragoza (which has been referred to as the MTZ strain). This strain, belonging to principal genetic group 3, caused a large unsuspected tuberculosis outbreak involving 85 patients in Zaragoza, Spain, in 2001 to 2004. The mapping of the points of insertion of IS
6110
in the genome of the Zaragoza strain offers clues for a better understanding of the adaptability and virulence of
M. tuberculosis.
Surprisingly, the presence of one copy of IS
6110
was found in
Rv2286c
, as was recently described for a successful Beijing sublineage. As a result of this analysis, a rapid method for detecting this particular
M. tuberculosis
strain has been designed.
Classical Molecular Tests Using Urine Samples as a Potential Screening Tool for Human Papillomavirus Detection in Human Immunodeficiency Virus-Infected Women
Authors: Munoz Marina , Camargo Milena , Soto-De Leon Sara C. , Sanchez Ricardo , Pineda-Peña Andrea C. , Perez-Prados Antonio , Patarroyo Manuel E. , Patarroyo Manuel A.
Published: August 2013

Human papillomavirus (HPV) is the main risk factor associated with the development of cervical cancer (CC); however, there are other factors, such as immunosuppression caused by the human immunodeficiency virus (HIV), that favor progression of the illness. This study was thus aimed at evaluating the functionality of classical PCR-based molecular tests for the generic identification of HPV DNA (GP5+/GP6+, MY09/MY11, and pU1M/2R primers, individually or in combination) using cervical and urine samples from 194 HIV-positive women. Infected samples were tested with type-specific primers for six high-risk types (HPV-16, -18, -31, -33, -45, and -58) and two low-risk types (HPV-6 and -11). HPV infection prevalence rates were 70.1% for the cervical samples and 63.9% for the urine samples. HPV-16 was the most prevalent viral type in the cervical and urine samples, with higher rates of multiple infections than single infections detected in such samples. HPV DNA detection by PCR (mainly with the pU1M/2R primer set) in urine samples was positively associated with abnormal cytological findings (atypical squamous cells of undetermined significance/squamous intraepithelial lesions [ASCUS/SIL]). It was determined that the operative characteristics for detection of cytological abnormalities were similar for cervical and urine samples. This suggested using PCR for the detection of HPV DNA in urine samples as a potential screening strategy for CC prevention in future prevention and control programs along with currently implemented strategies for reducing the impact of the disease, i.e., urine samples are economical, are easy to collect, have wide acceptability among women, and have operative characteristics similar to those of cervical samples.
National Surveillance of Methicillin-Resistant Staphylococcus aureus in China Highlights a Still-Evolving Epidemiology with 15 Novel Emerging Multilocus Sequence Types
Authors: Xiao Meng , Wang He , Zhao Ying , Mao Lei-Li , Brown Mitchell , Yu Yun-Song , O'Sullivan Matthew V. N. , Kong Fanrong , Xu Ying-Chun
Published: August 2013

The global spread of methicillin-resistant
Staphylococcus aureus
(MRSA) is a serious problem, particularly in mainland China. In order to better understand the national molecular epidemiology and resistance profiles of hospital-associated MRSA (HA-MRSA) in China, a laboratory-based multicenter surveillance study was conducted. Sixty-nine hospitals in 45 large cities in 27 provinces were involved, and a total of 1,141 HA-MRSA isolates were collected during the 6-month study period in 2011. All MRSA isolates were characterized by multilocus sequence typing (MLST), staphylococcal cassette chromosome
mec
(SCC
mec
) typing,
spa
typing, detection of the Panton-Valentine leukocidin (PVL) locus (
lukS-PV
and
lukF-PV
), and antibiogram analysis. ST239-III-t030, ST239-III-t037, and ST5-II-t002 were the predominant HA-MRSA clones (overall prevalence rates, 57.1%, 12.9%, and 8.1%, respectively), although the prevalence rates of these major clones varied markedly in different administrative regions. Of note, 6.6% of the HA-MRSA isolates were found to belong to ST59, which had typical community-associated MRSA (CA-MRSA) features, including carriage of SCC
mec
type IV or V and PVL and less antimicrobial resistance than other major HA-MRSA clones. Moreover, among 36 MLST sequence types (STs) identified, 15 STs, accounting for 3.5% of total isolates, were novel. A novel ST designated ST2590, which is a single-locus variant of ST5-II-t002, was identified in three hospitals in two large cities, with a total of 17 isolates. To further monitor trends in HA-MRSA prevalence, epidemic clonal shifts, clone emergence, and transmission between community and health care settings, longitudinal national MRSA surveillance is required.
Outbreak of Extensively Drug-Resistant Acinetobacter baumannii Indigo-Pigmented Strains
Authors: Vilacoba Elisabet , Almuzara Marisa , Gulone Lucia , Rodriguez Rocio , Pallone Elida , Bakai Romina , Centrón Daniela , Ramírez María Soledad
Published: August 2013

