bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface barrier layer effect in (In + Nb) co‐doped TiO2 ceramics: An alternative route to design low dielectric loss
Authors: Nachaithong Theeranuch , Kidkhunthod Pinit , Thongbai Prasit , Maensiri Santi
Published: January 2017

Giant dielectric permittivity (ε′) with low loss tangent (tanδ) was reported in (In + Nb) co‐doped TiO2 ceramics. Either of electron‐pinned defect‐dipole or internal barrier layer capacitor model was proposed to be the origin of this high dielectric performance. Here, we proposed an effectively alternative route for designing low‐tanδ in co‐doped TiO2 ceramics by creating a resistive outer surface layer. A pure rutile‐TiO2 phase with a dense microstructure and homogeneous dispersion of dopants was achieved in (In + Nb) co‐doped TiO2 ceramics prepared by a simple sol‐gel method. Two giant dielectric responses were observed in low‐ and high‐frequency ranges, corresponding to extremely high ε′≈106‐107 and large ε′≈104‐105, respectively. After annealing in air, a low‐frequency dielectric response disappeared and could be restored by removing the outer surface of the annealed sample, indicating the dominant electrode effect in the initial sample. Annealing can cause improved dielectric properties with a temperature‐ and frequency‐independent ε′ value of ≈1.9 × 104 and cause a decrease in tanδ from 0.1 to 0.035. High dielectric performance in (In0.5Nb0.5)xTi1−xO2 ceramics can be achieved by eliminating the electrode effect and forming a resistive outer surface layer.
“Breastfeeding” without baby: A longitudinal, qualitative investigation of how mothers perceive, feel about, and practice human milk expression
Authors: Felice Julia P. , Geraghty Sheela R. , Quaglieri Caroline W. , Yamada Rei , Wong Adriana J. , Rasmussen Kathleen M.
Published: January 2017

Most American mothers who produce human milk (HM) now pump in place of some or all feeding at the breast, and most American infants are now fed pumped HM. We aimed to investigate mothers' perceptions of, attitudes toward, and practices for pumping and providing pumped HM. Results related to pumping are reported here. We conducted in‐depth, semi‐structured interviews among a diverse sample of 20 mothers who pumped, following each from pregnancy through infant HM‐feeding cessation up to 1 year postpartum. Data were analyzed using thematic analysis with Atlas.ti. Mothers' reasons for pumping changed over time and reflected their needs and desires (e.g., latch difficulty, return to work, and increasing their milk supply). Mothers reported that pump type and quality were important to pumping success and that pumping was time‐consuming, costly, and unpleasant compared to feeding at the breast. Regardless of how often mothers pumped, most felt pumping was necessary to meet their infant HM‐feeding goals and was a welcome means of sharing with other caregivers the bonding opportunity and tasks they associated with feeding infants. Mothers interpreted output from pumping sessions to understand their ability to provide enough milk to meet their infants' needs. Mothers' reasons for pumping may signal constraints to infant HM feeding that may be addressed with policy changes. Mothers' attitudes and perceptions toward pumping indicate that, although pumping fills important and welcome roles for many mothers, the reality of its practice may make it an unacceptable or infeasible substitute for some.
Optimal Retail Return Policies with Wardrobing
Authors: Shang Guangzhi , Ghosh Bikram P. , Galbreth Michael R.
Published: January 2017

Many retailers offer refunds to consumers who, after a trial period, return a product that they find does not fit their needs. Some consumers are willing to use this return option opportunistically for short‐term consumption rather than its intended purpose of resolving fit uncertainty. Such behavior has been termed “wardrobing.” Restocking fees (partial refunds) can be used to combat wardrobing. However, there is a trade‐off involved, since partial refunds will be viewed negatively by consumers who return an item due to a true lack of fit. In this study, we consider how the extent of wardrobing (how many consumers consider such behavior) and the benefit of wardrobing (how much value can be extracted during the trial) impact firm pricing decisions and profits in this retail context. Our results imply that an increase in the extent of wardrobing is most detrimental to profits when the current extent of wardrobing is low. On the contrary, if the extent of wardrobing is already very high, and the benefit of wardrobing to consumers is also high, the retailer can set prices and refunds such that additional wardrobing actually increases firm profits. In a model extension, we show how a retailer can effectively screen wardrobers from ordinary consumers by offering a menu of price/refund pairs, and that such an approach can lead to increased profits if the extent of wardrobing is sufficiently high. Overall, our findings provide new insights into how retailers can set prices and refund policies to effectively manage opportunistic behavior by consumers.
Problem Solving Techniques Taught Through Validation of an Instantaneous Rigid Force Model
Authors: Mindek Richard B. , Guerrera Joseph M.
Published: January 2017

