bluuebunny/crossref_metadata_2025 huggingface dataset:
Three‐year analysis of repeated laboratory tests for the markers total cholesterol, ferritin, vitamin D, vitamin B12, and folate, in a large research and teaching hospital in Italy
Authors: Lanzoni Monica , Fornili Marco , Felicetta Irene , Maiavacca Rita , Biganzoli Elia , Castaldi Silvana
Published: January 2017

Rationale, aims and objectives

The increasing number of diagnostic tests requests all over the world is a problem that can partially be explained by inappropriate testing. Impact on the total costs of health systems becomes relevant when tests are performed in a large amount. In this paper, retesting of total cholesterol, ferritin, vitamin B12, vitamin D, and folate is assessed.

Methods

The Quality Unit of Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano (Fondazione) decided to perform a first assessment of the appropriate use of the laboratory tests cholesterol, ferritin, vitamin B12, vitamin D, and folate focusing on the retesting interval for the same patient in the time period January 1, 2012, to December 31, 2014, in every care setting. The minimum retesting intervals were chosen following the ACB recommendations.

The Fondazione is a research and teaching hospital with 3 emergency units (adult, pediatric, and obstetric), kidney, liver, lung, cornea, and bone marrow transplant centers and a medical school. Record linkage of laboratory records selected for the time interval January 1, 2012, to December 31, 2014, was applied using tax code. For each marker, the distribution of retesting intervals was evaluated for every year and the total period. With the same record linkage variable, requests on inpatients were identified from hospital discharge records. A cost analysis of inappropriate retesting was performed for every test.

Results

We examined 466 035 requests for 113 019 patients. Proportions of tests judged potentially inappropriate varied between 8.1% for 1,25‐dihydroxy vitamin D and 37.1% for total cholesterol. The rates of inappropriate tests from year to year never showed significant decrease, and the maximum increase corresponded to an odds ratio of 1.85 (95% CI, 1.36‐2.51) for 1,25‐dihydroxy vitamin D from 2012 to 2013. Calculated loss of money was approximately €500 000 in the 3 years.

Conclusions

Inappropriate requests represent a waste of time and money resources. Our analysis highlighted economically unacceptable rates of inappropriate retesting, with no evidence of decreasing trend. Actions to raise awareness in clinicians or automated electronic solutions are necessary to limit unnecessary test repetitions.
Coronary Procedures After TAVI With the Self‐Expanding Aortic Bioprosthesis Medtronic CoreValve™, Not an Easy Matter
Authors: Boukantar Madjid , Gallet Romain , Mouillet Gauthier , Belarbi Abdelkaoui , Rubimbura Vladimir , Ternacle Julien , Dubois‐Rande Jean‐Luc , Teiger Emmanuel
Published: January 2017

Objectives

To evaluate the feasibility of coronary procedures after transcatheter aortic valve implantation (TAVI) with the CoreValve™ device.

Background

Due to its design, CoreValve™ prosthesis may interfere with coronary procedures. Data on this issue are sparse.

Methods

Between 2007 and 2015, 550 patients underwent CoreValve™ TAVI in our hospital. Among them, 16 underwent coronary angiogram after TAVI and were included in our retrospective study. For each patient, we compared the characteristics of coronary angiograms performed before and after TAVI.

Results

Coronary angiogram was deemed successful in 9 patients. The mean number of different catheters used in attempts to cannulate the coronary arteries was 3.6 ± 1.4 and the rate of selective intubation was low. Fluoroscopy time (13.2 ± 5.8 vs. 7.2 ± 4.6 min, P = 0.003), dose area product (5,347 ± 4,919 vs. 3,433 ± 3,420 cGy/m2, P = 0.004), and contrast volume (157.7 ± 69.6 vs. 108.3 ± 42.6 mL, P = 0.006) were more important in coronary angiograms performed after CoreValve™ implantation. Percutaneous coronary intervention was successfully performed in 6 out of 7 patients who required it.