Acinetobacter baumannii
pigmented strains are not common in clinical settings. Here, we report an outbreak caused by indigo-pigmented
A. baumannii
strains isolated in an acute care hospital in Argentina from March to September 2012. Pan-PCR assays exposed a unique pattern belonging to the recently described regional CC113
B
/CC79
P
clonal complex that confirms the relevant relationships among the indigo-pigmented
A. baumannii
strains. All of them were extensively drug resistant and harbored different genetic elements associated with horizontal genetic transfer, such as the transposon Tn
2006
, class 2 integrons, AbaR-type islands, IS
125
, IS
26
,
strA
,
strB
,
florR
, and the small recombinase IS
CR2
associated with the
sul2
gene preceded by IS
Aba1
.
Detection of Cytomegalovirus Drug Resistance Mutations by Next-Generation Sequencing
Authors: Sahoo Malaya K. , Lefterova Martina I. , Yamamoto Fumiko , Waggoner Jesse J. , Chou Sunwen , Holmes Susan P. , Anderson Matthew W. , Pinsky Benjamin A.
Published: August 2013

Antiviral therapy for cytomegalovirus (CMV) plays an important role in the clinical management of solid organ and hematopoietic stem cell transplant recipients. However, CMV antiviral therapy can be complicated by drug resistance associated with mutations in the phosphotransferase UL97 and the DNA polymerase UL54. We have developed an amplicon-based high-throughput sequencing strategy for detecting CMV drug resistance mutations in clinical plasma specimens using a microfluidics PCR platform for multiplexed library preparation and a benchtop next-generation sequencing instrument. Plasmid clones of the UL97 and UL54 genes were used to demonstrate the low overall empirical error rate of the assay (0.189%) and to develop a statistical algorithm for identifying authentic low-abundance variants. The ability of the assay to detect resistance mutations was tested with mixes of wild-type and mutant plasmids, as well as clinical CMV isolates and plasma samples that were known to contain mutations that confer resistance. Finally, 48 clinical plasma specimens with a range of viral loads (394 to 2,191,011 copies/ml plasma) were sequenced using multiplexing of up to 24 specimens per run. This led to the identification of seven resistance mutations, three of which were present in <20% of the sequenced population. Thus, this assay offers more sensitive detection of minor variants and a higher multiplexing capacity than current methods for the genotypic detection of CMV drug resistance mutations.
Rapid Identification of Microbes in Positive Blood Cultures by Use of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System
Authors: Foster Arnold G. W.
Published: August 2013

Sepsis is a major cause of death worldwide among nonhospitalized people and hospitalized patients. A wide range of pathogens are involved, and the correct identification and correct antimicrobial therapy are critical to ensure optimal clinical outcomes. With the recent introduction of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), rapid identification of bacteria and fungi is now possible. The purpose of this study was to develop a rapid technique for identifying organisms in positive blood cultures using the Vitek MS system (bioMérieux). This technique is a lysis centrifugation method which involves a four-step washing and centrifugation procedure. A total of 253 positive monomicrobial blood cultures (Bactec Plus aerobic, anaerobic, and pediatric bottles) were tested using the Vitek MS system (KnowledgeBase version 2.0), with 92.1% and 88.1% of organisms overall being identified to the genus level and the species level, respectively. Of 161 Gram-positive bacterial isolates, 95.7% and 90.1% were identified to the genus level and the species level, respectively; of 92 Gram-negative bacterial isolates, 84.7% and 83.7% were identified to the genus level and the species level, respectively. The results obtained using this method demonstrate that the Vitek MS system can be used for rapid and effective identification of bacteria from positive blood cultures within 30 to 45 min after the positive signal has been provided by the Bactec FX blood culture system (Becton, Dickinson). This will lead to faster administration of the appropriate antimicrobial therapy and increase the chances for optimal clinical outcomes for patients.
Detection and Identification of Yeasts from Formalin-Fixed, Paraffin-Embedded Tissue by Use of PCR-Electrospray Ionization Mass Spectrometry
Authors: Simner Patricia J. , Buckwalter Seanne P. , Uhl James R. , Wengenack Nancy L. , Pritt Bobbi S.
Published: August 2013