Educating engineering students in the appropriate methods for analyzing and problem solving fundamental manufacturing processes is a challenge in undergraduate engineering education, given the increasingly limited room in the curriculum as well as the limited time and resources. Although junior and senior level laboratory courses have traditionally been used as a pedagogical platform for conveying this type of knowledge to undergraduate students, the broad range of manufacturing topics that can be covered along with the limited time within a laboratory course structure has sometimes limited the effectiveness of this approach. At the same time, some undergraduate students require a much deeper knowledge of certain manufacturing topics, practices or research techniques, especially those who may already be working in a manufacturing environment as part of a summer internship or part-time employment. The current work shows how modeling, actual machining tests and problem solving techniques were recently used to analyze a manufacturing process within a senior design project course. Specifically, an Instantaneous Rigid Force Model, originally put forward by Tlusty (1,2) was validated and used to assess cutting forces and the ability to detect tool defects during milling operations. Results from the tests showed that the model accurately predicts cutting forces during milling, but have some variation due to cutter vibration and deflection, which were not considered in the model. It was also confirmed that a defect as small as 0.050 inches by 0.025 inches was consistently detectable at multiple test conditions for a 0.5-inch diameter, 4-flute helical end mill. Based on the results, it is suggested that a force cutting model that includes the effect of cutter vibration be used in future work. The results presented demonstrate a level of knowledge in milling operations analysis beyond what can typically be taught in most undergraduate engineering laboratory courses.
Stress Analysis Along Tree Branches
Authors: Kaminski Allison , Mysliwiec Simon , Shahbazi Zahra , Evans Lance
Published: January 2017

Efforts have been made to develop various models to calculate the stress due to weight throughout tree branches. Most studies assumed a uniform modulus of elasticity throughout the branch as well as analyzing the branch as a tapered cantilever beam orientated horizontally or at an angle. However, previous studies show that branches located lower on the tree have a greater variance of modulus of elasticity values in the radial direction and that branches located lower on a tree are more curved. Also, different tree species have different morphologies, some with curvy branches. In this work we have developed a model which considers the curved shape and varying modulus of elasticity values in order to determine stress across the tree branches more accurately. To do this the cross sectional area was divided into rings and each ring was assigned a different modulus of elasticity. Next, the area of the rings was transformed according to their modulus of elasticity. We then considered the curved shape of the branch by generating a best fit line for the diameter of the tree branch in terms of distance from the end of the branch. The generated diameter equation was used in the stress calculations to provide more realistic results. Based on equations developed in this work, we have created a Graphical User Interface (GUI) in Matlab, which can be used as a tool to calculate stress within tree branches by biologists without getting involved with the mathematical and mechanical calculations. We also created a Finite Element Model (FEM) in Abaqus and compared results.
Research of Adhesive Effect Enhanced by Pounding Brush on Second Lining Pounding Procedure for Japanese Scrolls
Authors: Oka Yasuhiro , Goto Akihiko
Published: January 2017

Hanging scrolls are a traditional Japanese ornamental art, which allow paintings and calligraphy to be unrolled and hung on a wall or in an alcove for display, and rolled up and stored in a box. Hanging scrolls should hang straight when unrolled, and roll smoothly for proper storage, without damaging the artwork beneath. For this purpose, scrolls are lined with several layers of Japanese paper, and adhered together with a weak, aged paste made from wheat starch, which gives the paper the flexibility required when the scrolls are rolled up for storage. While this old paste facilitates winding a scroll because it does not become hard even when dried, it does not have sufficient adhesive effect to grip Japanese paper. In order to increase the adhesive power of this aged paste, craftsmen employ a traditional technique of pounding the paper with a special “pounding brush.”

This pounding technique is an important part of the fabrication process of hanging scrolls, but it is a difficult task for each generation to pass down the proper pounding technique. This study was intended to verify the effects of the pounding technique on aged paste and Japanese paper. We prepared samples with the pounding technique and investigated their adhesive properties of samples by peel text. In order to verify the importance of this traditional technique and the traditional materials, we compared and analyzed the differences in adhesion between craftsmen of different skill and differences introduced by paste concentration and backing paper quality.
Sustainable and Renewable Energy Undergraduate Research
Authors: Belu Radian , Chiou Richard , Tseng Tzu-Liang (Bill)
Published: January 2017

Energy is a continuous driving force for the social and technological prospective developments and a vital and essential ingredient for all human transactions. The world is facing an energy “crisis”, due to limited fossil fuel resources, growing energy demand and population. All these facts led to and increased interests in renewable energy sources and green manufacturing. Equipping engineering students with the skills and knowledge required to be successful global engineers in the 21st century is one of the primary objectives of academic educators. Enabling students to practice self-directed learning, find design solutions that are sustainable, and helping them recognize that they are part of a global community are just of few of our educational goals. Project-based learning provides the contextual environment making learning exciting and relevant, providing opportunities to explore technical problems from systems-level perspectives, with an appreciation for the inter-connectedness of science principles. The quest for knowledge is the driving force behind education no matter what field is being studied. This means a lot of reading from textbooks, completion of assignments, exams, lectures but quite little of this work involves original research. Active research experience is one of the most effective ways to attract and retain talented undergraduates in science and engineering. At our institutions, we are regularly modifying curriculum content to embrace sustainability and green energy concepts in learning outcomes. However this crosses over between a numbers of multi-disciplinary, multidimensional study areas that include philosophy and ethics. Consequently a major challenge for us is to encourage engineering students whose primary focus is purely technical to include sustainability and renewable energy topics in their designs. To join into this effort of equipping the future engineers and technologists with renewable energy background, we developed a set of project-based courses related to these topics and include them also in our senior project design course sequence. The main objectives of these curricula changes are to provide students with theoretical and practical knowledge reinforced by hands-on experience. These projects are also good examples of multi-disciplinary cooperation of different engineering disciplines as well as providing valuable hands-on and research experience. This paper presents the changes in the course structure, sample of projects, student survey of the course, as well as plans and expectations for future success. We are also discussing here the project team structure, plan and management, component selection, system simulation, and experimental result.
Papers of note in
Science
355
(6320)
Authors: VanHook Annalisa M.
Published: January 2017