Conclusion

Coronary procedures after CoreValve™ TAVI are feasible, but challenging. This problem is currently rare but will be more common as the indications of TAVI are expanded to younger patients with longer life expectancies. Recommendations for post‐TAVI coronary procedures are needed, particularly for centers unfamiliar with the management of post‐TAVI patients.
On the Frequency Variogram and on Frequency Domain Methods for the Analysis of Spatio‐Temporal Data
Authors: Subba Rao Tata , Terdik Gyorgy
Published: January 2017

In this article, we assume the spatio‐temporal process to be intrinsically stationary in time and stationary in space. Our objective here is to present an alternative way, based on frequency domain methods, for modelling the data. We consider the discrete Fourier transforms (DFTs) defined for the (intrinsic) time‐series data observed at several locations as our data. We use the well‐known property that DFTs are asymptotically uncorrelated and distributed as complex Gaussian in deriving many results. Our objective here is to emphasize the usefulness of the DFTs in the analysis of spatio‐temporal data. Under the assumption of intrinsic stationarity, we consider the estimation of frequency variogram (FV) and discuss its asymptotic sampling properties. We show that FV introduced earlier is a frequency decomposition of space–time variogram. The DFTs can be computed very fast using fast Fourier transform algorithms. Assuming that the DFTs of the incremental process satisfy a Laplacian model, an analytic expression for the space–time spectral density and an expression for the FV in terms of the spectral density function for the intrinsic stationary process are derived. The estimation of the parameters of the spectral density is also considered. A statistical test for spatial independence of spatio‐temporal data is proposed.
Fiscal Incidence in Ghana
Authors: Younger Stephen D. , Osei‐Assibey Eric , Oppong Felix
Published: January 2017

We use methods developed by the Commitment to Equity Institute to assess the effects of government taxation, social spending and indirect subsidies on poverty and inequality in Ghana. We also simulate several policy reforms to assess their distributional consequences. Results show that, although the country has some very progressive taxes and well‐targeted expenditures, the extent of fiscal redistribution is small, but about what one would expect given Ghana's income level and relatively low initial inequality. Results for poverty reduction are less encouraging: were it not for the in‐kind benefits from health and education spending, the overall effect of government spending and taxation would actually increase poverty in Ghana. Eliminating energy subsidies and at the same time reallocating part of the savings to well‐targeted transfer programs could lower the fiscal deficit while reducing inequality and protecting the poor.
A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and F‐actin organization resulting in dwarf, lintless cotton plants
Authors: Thyssen Gregory N. , Fang David D. , Turley Rickie B. , Florane Christopher B. , Li Ping , Mattison Christopher P. , Naoumkina Marina
Published: January 2017

Actin polymerizes to form part of the cytoskeleton and organize polar growth in all eukaryotic cells. Species with numerous actin genes are especially useful for the dissection of actin molecular function due to redundancy and neofunctionalization. Here, we investigated the role of a cotton (Gossypium hirsutum) actin gene in the organization of actin filaments in lobed cotyledon pavement cells and the highly elongated single‐celled trichomes that comprise cotton lint fibers. Using mapping‐by‐sequencing, virus‐induced gene silencing, and molecular modeling, we identified the causative mutation of the dominant dwarf Ligon lintless Li1 short fiber mutant as a single Gly65Val amino acid substitution in a polymerization domain of an actin gene, GhACT_LI1 (Gh_D04G0865). We observed altered cell morphology and disrupted organization of F‐actin in Li1 plant cells by confocal microscopy. Mutant leaf cells lacked interdigitation of lobes and F‐actin did not uniformly decorate the nuclear envelope. While wild‐type lint fiber trichome cells contained long longitudinal actin cables, the short Li1 fiber cells accumulated disoriented transverse cables. The polymerization‐defective Gly65Val allele in Li1 plants likely disrupts processive elongation of F‐actin, resulting in a disorganized cytoskeleton and reduced cell polarity, which likely accounts for the dominant gene action and diverse pleiotropic effects associated with the Li1 mutation. Lastly, we propose a model to account for these effects, and underscore the roles of actin organization in determining plant cell polarity, shape and plant growth.
Artificial bee colony algorithm variants on constrained optimization
Authors: Akay Bahriye Basturk , Karaboga Dervis
Published: January 2017