Diagnosis of yeast infection is typically accomplished by fungal smear and culture, histopathologic examination, and/or serologic studies. Newer assays based on mass spectrometry may be useful for yeast identification when histologic examination is inconclusive, fungal cultures are not ordered, or cultures fail to yield a causative agent. The purpose of this study was to evaluate the ability of the PLEX-ID broad fungal assay to accurately detect and identify yeasts in formalin-fixed paraffin-embedded (FFPE) tissues. Tissue samples from 78 FFPE specimens with both histopathology and corresponding culture results for a variety of yeasts were tested using the PLEX-ID broad fungal assay. A 40-μm FFPE tissue section from each specimen was digested with proteinase K followed by nucleic acid extraction and PCR using broad-range fungal primers. Yeast DNA in amplified products was identified using electrospray ionization mass spectrometry. Discordant results were resolved by D2 rRNA gene sequencing. PLEX-ID analysis detected yeast DNA in 78.2% (61/78) of the cases, of which 91.8% (56/61) were concordant with culture results. Of the 5 discordant positive results, 4 PLEX-ID results were considered to result from environmental contaminants, while 1 clinically important discrepancy was observed (
Blastomyces dermatitidis
by culture and
Cryptococcus neoformans
by PLEX-ID). Sequencing of the discordant sample was unsuccessful. The majority of histopathology results (89.7% [70/78]) correlated with culture results. The PLEX-ID broad fungal assay identifies fungi directly from FFPE tissues and can be a useful adjunct to traditional culture and histopathology tests.
Molecular Detection of Culture-Confirmed Bacterial Bloodstream Infections with Limited Enrichment Time
Authors: Moore Miranda S. , McCann Chase D. , Jordan Jeanne A.
Published: August 2013

Conventional blood culturing using automated instrumentation with phenotypic identification requires a significant amount of time to generate results. This study investigated the speed and accuracy of results generated using PCR and pyrosequencing compared to the time required to obtain Gram stain results and final culture identification for cases of culture-confirmed bloodstream infections. Research and physician-ordered blood cultures were drawn concurrently. Aliquots of the incubating research blood culture fluid were removed hourly between 5 and 8 h, at 24 h, and again at 5 days. DNA was extracted from these 6 time point aliquots and analyzed by PCR and pyrosequencing for bacterial rRNA gene targets. These results were then compared to those of the physician-ordered blood culture. PCR and pyrosequencing accurately identified 92% of all culture-confirmed cases after a mean enrichment time of 5.8 ± 2.9 h. When the time needed to complete sample processing was included for PCR and pyrosequencing protocols, the molecular approach yielded results in 11.8 ± 2.9 h compared to means of 27.9 ± 13.6 h to obtain the Gram stain results and 81.6 ± 24.0 h to generate the final culture-based identification. The molecular approach enabled accurate detection of most bacteria present in incubating blood culture bottles on average about 16 h sooner than Gram stain results became available and approximately 3 days sooner than the phenotypic identification was entered in the Laboratory Information System. If implemented, this more rapid molecular approach could minimize the number of doses of unnecessary or ineffective antibiotics administered to patients.
Herpes Simplex Virus 1 Ubiquitin-Specific Protease UL36 Inhibits Beta Interferon Production by Deubiquitinating TRAF3
Authors: Wang Shuai , Wang Kezhen , Li Jie , Zheng Chunfu
Published: August 2013

Interferon (IFN)-mediated innate immune defense is a potent antiviral mechanism. Viruses evade innate immunity and limit secretion of beta interferon (IFN-β) to replicate and survive in the host. The largest tegument protein of herpes simplex virus 1 (HSV-1), UL36, contains a novel deubiquitinase (DUB) motif embedded in its N terminus, denoted UL36 ubiquitin-specific protease (UL36USP). In the present study, we demonstrate that HSV-1 UL36USP inhibits Sendai virus (SeV)-induced interferon regulatory factor 3 (IRF3) dimerization, promoter activation, and transcription of IFN-β. The DUB activity of UL36USP is essential to block IFN-β production. UL36USP also inhibited IFN-β promoter activity induced by overexpression of the N terminus of RIG-I (RIG-IN) and MAVS, but not TBK-1, IκB kinase ε (IKKε), and IRF3/5D. UL36USP was subsequently shown to deubiquitinate TRAF3 and prevent the recruitment of the downstream adaptor TBK1. The recombinant HSV-1 lacking UL36USP DUB activity was generated. Cells infected with the mutant virus produced more IFN-β than wild-type (WT) HSV-1-infected cells. These findings demonstrate HSV-1 UL36USP removes polyubiquitin chains on TRAF3 and counteracts the IFN-β pathway.
Cytokine-Dependent Induction of CD4+T cells with Cytotoxic Potential during Influenza Virus Infection
Authors: Hua Laiqing , Yao Shuyu , Pham Duy , Jiang Li , Wright Jeffrey , Sawant Deepali , Dent Alexander L. , Braciale Thomas J. , Kaplan Mark H. , Sun Jie
Published: August 2013