This week’s articles demonstrate that prostate cancer cells become resistant to androgen-deprivation therapy by changing their identity.
Antimicrobial Activity of Ceftazidime-Avibactam against Gram-Negative Bacteria Isolated from Patients Hospitalized with Pneumonia in U.S. Medical Centers, 2011 to 2015
Authors: Sader Helio S. , Castanheira Mariana , Flamm Robert K.
Published: January 2017

Bacterial isolates were collected from patients hospitalized with pneumonia (PHP), including ventilator-associated pneumonia (VAP), from 76 U.S. medical centers in 2011 to 2015. The Gram-negative organisms (
n
= 11,185, including 1,097 from VAP) were tested for susceptibility to ceftazidime-avibactam and comparators by the broth microdilution method. β-Lactamase-encoding genes were screened using a microarray-based assay on selected isolates.
Pseudomonas aeruginosa
and
Klebsiella
spp. were the most common Gram-negative bacteria isolated from PHP and VAP. Ceftazidime-avibactam was very active against
P. aeruginosa
(
n
= 3,402; MIC
50
/MIC
90
, 2 and 4 μg/ml; 96.6% susceptible), including isolates nonsusceptible to meropenem (86.3% susceptible to ceftazidime-avibactam), piperacillin-tazobactam (85.6% susceptible), or ceftazidime (80.6% susceptible). Ceftazidime-avibactam was also highly active against
Enterobacteriaceae
(MIC
50
/MIC
90
, 0.12 and 0.5 μg/ml; 99.9% susceptible), including carbapenem-resistant
Enterobacteriaceae
(CRE) (
n
= 189; MIC
50
/MIC
90
, 0.5 and 2 μg/ml; 98.0% susceptible) and multidrug-resistant (MDR) (
n
= 674; MIC
50
/MIC
90
, 0.25 and 1 μg/ml; 98.8% susceptible) and extensively drug-resistant (XDR) (
n
= 156; MIC
50
/MIC
90
, 0.5 and 2 μg/ml; 98.1% susceptible)
Enterobacteriaceae
isolates, as well as
Klebsiella
species isolates showing an extended-spectrum β-lactamase (ESBL) screening-positive phenotype (
n
= 433; MIC
50
/MIC
90
, 0.25 and 1 μg/ml; 99.5% susceptible). Among
Enterobacter
spp. (24.8% ceftazidime nonsusceptible), 99.8% of the isolates, including 99.4% of ceftazidime-nonsusceptible isolates, were susceptible to ceftazidime-avibactam. The most common β-lactamases detected among
Klebsiella pneumoniae
and
E. coli
isolates were
K. pneumoniae
carbapenemase (KPC)-like and CTX-M-15, respectively. Only 8 of 6,209
Enterobacteriaceae
isolates (0.1%) were ceftazidime-avibactam nonsusceptible, three NDM-1-producing strains with ceftazidime-avibactam MIC values of >32 μg/ml and five isolates with ceftazidime-avibactam MIC values of 16 μg/ml and negative results for all β-lactamases tested. Susceptibility rates among isolates from VAP were generally similar or slightly higher than those from all PHP.
MUC2 Mucin and Butyrate Contribute to the Synthesis of the Antimicrobial Peptide Cathelicidin in Response to Entamoeba histolytica- and Dextran Sodium Sulfate-Induced Colitis
Authors: Cobo Eduardo R. , Kissoon-Singh Vanessa , Moreau France , Holani Ravi , Chadee Kris
Published: January 2017