Optimization problems are generally classified into two main groups:unconstrained and constrained. In the case of constrainedoptimization, special techniques are required to handle withconstraints and produce solutions in the feasible space. Intelligentoptimization techniques that do not make assumptions on the problemcharacteristics are preferred to produce acceptable solutions to theconstrained optimization problems. In this study, the performance ofartificial bee colony algorithm (ABC), one of the intelligentoptimization techniques, is investigated on constrained problems andthe effect of some modifications on the performance of the algorithmis examined. Different variants of the algorithm have been proposedand compared in terms of efficiency and stability. Depending on theresults, when DE operators were integrated into ABC algorithm'sonlooker phase while the employed bee phase is retained as in ABCalgorithm, an improvement in the performance was gained in terms ofthe best solution in addition to preserving the stability of thebasic ABC. The ABC algorithm is a simple optimization algorithm thatcan be used for constrained optimization without requiring a prioriknowledge.
Ghrelin ameliorates blood–brain barrier disruption during systemic hypoxia
Authors: Mohaddes Gisou , Abdolalizadeh Jalal , Babri Shirin , Hossienzadeh Fezzeh
Published: January 2017

New Findings

What is the central question of this study?

Is an anti‐oedematous effect of ghrelin associated with increased expression of tight junction proteins in the hypoxic brain?

What is the main finding and its importance?

We showed that injection of ghrelin during acute and chronic systemic hypoxia is associated with increased expression of tight junction proteins and protection of the blood–brain barrier. Ghrelin appears to be a new therapeutic strategy for protection of the blood–brain barrier from disruption and prevention of brain oedema in hypoxic conditions.

The blood–brain barrier, which serves to protect the homeostasis of the CNS, is formed by tight junction proteins. Several studies have indicated that systemic hypoxia leads to cerebral oedema through disruption of tight junction proteins, such as occludin and zonula occludens‐1 (ZO‐1). According to our previous studies, ghrelin attenuates cerebral oedema in the hypoxic brain. However, the mechanism is not completely understood. The present study was designed to determine the effect of ghrelin on occludin and ZO‐1 in the hypoxic brain. Adult male Wistar rats were divided into acute and chronic control, acute or chronic hypoxia, and ghrelin‐treated acute or chronic hypoxia groups. Hypoxic groups were kept in a hypoxic chamber (10–11% O2) for 2 (acute) or 10 days (chronic). Effects of ghrelin on occludin and ZO‐1 protein levels were assessed using Western blotting. Western blot analysis revealed that the protein expression of ZO‐1 and occludin decreased significantly in acute and chronic hypoxia. Ghrelin significantly increased ZO‐1 protein expression in both acute and chronic hypoxia (P < 0.05). Ghrelin also increased occludin protein expression in chronic hypoxia (P < 0.05) but did not effectively change it in acute hypoxia. Our data showed that ghrelin injection maintains occludin and ZO‐1 tight junction proteins, which may improve the integrity of the blood–brain barrier in hypoxic conditions.
Visualization of Brushing in “Shibo” Production of Hand-Made Japanese Paper
Authors: Nojima Shinji , Yoshikawa Takashi , Imajo Akihiko , Tsujinaka Takeshi
Published: January 2017

We deal with “Danshi” that has a special wrinkle called “Shibo” on the surface structure of the Japanese paper. Three sheets of wet papers are superimposed to make the Shibo. Wet papers are extended the slack by brushing. Superimposed wet papers are made the Shibo by especial pulling movement. This time, we investigate about the movement of brushing for extending the slack.

Subjects are two people which are wearing 18 reflecting markers on the body. An expert has manufactured Danshi for 23 years of experience and a non-expert has done less than 1 year of experience. The movement of brushing process is measured as sampling time of 100 [Hz]. We will investigate differences of the physical movement between the expert and the non-expert.

We make a hearing about the differences and work on visualization about the skill of the expert.

The method of making Shibo structure has five procedures. First, one piece of wet paper is placed on the inclined work table. Second, wrinkles of the paper are extended by brushing. Third, next wet paper is put on the first sheet, it is extended the slack again. Fourth, moreover third wet paper is put on the second sheet, it is extended the slack by brushing again. Fifth, the Shibo structures are produced by pulling in a state of three superimposed sheets.

We compared the number of brushing in each sheets. There was not difference in the number of brushing in each sheet in a non-expert. In other hand, number of brushing by the expert was two times that of first and second sheets in third sheet. The number of brushing in first and second sheets did not change by the expert. In consequence, he was a notion that important things for making the clear Shibo structure are not only extending the slack, but also pulling out the bubbles.