Recent evidence has identified the role of granzyme B- and perforin-expressing CD4+T cells with cytotoxic potential in antiviral immunity. However, thein vivocytokine cues and downstream pathways governing the differentiation of these cells are unclear. Here, we have identified that CD4+T cells with cytotoxic potential are specifically induced at the site of infection during influenza virus infection. The development of CD4+T cells with cytotoxic potentialin vivowas dependent on the cooperation of the STAT2-dependent type I interferon signaling and the interleukin-2/interleukin-2 receptor alpha pathway for the induction of the transcription factors T-bet and Blimp-1. We showed that Blimp-1 promoted the binding of T-bet to the promoters of cytolytic genes in CD4+T cells and was required for the cytolytic function of thein vitro- andin vivo-generated CD4+T cells with cytotoxic potential. Thus, our data define the molecular basis of regulation of thein vivodevelopment of this functionally cytotoxic Th subset during acute respiratory virus infection. The potential implications for the functions of these cells are discussed.
A Host YB-1 Ribonucleoprotein Complex Is Hijacked by Hepatitis C Virus for the Control of NS3-Dependent Particle Production
Authors: Chatel-Chaix Laurent , Germain Marie-Anne , Motorina Alena , Bonneil Éric , Thibault Pierre , Baril Martin , Lamarre Daniel
Published: August 2013

Hepatitis C virus (HCV) orchestrates the different stages of its life cycle in time and space through the sequential participation of HCV proteins and cellular machineries; hence, these represent tractable molecular host targets for HCV elimination by combination therapies. We recently identified multifunctional Y-box-binding protein 1 (YB-1 or YBX1) as an interacting partner of NS3/4A protein and HCV genomic RNA that negatively regulates the equilibrium between viral translation/replication and particle production. To identify novel host factors that regulate the production of infectious particles, we elucidated the YB-1 interactome in human hepatoma cells by a quantitative mass spectrometry approach. We identified 71 YB-1-associated proteins that included previously reported HCV regulators DDX3, heterogeneous nuclear RNP A1, and ILF2. Of the potential YB-1 interactors, 26 proteins significantly modulated HCV replication in a gene-silencing screening. Following extensive interaction and functional validation, we identified three YB-1 partners, C1QBP, LARP-1, and IGF2BP2, that redistribute to the surface of core-containing lipid droplets in HCV JFH-1-expressing cells, similarly to YB-1 and DDX6. Importantly, knockdown of these proteins stimulated the release and/or egress of HCV particles without affecting virus assembly, suggesting a functional YB-1 protein complex that negatively regulates virus production. Furthermore, a JFH-1 strain with the NS3 Q221L mutation, which promotes virus production, was less sensitive to this negative regulation, suggesting that this HCV-specific YB-1 protein complex modulates an NS3-dependent step in virus production. Overall, our data support a model in which HCV hijacks host cell machinery containing numerous RNA-binding proteins to control the equilibrium between viral RNA replication and NS3-dependent late steps in particle production.
Quantifying Selection against Synonymous Mutations in HIV-1
env
Evolution
Authors: Zanini Fabio , Neher Richard A.
Published: August 2013