Embedded in the colonic mucus are cathelicidins, small cationic peptides secreted by colonic epithelial cells. Humans and mice have one cathelicidin-related antimicrobial peptide (CRAMP) each, LL-37/hCAP-18 and Cramp, respectively, with related structure and functions. Altered production of MUC2 mucin and antimicrobial peptides is characteristic of intestinal amebiasis. The interactions between MUC2 mucin and cathelicidins in conferring innate immunity againstEntamoeba histolyticaare not well characterized. In this study, we quantified whether MUC2 expression and release could regulate the expression and secretion of cathelicidin LL-37 in colonic epithelial cells and in the colon. The synthesis of LL-37 was enhanced with butyrate (a product of bacterial fermentation) and interleukin-1β (IL-1β) (a proinflammatory cytokine in colitis) in the presence of exogenously added purified MUC2. The LL-37 responses to butyrate and IL-1β were higher in high-MUC2-producing cells than in lentivirus short hairpin RNA (shRNA) MUC2-silenced cells. Activation of cyclic adenylyl cyclase (AMP) and mitogen-activated protein kinase (MAPK) signaling pathways was necessary for the simultaneous expression of MUC2 and cathelicidins. In Muc2 mucin-deficient (Muc2−/−) mice, murine cathelicidin (Cramp) was significantly reduced compared to that inMuc2+/−andMuc2+/+littermates.E. histolytica-induced acute inflammation in colonic loops stimulated high levels of cathelicidin inMuc2+/+but not inMuc2−/−littermates. In dextran sodium sulfate (DSS)-induced colitis inMuc2+/+mice, which depletes the mucus barrier and goblet cell mucin,Crampexpression was significantly enhanced during restitution. These studies demonstrate regulatory mechanisms between MUC2 and cathelicidins in the colonic mucosa where an intact mucus barrier is essential for expression and secretion of cathelicidins in response toE. histolytica-and DSS-induced colitis.
Transcriptional Activation of Virulence Genes of Rhizobium etli
Authors: Wang Luyao , Lacroix Benoît , Guo Jianhua , Citovsky Vitaly
Published: January 2017

Recently,
Rhizobium etli
, in addition to
Agrobacterium
spp., has emerged as a prokaryotic species whose genome encodes a functional machinery for DNA transfer to plant cells. To understand this
R. etli
-mediated genetic transformation, it would be useful to define how its
vir
genes respond to the host plants. Here, we explored the transcriptional activation of the
vir
genes contained on the
R. etli
p42a plasmid. Using a reporter construct harboring
lacZ
under the control of the
R. etli virE
promoter, we show that the signal phenolic molecule acetosyringone (AS) induces
R. etli vir
gene expression both in an
R. etli
background and in an
Agrobacterium tumefaciens
background. Furthermore, in both bacterial backgrounds, the p42a plasmid also promoted plant genetic transformation with a reporter transfer DNA (T-DNA). Importantly, the
R. etli vir
genes were transcriptionally activated by AS in a bacterial species-specific fashion in regard to the VirA/VirG signal sensor system, and this activation was induced by signals from the natural host species of this bacterium but not from nonhost plants. The early kinetics of transcriptional activation of the major
vir
genes of
R. etli
also revealed several features distinct from those known for
A. tumefaciens
: the expression of the
virG
gene reached saturation relatively quickly, and
virB2
, which in
R. etli
is located outside the
virB
operon, was expressed only at low levels and did not respond to AS. These differences in
vir
gene transcription may contribute to the lower efficiency of T-DNA transfer of
R. etli
p42a than of T-DNA transfer of pTiC58 of
A. tumefaciens
.

IMPORTANCE
The region encoding homologs of
Agrobacterium tumefaciens
virulence genes in the
Rhizobium etli
CE3 p42a plasmid was the first endogenous virulence system encoded by the genome of a non-
Agrobacterium
species demonstrated to be functional in DNA transfer and stable integration into the plant cell genome. In this study, we explored the transcriptional regulation and induction of virulence genes in
R. etli
and show similarities to and differences from those of their
A. tumefaciens
counterparts, contributing to an understanding and a comparison of these two systems. Whereas most
vir
genes in
R. etli
follow an induction pattern similar to that of
A. tumefaciens vir
genes, a few significant differences may at least in part explain the variations in T-DNA transfer efficiency.
Detection of Antigenic Variants of Subtype H3 Swine Influenza A Viruses from Clinical Samples
Authors: Martin Brigitte E. , Bowman Andrew S. , Li Lei , Nolting Jacqueline M. , Smith David R. , Hanson Larry A. , Wan Xiu-Feng
Published: January 2017

A large population of genetically and antigenically diverse influenza A viruses (IAVs) are circulating among the swine population, playing an important role in influenza ecology. Swine IAVs not only cause outbreaks among swine but also can be transmitted to humans, causing sporadic infections and even pandemic outbreaks. Antigenic characterizations of swine IAVs are key to understanding the natural history of these viruses in swine and to selecting strains for effective vaccines. However, influenza outbreaks generally spread rapidly among swine, and the conventional methods for antigenic characterization require virus propagation, a time-consuming process that can significantly reduce the effectiveness of vaccination programs. We developed and validated a rapid, sensitive, and robust method, the polyclonal serum-based proximity ligation assay (polyPLA), to identify antigenic variants of subtype H3N2 swine IAVs. This method utilizes oligonucleotide-conjugated polyclonal antibodies and quantifies antibody-antigen binding affinities by quantitative reverse transcription-PCR (RT-PCR). Results showed the assay can rapidly detect H3N2 IAVs directly from nasal wash or nasal swab samples collected from laboratory-challenged animals or during influenza surveillance at county fairs. In addition, polyPLA can accurately separate the viruses at two contemporary swine IAV antigenic clusters (H3N2 swine IAV-α and H3N2 swine IAV-ß) with a sensitivity of 84.9% and a specificity of 100.0%. The polyPLA can be routinely used in surveillance programs to detect antigenic variants of influenza viruses and to select vaccine strains for use in controlling and preventing disease in swine.
BRD4 Couples NF-κB/RelA with Airway Inflammation and the IRF-RIG-I Amplification Loop in Respiratory Syncytial Virus Infection
Authors: Tian Bing , Yang Jun , Zhao Yingxin , Ivanciuc Teodora , Sun Hong , Garofalo Roberto P. , Brasier Allan R.
Published: January 2017