We divided brushing movement into eight directions. In third sheet of the expert, the number of brushing to body direction has increased over 10%. It was found that the expert removed air bubbles from the corner of the top right. Furthermore, we investigated the change of angle of the right wrist in the expert and the non-expert. It became clear that angle of the wrist is reduced when the expert is brushing forward.
Fostering Sustainable Development Thinking Through Lean Engineering Education
Authors: Alves Anabela C. , Kahlen Franz-Josef , Flumerfelt Shannon , Siriban-Manalang Anna Bella
Published: January 2017

An implementation plan for the UN Decade of Education for Sustainable Development (ESD) by the implementing agency UNESCO, launched in 2005 to build partnerships with various partners mainly aimed to reflect the great diversity of interests, concerns, and challenges for ESD. Embedded in this UN program is the challenge to academic engineering programs to develop a technical workforce which is capable of designing and continually developing sustainable processes and products. ESD therefore requires engineers to be able to learn and perform in an interdisciplinary work environment as critical thinkers and problem solvers, to be value-driven and to practice participatory and transparent decision making. Taking these challenges back into curriculum development, the authors of this paper propose that their Lean Engineering Education (LEE) initiative be examined and scrutinized as a contribution to ESD. Thus, this paper reviews ESD roots and partnerships and, then, present, succinctly, LEE as a curricular innovation for engineering courses that promotes the behavior intended for future engineers, to foster a ESD and the Sustainable Development thinking.
Early formation of the Moon 4.51 billion years ago
Authors: Barboni Melanie , Boehnke Patrick , Keller Brenhin , Kohl Issaku E. , Schoene Blair , Young Edward D. , McKeegan Kevin D.
Published: January 2017

Data on lunar zircons require the formation of the Moon by 4.51 Gy, therefore within the first 60 My of the solar system.
Pioneering study images activity in fetal brains
Authors: Miller Greg
Published: January 2017

Altered brain function found in fetuses that go on to be born prematurely.
Combining theory and experiment in electrocatalysis: Insights into materials design
Authors: Seh Zhi Wei , Kibsgaard Jakob , Dickens Colin F. , Chorkendorff Ib , Nørskov Jens K. , Jaramillo Thomas F.
Published: January 2017

Better living through water-splitting

Chemists have known how to use electricity to split water into hydrogen and oxygen for more than 200 years. Nonetheless, because the electrochemical route is inefficient, most of the hydrogen made nowadays comes from natural gas. Seh
et al.
review recent progress in electrocatalyst development to accelerate water-splitting, the reverse reactions that underlie fuel cells, and related oxygen, nitrogen, and carbon dioxide reductions. A unified theoretical framework highlights the need for catalyst design strategies that selectively stabilize distinct reaction intermediates relative to each other.

Science
, this issue p.
10.1126/science.aad4998
Superficial layers of the medial entorhinal cortex replay independently of the hippocampus
Authors: O’Neill J. , Boccara C.N. , Stella F. , Schoenenberger P. , Csicsvari J.
Published: January 2017

Parallel computation in memory-making

The hippocampus plays a central role in the encoding, consolidation, and recall of memories. Consolidation and recall are thought to be executed by the replay of previously acquired memory traces by hippocampal cell assemblies. The hippocampus is thus considered to be the initiator of memory redistribution processes. However, O'Neill
et al.
now report that the superficial layers of the medial entorhinal cortex show replay events that are independent of hippocampal activity (see the Perspective by Moser and Gardner). Computations in memory systems may thus be organized in a less hierarchical, more parallel way than previously thought.

Science
, this issue p.
184
; see also p.
131
Plant-soil feedbacks and mycorrhizal type influence temperate forest population dynamics
Authors: Bennett Jonathan A. , Maherali Hafiz , Reinhart Kurt O. , Lekberg Ylva , Hart Miranda M. , Klironomos John
Published: January 2017

Soil biota and plant diversity

Soil biota, including symbionts such as mycorrhizal fungi and nitrogen-fixing bacteria, as well as fungal and bacterial pathogens, affect terrestrial plant diversity and growth patterns (see the Perspective by van der Putten). Teste
et al.
monitored growth and survival in Australian shrubland plant species paired with soil biota from plants of the same species and from other plants that use different nutrient acquisition strategies. Plant-soil feedbacks appear to drive local plant diversity through interactions between the different types of plants and their associated soil biota. Bennett
et al.
studied plant-soil feedbacks in soil and seeds from 550 populations of 55 species of North American trees. Feedbacks ranged from positive to negative, depending on the type of mycorrhizal association, and were related to how densely the same species occurred in natural populations.