Intrapatient evolution of human immunodeficiency virus type 1 (HIV-1) is driven by the adaptive immune system resulting in rapid change of HIV-1 proteins. When cytotoxic CD8
+
T cells or neutralizing antibodies target a new epitope, the virus often escapes via nonsynonymous mutations that impair recognition. Synonymous mutations do not affect this interplay and are often assumed to be neutral. We test this assumption by tracking synonymous mutations in longitudinal intrapatient data from the C2-V5 part of the
env
gene. We find that most synonymous variants are lost even though they often reach high frequencies in the viral population, suggesting a cost to the virus. Using published data from SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) assays, we find that synonymous mutations that disrupt base pairs in RNA stems flanking the variable loops of gp120 are more likely to be lost than other synonymous changes: these RNA hairpins might be important for HIV-1. Computational modeling indicates that, to be consistent with the data, a large fraction of synonymous mutations in this genomic region need to be deleterious with a cost on the order of 0.002 per day. This weak selection against synonymous substitutions does not result in a strong pattern of conservation in cross-sectional data but slows down the rate of evolution considerably. Our findings are consistent with the notion that large-scale patterns of RNA structure are functionally relevant, whereas the precise base pairing pattern is not.
Middle East Respiratory Syndrome Coronavirus Spike Protein Delivered by Modified Vaccinia Virus Ankara Efficiently Induces Virus-Neutralizing Antibodies
Authors: Song Fei , Fux Robert , Provacia Lisette B. , Volz Asisa , Eickmann Markus , Becker Stephan , Osterhaus Albert D. M. E. , Haagmans Bart L. , Sutter Gerd
Published: August 2013

Middle East respiratory syndrome coronavirus (MERS-CoV) has recently emerged as a causative agent of severe respiratory disease in humans. Here, we constructed recombinant modified vaccinia virus Ankara (MVA) expressing full-length MERS-CoV spike (S) protein (MVA-MERS-S). The genetic stability and growth characteristics of MVA-MERS-S make it a suitable candidate vaccine for clinical testing. Vaccinated mice produced high levels of serum antibodies neutralizing MERS-CoV. Thus, MVA-MERS-S may serve for further development of an emergency vaccine against MERS-CoV.
The Open Chromatin Landscape of Kaposi's Sarcoma-Associated Herpesvirus
Authors: Hilton Isaac B. , Simon Jeremy M. , Lieb Jason D. , Davis Ian J. , Damania Blossom , Dittmer Dirk P.
Published: August 2013

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus which establishes latent infection in endothelial and B cells, as well as in primary effusion lymphoma (PEL). During latency, the viral genome exists as a circular DNA minichromosome (episome) and is packaged into chromatin analogous to human chromosomes. Only a small subset of promoters, those which drive latent RNAs, are active in latent episomes. In general, nucleosome depletion (“open chromatin”) is a hallmark of eukaryotic regulatory elements such as promoters and transcriptional enhancers or insulators. We applied formaldehyde-assisted isolation of regulatory elements (FAIRE) followed by next-generation sequencing to identify regulatory elements in the KSHV genome and integrated these data with previously identified locations of histone modifications, RNA polymerase II occupancy, and CTCF binding sites. We found that (i) regions of open chromatin were not restricted to the transcriptionally defined latent loci; (ii) open chromatin was adjacent to regions harboring activating histone modifications, even at transcriptionally inactive loci; and (iii) CTCF binding sites fell within regions of open chromatin with few exceptions, including the constitutive LANA promoter and the vIL6 promoter. FAIRE-identified nucleosome depletion was similar among B and endothelial cell lineages, suggesting a common viral genome architecture in all forms of latency.
Promyelocytic Leukemia Protein Modulates Establishment and Maintenance of Latent Gammaherpesvirus Infection in Peritoneal Cells
Authors: Sewatanon Jaturong , Liu Hao , Ling Paul D.
Published: August 2013

Promyelocytic leukemia protein (PML) is an essential organizer of PML nuclear bodies (NBs), which carry out a variety of activities, including antiviral functions. Herpesviruses from all subfamilies encode proteins that counteract PML NB-mediated antiviral defenses by multiple mechanisms. However, because of the species specificity of herpesviruses, only a limited number of
in vivo
studies have been undertaken to investigate the effect of PML or PML NBs on herpesvirus infection. To address this central issue in herpesvirus biology, we studied the course of infection in wild-type and
PML
−/−
mice using murine gammaherpesvirus 68 (MHV68), which encodes a tegument protein that induces PML degradation. While acute infection in
PML
−/−
mice progressed similarly to that in wild-type mice, the lytic reactivation frequency was higher in peritoneal exudate cells, due to both an increase of MHV68 genome-positive cells and greater reactivation efficiency. We also detected a higher frequency of persistent infection in
PML
−/−
peritoneal cells. These findings suggest that the PML protein can repress the establishment or maintenance of gammaherpesvirus latency
in vivo
. Further use of the
PML
−/−
mouse model should aid in dissecting the molecular mechanisms that underlie the role of PML in gammaherpesvirus latency and may yield clues for how PML modulates herpesvirus latency in general.
Kaposi's Sarcoma-Associated Herpesvirus-Positive Primary Effusion Lymphoma Tumor Formation in NOD/SCID Mice Is Inhibited by Neomycin and Neamine Blocking Angiogenin's Nuclear Translocation
Authors: Bottero Virginie , Sadagopan Sathish , Johnson Karen E. , Dutta Sujoy , Veettil Mohanan Valiya , Chandran Bala
Published: August 2013