The airway mucosa expresses protective interferon (IFN) and inflammatory cytokines in response to respiratory syncytial virus (RSV) infection. In this study, we examine the role of bromodomain containing 4 (BRD4) in mediating this innate immune response in human small airway epithelial cells. We observe that RSV induces BRD4 to complex with NF-κB/RelA. BRD4 is functionally required for expression of the NF-κB-dependent inflammatory gene regulatory network (GRN), including the IFN response factor 1 (IRF1) and IRF7, which mediate a cross talk pathway for RIG-I upregulation. Mechanistically, BRD4 is required for cyclin-dependent kinase 9 (CDK9) recruitment and phospho-Ser 2 carboxy-terminal domain (CTD) RNA polymerase (Pol) II formation on the promoters of
IRF1
,
IRF7
, and
RIG-I
, producing their enhanced expression by transcriptional elongation. We also find that BRD4 independently regulates CDK9/phospho-Ser 2 CTD RNA Pol II recruitment to the IRF3-dependent IFN-stimulated genes (ISGs).
In vivo
, poly(I·C)-induced neutrophilia and mucosal chemokine production are blocked by a small-molecule BRD4 bromodomain inhibitor. Similarly, BRD4 inhibition reduces RSV-induced neutrophilia, mucosal CXC chemokine expression, activation of the IRF7-RIG-I autoamplification loop, mucosal IFN expression, and airway obstruction. RSV infection activates BRD4 acetyltransferase activity on histone H3 Lys (K) 122, demonstrating that RSV infection activates BRD4
in vivo
. These data validate BRD4 as a major effector of RSV-induced inflammation and disease. BRD4 is required for coupling NF-κB to expression of inflammatory genes and the IRF-RIG-I autoamplification pathway and independently facilitates antiviral ISG expression. BRD4 inhibition may be a strategy to reduce exuberant virus-induced mucosal airway inflammation.

IMPORTANCE
In the United States, 2.1 million children annually require medical attention for RSV infections. A first line of defense is the expression of the innate gene network by infected epithelial cells. Expression of the innate response requires the recruitment of transcriptional elongation factors to rapidly induce innate response genes through an unknown mechanism. We discovered that RSV infection induces a complex of bromodomain containing 4 (BRD4) with NF-κB and cyclin-dependent kinase 9 (CDK9). BRD4 is required for stable CDK9 binding, phospho-Ser 2 RNA Pol II formation, and histone acetyltransferase activity. Inhibition of BRD4 blocks Toll-like receptor 3 (TLR3)-dependent neutrophilia and RSV-induced inflammation, demonstrating its importance in the mucosal innate response
in vivo
. Our study shows that BRD4 plays a central role in inflammation and activation of the IRF7-RIG-I amplification loop vital for mucosal interferon expression. BRD4 inhibition may be a strategy for modulating exuberant mucosal airway inflammation.
Latent Membrane Protein 1 (LMP1) and LMP2A Collaborate To Promote Epstein-Barr Virus-Induced B Cell Lymphomas in a Cord Blood-Humanized Mouse Model but Are Not Essential
Authors: Ma Shi-Dong , Tsai Ming-Han , Romero-Masters James C. , Ranheim Erik A. , Huebner Shane M. , Bristol Jillian A. , Delecluse Henri-Jacques , Kenney Shannon C.
Published: January 2017