Science
, this issue p.
134
, p.
173
; see also p.
181
Plant-soil feedback and the maintenance of diversity in Mediterranean-climate shrublands
Authors: Teste François P. , Kardol Paul , Turner Benjamin L. , Wardle David A. , Zemunik Graham , Renton Michael , Laliberté Etienne
Published: January 2017

Soil biota and plant diversity

Soil biota, including symbionts such as mycorrhizal fungi and nitrogen-fixing bacteria, as well as fungal and bacterial pathogens, affect terrestrial plant diversity and growth patterns (see the Perspective by van der Putten). Teste
et al.
monitored growth and survival in Australian shrubland plant species paired with soil biota from plants of the same species and from other plants that use different nutrient acquisition strategies. Plant-soil feedbacks appear to drive local plant diversity through interactions between the different types of plants and their associated soil biota. Bennett
et al.
studied plant-soil feedbacks in soil and seeds from 550 populations of 55 species of North American trees. Feedbacks ranged from positive to negative, depending on the type of mycorrhizal association, and were related to how densely the same species occurred in natural populations.

Science
, this issue p.
134
, p.
173
; see also p.
181
Vectorial representation of spatial goals in the hippocampus of bats
Authors: Sarel Ayelet , Finkelstein Arseny , Las Liora , Ulanovsky Nachum
Published: January 2017

How to get to place B

We constantly navigate around our environment. This means moving from our current location, place A, to a new goal, place B. We have recently learned much about spatial maps in the brain in which place cells indicate current location. However, it is unclear how navigational goals are represented in the brain. Sarel
et al.
describe a group of neurons in the brains of bats that are tuned to goal direction and distance relative to the bat's current position as it flies toward its goal. The finding elucidates the computations involved in spatial navigation.

Science
, this issue p.
176
Hydrogen positions in single nanocrystals revealed by electron diffraction
Authors: Palatinus L. , Brázda P. , Boullay P. , Perez O. , Klementová M. , Petit S. , Eigner V. , Zaarour M. , Mintova S.
Published: January 2017

Pin the tail on the hydrogens

X-ray diffraction has been the method of choice for determining the positions of atoms within a crystal. However, the technique works better for atoms with higher atomic numbers and requires single crystals of a minimum size. Palatinus
et al.
used electron diffraction, a technique of increasing importance for analyzing very small crystals, to identify the positions of hydrogen atoms in organic and inorganic materials (see the Perspective by McCusker).

Science
, this issue p.
166
; see also p.
136
Assembly of a nucleus-like structure during viral replication in bacteria
Authors: Chaikeeratisak Vorrapon , Nguyen Katrina , Khanna Kanika , Brilot Axel F. , Erb Marcella L. , Coker Joanna K. C. , Vavilina Anastasia , Newton Gerald L. , Buschauer Robert , Pogliano Kit , Villa Elizabeth , Agard David A. , Pogliano Joe
Published: January 2017

Phages build themselves a wall

The compartmentalization of DNA replication away from other cytoplasmic events is a key feature of the cell nucleus. Chaikeeratisak
et al.
studied the replication of the very large
Pseudomonas
bacteriophage 201φ2-1 by using fluorescence microscopy and cryo–electron tomography. They found that the phage assembled a nucleus-like compartment when it infected a bacterial cell. The phage genome was completely enclosed by an apparently contiguous protein shell, within which DNA replication, recombination, and transcription occurred. Translation, precursor biosynthesis, and viral assembly occurred outside the structure.

Science
, this issue p.
194
Multiple mechanisms for memory replay?
Authors: Gardner Richard J. , Moser May-Britt
Published: January 2017

Independent repetition of experiences occurs in two regions of the brain's memory system
Global clean energy in 2017
Authors: King David
Published: January 2017

During the November 2016 Climate Change Conference in Marrakesh, much talk centered on implementation of the political commitments made in Paris in 2015. Governments are now focused on putting their words into action as they prepare for the first official stocktake in 2018. Innovation will have an essential role to play.
Antimicrobial Susceptibility Patterns among a Large, Nationwide Cohort of Abiotrophia and Granulicatella Clinical Isolates
Authors: Prasidthrathsint Kunatum , Fisher Mark A.
Published: January 2017