Angiogenin (ANG) is a 14-kDa multifunctional proangiogenic secreted protein whose expression level correlates with the aggressiveness of several tumors. We observed increased ANG expression and secretion in endothelial cells during
de novo
infection with Kaposi's sarcoma-associated herpesvirus (KSHV), in cells expressing only latency-associated nuclear antigen 1 (LANA-1) protein, and in KSHV latently infected primary effusion lymphoma (PEL) BCBL-1 and BC-3 cells. Inhibition of phospholipase Cγ (PLCγ) mediated ANG's nuclear translocation by neomycin, an aminoglycoside antibiotic (not G418-neomicin), resulted in reduced KSHV latent gene expression, increased lytic gene expression, and increased cell death of KSHV
+
PEL and endothelial cells. ANG detection in significant levels in KS and PEL lesions highlights its importance in KSHV pathogenesis. To assess the
in vivo
antitumor activity of neomycin and neamine (a nontoxic derivative of neomycin), BCBL-1 cells were injected intraperitoneally into NOD/SCID mice. We observed significant extended survival of mice treated with neomycin or neamine. Markers of lymphoma establishment, such as increases in animal body weight, spleen size, tumor cell spleen infiltration, and ascites volume, were observed in nontreated animals and were significantly diminished by neomycin or neamine treatments. A significant decrease in LANA-1 expression, an increase in lytic gene expression, and an increase in cleaved caspase-3 were also observed in neomycin- or neamine-treated animal ascitic cells. These studies demonstrated that ANG played an essential role in KSHV latency maintenance and BCBL-1 cell survival
in vivo
, and targeting ANG function by neomycin/neamine to induce the apoptosis of cells latently infected with KSHV is an attractive therapeutic strategy against KSHV-associated malignancies.
Mitochondrial Nucleases ENDOG and EXOG Participate in Mitochondrial DNA Depletion Initiated by Herpes Simplex Virus 1 UL12.5
Authors: Duguay Brett A. , Smiley James R.
Published: August 2013

Herpes simplex virus 1 (HSV-1) rapidly eliminates mitochondrial DNA (mtDNA) from infected cells, an effect that is mediated by UL12.5, a mitochondrial isoform of the viral alkaline nuclease UL12. Our initial hypothesis was that UL12.5 directly degrades mtDNA via its nuclease activity. However, we show here that the nuclease activities of UL12.5 are not required for mtDNA loss. This observation led us to examine whether cellular nucleases mediate the mtDNA loss provoked by UL12.5. We provide evidence that the mitochondrial nucleases endonuclease G (ENDOG) and endonuclease G-like 1 (EXOG) play key redundant roles in UL12.5-mediated mtDNA depletion. Overall, our data indicate that UL12.5 deploys cellular proteins, including ENDOG and EXOG, to destroy mtDNA and contribute to a growing body of literature highlighting roles for ENDOG and EXOG in mtDNA maintenance.
Cold finger: urban frostbite in the UK
Authors: Mulgrew Stephen , Khoo Anna , Oxenham Tom , James Nick
Published: August 2013

A 24-year-old man, presented to the accident and emergency (A&E) department 48 h after a social evening where excess alcohol had been consumed. He had fallen asleep outside then made a visit to the A&E department once his finger became painful. His diagnosis was frostbite.
Finger prosthesis: a boon to handicapped
Authors: Gupta Ridhima , Kumar Lakshya , Rao Jitendra , Singh Kamleshwar
Published: August 2013

This is a clinical case report of a 52-year-old male patient with four partially missing fingers of the left hand. The article describes the clinical and laboratory procedure of making prosthesis with modern silicone material. A wax pattern was fabricated using the right hand of the patient. A special type of wax was formulated to make the pattern so that it can be easily moulded and carved. Intrinsic and extrinsic staining was also performed to match the adjacent skin colour. The patient was given the finger prosthesis and was asked to use a half glove (sports) to mask the junction between the prosthesis and the normal tissue. It also provides additional retention to the artificial fingers. The patient felt his social acceptance improved after wearing the finger prosthesis.