Epstein-Barr virus (EBV) infection is associated with B cell lymphomas in humans. The ability of EBV to convert human B cells into long-lived lymphoblastoid cell lines (LCLs)
in vitro
requires the collaborative effects of EBNA2 (which hijacks Notch signaling), latent membrane protein 1 (LMP1) (which mimics CD40 signaling), and EBV-encoded nuclear antigen 3A (EBNA3A) and EBNA3C (which inhibit oncogene-induced senescence and apoptosis). However, we recently showed that an LMP1-deleted EBV mutant induces B cell lymphomas in a newly developed cord blood-humanized mouse model that allows EBV-infected B cells to interact with CD4 T cells (the major source of CD40 ligand). Here we examined whether the EBV LMP2A protein, which mimics constitutively active B cell receptor signaling, is required for EBV-induced lymphomas in this model. We find that the deletion of LMP2A delays the onset of EBV-induced lymphomas but does not affect the tumor phenotype or the number of tumors. The simultaneous deletion of both LMP1 and LMP2A results in fewer tumors and a further delay in tumor onset. Nevertheless, the LMP1/LMP2A double mutant induces lymphomas in approximately half of the infected animals. These results indicate that neither LMP1 nor LMP2A is absolutely essential for the ability of EBV to induce B cell lymphomas in the cord blood-humanized mouse model, although the simultaneous loss of both LMP1 and LMP2A decreases the proportion of animals developing tumors and increases the time to tumor onset. Thus, the expression of either LMP1 or LMP2A may be sufficient to promote early-onset EBV-induced tumors in this model.

IMPORTANCE
EBV causes human lymphomas, but few models are available for dissecting how EBV causes lymphomas
in vivo
in the context of a host immune response. We recently used a newly developed cord blood-humanized mouse model to show that EBV can cooperate with human CD4 T cells to cause B cell lymphomas even when a major viral transforming protein, LMP1, is deleted. Here we examined whether the EBV protein LMP2A, which mimics B cell receptor signaling, is required for EBV-induced lymphomas in this model. We find that the deletion of LMP2A alone has little effect on the ability of EBV to cause lymphomas but delays tumor onset. The deletion of both LMP1 and LMP2A results in a smaller number of lymphomas in infected animals, with an even more delayed time to tumor onset. These results suggest that LMP1 and LMP2A collaborate to promote early-onset lymphomas in this model, but neither protein is absolutely essential.
Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing
Authors: Ho Cynthia K. Y. , Raghwani Jayna , Koekkoek Sylvie , Liang Richard H. , Van der Meer Jan T. M. , Van Der Valk Marc , De Jong Menno , Pybus Oliver G. , Schinkel Janke , Molenkamp Richard
Published: January 2017

In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However,
in vitro
recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms.

IMPORTANCE
Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations.
RNA Interference in Fungi: Retention and Loss
Authors: Nicolás Francisco E. , Garre Victoriano
Published: January 2017

RNA interference (RNAi) is a mechanism conserved in eukaryotes, including fungi, that represses gene expression by means of small noncoding RNAs (sRNAs) of about 20 to 30 nucleotides. Its discovery is one of the most important scientific breakthroughs of the past 20 years, and it has revolutionized our perception of the functioning of the cell. Initially described and characterized in
Neurospora crassa
, the RNAi is widespread in fungi, suggesting that it plays important functions in the fungal kingdom. Several RNAi-related mechanisms for maintenance of genome integrity, particularly protection against exogenous nucleic acids such as mobile elements, have been described in several fungi, suggesting that this is the main function of RNAi in the fungal kingdom. However, an increasing number of fungal sRNAs with regulatory functions generated by specific RNAi pathways have been identified. Several mechanistic aspects of the biogenesis of these sRNAs are known, but their function in fungal development and physiology is scarce, except for remarkable examples such as
Mucor circinelloides
, in which specific sRNAs clearly regulate responses to environmental and endogenous signals. Despite the retention of RNAi in most species, some fungal groups and species lack an active RNAi mechanism, suggesting that its loss may provide some selective advantage. This article summarizes the current understanding of RNAi functions in the fungal kingdom.
Lichenized Fungi and the Evolution of Symbiotic Organization
Authors: Grube Martin , Wedin Mats
Published: January 2017

Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens. Microscopy has revealed various ways these fungi interact with their hosts. Besides the morphologically recognizable diversity of the lichen mycobionts and lichenicolous (lichen-inhabiting) fungi, many other microorganisms including other fungi and bacterial communities are now detected in lichens by culture-dependent and culture-independent approaches. The application of multi-omics approaches, refined microscopic techniques, and physiological studies has added to our knowledge of lichens, not only about the taxa involved in the lichen interactions, but also about their functions.
Evolution of Cell-Autonomous Effector Mechanisms in Macrophages versus Non-Immune Cells
Authors: Gaudet Ryan G. , Bradfield Clinton J. , MacMicking John D.
Published: January 2017

Specialized adaptations for killing microbes are synonymous with phagocytic cells including macrophages, monocytes, inflammatory neutrophils, and eosinophils. Recent genome sequencing of extant species, however, reveals that analogous antimicrobial machineries exist in certain non-immune cells and also within species that ostensibly lack a well-defined immune system. Here we probe the evolutionary record for clues about the ancient and diverse phylogenetic origins of macrophage killing mechanisms and how some of their properties are shared with cells outside the traditional bounds of immunity in higher vertebrates such as mammals.
Clinical Testing of Tuberculosis Vaccine Candidates
Authors: Hatherill Mark , Tait Dereck , McShane Helen
Published: January 2017