Antimicrobial susceptibility patterns from 599
A. defectiva
,
G. adiacens
, and
G. elegans
clinical isolates were determined by broth microdilution. We observed significant differences in susceptibility across species, particularly to penicillin and ceftriaxone, and across geographical regions.
A. defectiva
was the least susceptible species overall to penicillin. All isolates were susceptible to vancomycin and >90% were susceptible to levofloxacin.
Adenovirus Modulates Toll-Like Receptor 4 Signaling by Reprogramming ORP1L-VAP Protein Contacts for Cholesterol Transport from Endosomes to the Endoplasmic Reticulum
Authors: Cianciola Nicholas L. , Chung Stacey , Manor Danny , Carlin Cathleen R.
Published: January 2017

Human adenoviruses (Ads) generally cause mild self-limiting infections but can lead to serious disease and even be fatal in high-risk individuals, underscoring the importance of understanding how the virus counteracts host defense mechanisms. This study had two goals. First, we wished to determine the molecular basis of cholesterol homeostatic responses induced by the early region 3 membrane protein RIDα via its direct interaction with the sterol-binding protein ORP1L, a member of the evolutionarily conserved family of oxysterol-binding protein (OSBP)-related proteins (ORPs). Second, we wished to determine how this interaction regulates innate immunity to adenovirus. ORP1L is known to form highly dynamic contacts with endoplasmic reticulum-resident VAP proteins that regulate late endosome function under regulation of Rab7-GTP. Our studies have demonstrated that ORP1L-VAP complexes also support transport of LDL-derived cholesterol from endosomes to the endoplasmic reticulum, where it was converted to cholesteryl esters stored in lipid droplets when ORP1L was bound to RIDα. The virally induced mechanism counteracted defects in the predominant cholesterol transport pathway regulated by the late endosomal membrane protein Niemann-Pick disease type C protein 1 (NPC1) arising during early stages of viral infection. However, unlike NPC1, RIDα did not reconstitute transport to endoplasmic reticulum pools that regulate SREBP transcription factors. RIDα-induced lipid trafficking also attenuated proinflammatory signaling by Toll-like receptor 4, which has a central role in Ad pathogenesis and is known to be tightly regulated by cholesterol-rich “lipid rafts.” Collectively, these data show that RIDα utilizes ORP1L in a way that is distinct from its normal function in uninfected cells to fine-tune lipid raft cholesterol that regulates innate immunity to adenovirus in endosomes.

IMPORTANCE
Early region 3 proteins encoded by human adenoviruses that attenuate immune-mediated pathology have been a particularly rich source of information regarding intracellular protein trafficking. Our studies with the early region 3-encoded RIDα protein also provided fundamental new information regarding mechanisms of nonvesicular lipid transport and the flow of molecular information at membrane contacts between different organelles. We describe a new pathway that delivers cholesterol from endosomes to the endoplasmic reticulum, where it is esterified and stored in lipid droplets. Although lipid droplets are attracting renewed interest from the standpoint of normal physiology and human diseases, including those resulting from viral infections, experimental model systems for evaluating how and why they accumulate are still limited. Our studies also revealed an intriguing relationship between lipid droplets and innate immunity that may represent a new paradigm for viruses utilizing these organelles.
Neutralization of Diverse Human Cytomegalovirus Strains Conferred by Antibodies Targeting Viral gH/gL/pUL128-131 Pentameric Complex
Authors: Ha Sha , Li Fengsheng , Troutman Matthew C. , Freed Daniel C. , Tang Aimin , Loughney John W. , Wang Dai , Wang I-Ming , Vlasak Josef , Nickle David C. , Rustandi Richard R. , Hamm Melissa , DePhillips Pete A. , Zhang Ningyan , McLellan Jason S. , Zhu Hua , Adler Stuart P. , McVoy Michael A. , An Zhiqiang , Fu Tong-Ming
Published: January 2017