It is almost 100 years since the development of bacille Calmette-Guérin (BCG), the only licensed vaccine against tuberculosis (TB). While BCG does confer consistent protection against disseminated disease, there is an urgent need for a more effective vaccine against pulmonary disease. There are several indications for such an improved vaccine, including prevention of infection, prevention of disease, and a therapeutic vaccine to prevent recurrent disease. The two main approaches to TB vaccine development are developing an improved whole mycobacterial priming agent to replace BCG and/or developing a subunit booster vaccine to be administered after a BCG or BCG replacement priming vaccination. In this article we review the status of the current candidate vaccines being evaluated in clinical trials. The critical challenges to successful TB vaccine development are the uncertain predictive value of the preclinical animal models and the lack of a validated immune correlate of protection. While it is relatively simple to evaluate safety and immunogenicity in phase 1/2 studies, the evaluation of efficacy requires complex studies with large numbers of subjects and long periods of follow-up. This article reviews the potential role for human Experimental Medicine studies, in parallel with product development, to help improve the predictive value of the early-stage trials.
Invasion of Host Cells and Tissues by Uropathogenic Bacteria
Authors: Lewis Adam J. , Richards Amanda C. , Mulvey Matthew A.
Published: January 2017

Within the mammalian urinary tract uropathogenic bacteria face many challenges, including the shearing flow of urine, numerous antibacterial molecules, the bactericidal effects of phagocytes, and a scarcity of nutrients. These problems may be circumvented in part by the ability of uropathogenic
Escherichia coli
and several other uropathogens to invade the epithelial cells that line the urinary tract. By entering host cells, uropathogens can gain access to additional nutrients and protection from both host defenses and antibiotic treatments. Translocation through host cells can facilitate bacterial dissemination within the urinary tract, while the establishment of stable intracellular bacterial populations may create reservoirs for relapsing and chronic urinary tract infections. Here we review the mechanisms and consequences of host cell invasion by uropathogenic bacteria, with consideration of the defenses that are brought to bear against facultative intracellular pathogens within the urinary tract. The relevance of host cell invasion to the pathogenesis of urinary tract infections in human patients is also assessed, along with some of the emerging treatment options that build upon our growing understanding of the infectious life cycle of uropathogenic
E. coli
and other uropathogens.
The Case for Adopting the “Species Complex” Nomenclature for the Etiologic Agents of Cryptococcosis
Authors: Kwon-Chung Kyung J. , Bennett John E. , Wickes Brian L. , Meyer Wieland , Cuomo Christina A. , Wollenburg Kurt R. , Bicanic Tihana A. , Castañeda Elizabeth , Chang Yun C. , Chen Jianghan , Cogliati Massimo , Dromer Françoise , Ellis David , Filler Scott G. , Fisher Matthew C. , Harrison Thomas S. , Holland Steven M. , Kohno Shigeru , Kronstad James W. , Lazera Marcia , Levitz Stuart M. , Lionakis Michail S. , May Robin C. , Ngamskulrongroj Popchai , Pappas Peter G. , Perfect John R. , Rickerts Volker , Sorrell Tania C. , Walsh Thomas J. , Williamson Peter R. , Xu Jianping , Zelazny Adrian M. , Casadevall Arturo
Published: January 2017

Cryptococcosis is a potentially lethal disease of humans/animals caused by
Cryptococcus neoformans
and
Cryptococcus gattii
. Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that
C. neoformans
be divided into two species and
C. gattii
into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species. Naming every clade as a separate species at this juncture will lead to continuing nomenclatural instability. In the absence of biological differences between clades and no consensus about how DNA sequence alone can delineate a species, we recommend using “
Cryptococcus neoformans
species complex” and “
C. gattii
species complex” as a practical intermediate step, rather than creating more species. This strategy recognizes genetic diversity without creating confusion.
The Mw 8.3 Illapel earthquake (Chile): Preseismic and postseismic activity associated with hydrated slab structures
Authors: Poli Piero , Maksymowicz Andrei , Ruiz Sergio
Published: January 2017

The accumulated stress in subduction zones is discharged with earthquake and aseismic activity; the latter is hosted in rheological complex regions, characterized by high pore fluid pressure, and is often accompanied by repeated earthquakes and earthquake swarms. The spatiotemporal analysis of seismic activity can reveal the presence of aseismic transients associated with large earthquakes. Here we study 20 years of seismicity prior to and after the Mw 8.3 earthquake that occurred in A.D. 2015 in central Chile. We identified several earthquake swarms before the main shock and repeating aftershocks at the border of the main slip area. Spatial clustering of the seismic activity shares similar orientation with the main fracture zones observed on the outer rise of the subducting Nazca plate. Our findings suggest that the fracture zones enclosing the rupture are playing a major role in accommodating the pre and post–main shock stress evolution. We further recognize how fracture regions have acted as barriers to the propagation of large earthquakes in the region.
Bacterial sulfur disproportionation constrains timing of Neoproterozoic oxygenation
Authors: Kunzmann Marcus , Bui Thi Hao , Crockford Peter W. , Halverson Galen P. , Scott Clint , Lyons Timothy W. , Wing Boswell A.
Published: January 2017

Various geochemical records suggest that atmospheric O2 increased in the Ediacaran (635–541 Ma), broadly coincident with the emergence and diversification of large animals and increasing marine ecosystem complexity. Furthermore, geochemical proxies indicate that seawater sulfate levels rose at this time too, which has been hypothesized to reflect increased sulfide oxidation in marine sediments caused by sediment mixing of the newly evolved macrofauna. However, the exact timing of oxygenation is not yet understood, and there are claims for significant oxygenation prior to the Ediacaran. Furthermore, recent evidence suggests that physical mixing of sediments did not become important until the late Silurian. Here we report a multiple sulfur isotope record from a ca. 835–630 Ma succession from Svalbard, further supported by data from Proterozoic strata in Canada, Australia, Russia, and the United States, in order to investigate the timing of oxygenation. We present isotopic evidence for onset of globally significant bacterial sulfur disproportionation and reoxidative sulfur cycling following the 635 Ma Marinoan glaciation. Widespread sulfide oxidation helps to explain the observed first-order increase in seawater sulfate concentration from the earliest Ediacaran to the Precambrian-Cambrian boundary by reducing the amount of sulfur buried as pyrite. Expansion of reoxidative sulfur cycling to a global scale also indicates increasing environmental O2 levels. Thus, our data suggest that increasing atmospheric O2 levels may have played a role in the emergence of the Ediacaran macrofauna and increasing marine ecosystem complexity.
Flexible and responsive growth strategy of the Ediacaran skeletal Cloudina from the Nama Group, Namibia
Authors: Wood Rachel , Curtis Andrew , Penny Amelia , Zhuravlev Andrey Yu. , Curtis-Walcott Shona , Iipinge Secilie , Bowyer Frederick
Published: January 2017

The Ediacaran skeletal tubular putative metazoan Cloudina occurs globally in carbonate settings, which both provided lithified substrates and minimized the cost of skeletonization. Habitat and substrate preferences and the relationship of Cloudina to other metazoans have not been fully documented, so we know little as to its ecological demands or community dynamics. In situ Cloudina from the Nama Group, Namibia (ca. 550–541 Ma), formed mutually attached reefs composed of successive assemblages in shallow, high-energy environments, and also communities attached to either stromatolites in storm-influenced deep inner-ramp settings or thin microbial mats in lower-energy habitats. Each assemblage shows statistically distinct tube diameter cohorts, but in sum, Cloudina shows an exponential frequency distribution of diameter size. In reefs, we document a periodicity of size variation, where mean, minimum, and maximum tube diameters vary together and show a systematic increase toward the top of each assemblage. We conclude that most Nama Group Cloudina represent one ecologically generalist taxon with highly variable size, that size was environmentally mediated, and that Cloudina could respond rapidly to periodic environmental changes. While Nama Group skeletal metazoans coexisted with soft-bodied biota, there was no apparent ecological interaction, as they were segregated into lithified carbonate and non-lithified clastic microbial mat communities, respectively. We infer that ecological flexibility allowed Cloudina to form varied communities that colonized diverse carbonate substrates under low levels of interspecific substrate competition. This is in notable contrast to the earliest Cambrian skeletal epibenthos that formed biodiverse reef communities with specialist niche occupancy.
Taking the health aid debate to the subnational level: the impact and allocation of foreign health aid in Malawi
Authors: Marty Robert , Dolan Carrie B , Leu Matthias , Runfola Daniel
Published: January 2017

Objective

Cross-national studies provide inconclusive results as to the effectiveness of foreign health aid. We highlight a novel application of using subnational data to evaluate aid impacts, using Malawi as a case study.

Design

We employ two rounds of nationally representative household surveys (2004/2005 and 2010/2011) and geo-referenced foreign aid data. We examine the determinants of Malawi's traditional authorities receiving aid according to health, environmental risk, socioeconomic and political factors. We use two approaches to estimate the impact of aid on reducing malaria prevalence and increasing healthcare quality: difference-in-difference models, which include traditional authority and month-of-interview fixed effects and control for individual and household level time-varying factors, and entropy balancing, where models balance on health-related and socioeconomic baseline characteristics. General health aid and four specific health aid sectors are examined.

Results

Traditional authorities with greater proportions of individuals living in urban areas, more health facilities and greater proportions of those in major ethnic groups were more likely to receive aid. Difference-in-difference models show health infrastructure and parasitic disease control aid reduced malaria prevalence by 1.20 (95% CI −0.36 to 2.76) and 2.20 (95% CI 0.43 to 3.96) percentage points, respectively, and increased the likelihood of individuals reporting healthcare as more than adequate by 12.1 (95% CI 1.51 to 22.68) and 14.0 (95% CI 0.11 to 28.11) percentage points. Entropy balancing shows similar results.

Conclusions

Aid was targeted to areas with greater existing health infrastructure rather than areas most in need, but still effectively reduced malaria prevalence and enhanced self-reported healthcare quality.