Human cytomegalovirus (HCMV) is the leading cause of congenital viral infection, and developing a prophylactic vaccine is of high priority to public health. We recently reported a replication-defective human cytomegalovirus with restored pentameric complex glycoprotein H (gH)/gL/pUL128-131 for prevention of congenital HCMV infection. While the quantity of vaccine-induced antibody responses can be measured in a viral neutralization assay, assessing the quality of such responses, including the ability of vaccine-induced antibodies to cross-neutralize the field strains of HCMV, remains a challenge. In this study, with a panel of neutralizing antibodies from three healthy human donors with natural HCMV infection or a vaccinated animal, we mapped eight sites on the dominant virus-neutralizing antigen—the pentameric complex of glycoprotein H (gH), gL, and pUL128, pUL130, and pUL131. By evaluating the site-specific antibodies in vaccine immune sera, we demonstrated that vaccination elicited functional antiviral antibodies to multiple neutralizing sites in rhesus macaques, with quality attributes comparable to those of CMV hyperimmune globulin. Furthermore, these immune sera showed antiviral activities against a panel of genetically distinct HCMV clinical isolates. These results highlighted the importance of understanding the quality of vaccine-induced antibody responses, which includes not only the neutralizing potency in key cell types but also the ability to protect against the genetically diverse field strains.

IMPORTANCE
HCMV is the leading cause of congenital viral infection, and development of a preventive vaccine is a high public health priority. To understand the strain coverage of vaccine-induced immune responses in comparison with natural immunity, we used a panel of broadly neutralizing antibodies to identify the immunogenic sites of a dominant viral antigen—the pentameric complex. We further demonstrated that following vaccination of a replication-defective virus with the restored pentameric complex, rhesus macaques can develop broadly neutralizing antibodies targeting multiple immunogenic sites of the pentameric complex. Such analyses of site-specific antibody responses are imperative to our assessment of the quality of vaccine-induced immunity in clinical studies.
Klebsiella Phage ΦK64-1 Encodes Multiple Depolymerases for Multiple Host Capsular Types
Authors: Pan Yi-Jiun , Lin Tzu-Lung , Chen Ching-Ching , Tsai Yun-Ting , Cheng Yi-Hsiang , Chen Yi-Yin , Hsieh Pei-Fang , Lin Yi-Tsung , Wang Jin-Town
Published: January 2017

The genome of the multihost bacteriophage ΦK64-1, capable of infecting
Klebsiella
capsular types K1, K11, K21, K25, K30, K35, K64, and K69, as well as new capsular types KN4 and KN5, was analyzed and revealed that 11 genes (
S1-1
,
S1-2
,
S1-3
,
S2-1
,
S2-2
,
S2-3
,
S2-4
,
S2-5
,
S2-6
,
S2-7
, and
S2-8
) encode proteins with amino acid sequence similarity to tail fibers/spikes or lyases.
S2-5
previously was shown to encode a K64 capsule depolymerase (K64dep). Specific capsule-degrading activities of an additional eight putative capsule depolymerases (S2-4 against K1, S1-1 against K11, S1-3 against K21, S2-2 against K25, S2-6 against K30/K69, S2-3 against K35, S1-2 against KN4, and S2-1 against KN5) was demonstrated by expression and purification of the recombinant proteins. Consistent with the capsular type-specific depolymerization activity of these gene products, phage mutants of
S1-2
,
S2-2
,
S2-3
, or
S2-6
lost infectivity for KN4, K25, K35, or K30/K69, respectively, indicating that capsule depolymerase is crucial for infecting specific hosts. In conclusion, we identified nine functional capsule depolymerase-encoding genes in a bacteriophage and correlated activities of the gene products to all ten hosts of this phage, providing an example of type-specific host infection mechanisms in a multihost bacteriophage.

IMPORTANCE
We currently identified eight novel capsule depolymerases in a multihost
Klebsiella
bacteriophage and correlated the activities of the gene products to all hosts of this phage, providing an example of carriage of multiple depolymerases in a phage with a wide capsular type host spectrum. Moreover, we also established a recombineering system for modification of
Klebsiella
bacteriophage genomes and demonstrated the importance of capsule depolymerase for infecting specific hosts. Based on the powerful tool for modification of phage genome, further studies can be conducted to improve the understanding of mechanistic details of
Klebsiella
phage infection. Furthermore, the newly identified capsule depolymerases will be of great value for applications in capsular typing.
HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer+Gag-Specific CD4+T Cells in Chronic Clade C HIV-1 Infection
Authors: Laher Faatima , Ranasinghe Srinika , Porichis Filippos , Mewalal Nikoshia , Pretorius Karyn , Ismail Nasreen , Buus Søren , Stryhn Anette , Carrington Mary , Walker Bruce D. , Ndung'u Thumbi , Ndhlovu Zaza M.
Published: January 2017

Immune control of viral infections is heavily dependent on helper CD4+T cell function. However, the understanding of the contribution of HIV-specific CD4+T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4+T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4+T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4+T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4+T cells in HIV controllers than progressors (P= 0.0001), and these expanded Gag-specific CD4+T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control (r= −0.5,P= 0.02). These data identify an association between HIV-specific CD4+T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4+T cell responses in natural infections.

IMPORTANCEIncreasing evidence suggests that virus-specific CD4+T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4+T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV infections worldwide. Understanding the contribution of HIV-specific CD4+T cell responses in clade C infection is particularly important for developing vaccines that would be efficacious in sub-Saharan Africa, where clade C infection is dominant. Here, we employed MHC class II tetramers designed to immunodominant Gag epitopes and used them to characterize CD4+T cell responses in HIV-1 clade C infection. Our results demonstrate an association between the frequency of HIV-specific CD4+T cell responses targeting an immunodominant DRB1*11-Gag41 complex and HIV control, highlighting the important contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infections.
Characterizing HIV-1 Splicing by Using Next-Generation Sequencing
Authors: Emery Ann , Zhou Shuntai , Pollom Elizabeth , Swanstrom Ronald
Published: January 2017

Full-length human immunodeficiency virus type 1 (HIV-1) RNA serves as the genome or as an mRNA, or this RNA undergoes splicing using four donors and 10 acceptors to create over 50 physiologically relevant transcripts in two size classes (1.8 kb and 4 kb). We developed an assay using Primer ID-tagged deep sequencing to quantify HIV-1 splicing. Using the lab strain NL4-3, we found that A5 (
env
/
nef
) is the most commonly used acceptor (about 50%) and A3 (
tat
) the least used (about 3%). Two small exons are made when a splice to acceptor A1 or A2 is followed by activation of donor D2 or D3, and the high-level use of D2 and D3 dramatically reduces the amount of
vif
and
vpr
transcripts. We observed distinct patterns of temperature sensitivity of splicing to acceptors A1 and A2. In addition, disruption of a conserved structure proximal to A1 caused a 10-fold reduction in all transcripts that utilized A1. Analysis of a panel of subtype B transmitted/founder viruses showed that splicing patterns are conserved, but with surprising variability of usage. A subtype C isolate was similar, while a simian immunodeficiency virus (SIV) isolate showed significant differences. We also observed transsplicing from a downstream donor on one transcript to an upstream acceptor on a different transcript, which we detected in 0.3% of 1.8-kb RNA reads. There were several examples of splicing suppression when the
env
intron was retained in the 4-kb size class. These results demonstrate the utility of this assay and identify new examples of HIV-1 splicing regulation.

IMPORTANCE
During HIV-1 replication, over 50 conserved spliced RNA variants are generated. The splicing assay described here uses new developments in deep-sequencing technology combined with Primer ID-tagged cDNA primers to efficiently quantify HIV-1 splicing at a depth that allows even low-frequency splice variants to be monitored. We have used this assay to examine several features of HIV-1 splicing and to identify new examples of different mechanisms of regulation of these splicing patterns. This splicing assay can be used to explore in detail how HIV-1 splicing is regulated and, with moderate throughput, could be used to screen for structural elements, small molecules, and host factors that alter these relatively conserved splicing patterns.
The Role and Function of Fcγ Receptors on Myeloid Cells
Authors: Bournazos Stylianos , Wang Taia T. , Ravetch Jeffrey V.
Published: January 2017

A key determinant for the survival of organisms is their capacity to recognize and respond efficiently to foreign antigens. This is largely accomplished by the orchestrated activity of the innate and adaptive branches of the immune system. Antibodies are specifically generated in response to foreign antigens, facilitating thereby the specific recognition of antigens of almost infinite diversity. Receptors specific for the Fc domain of antibodies, Fc receptors, are expressed on the surface of the various myeloid leukocyte populations and mediate the binding and recognition of antibodies by innate leukocytes. By directly linking the innate and the adaptive components of immunity, Fc receptors play a central role in host defense and the maintenance of tissue homeostasis through the induction of diverse proinflammatory, anti-inflammatory, and immunomodulatory processes that are initiated upon engagement by the Fc domain. In this chapter, we discuss the mechanisms that regulate Fc domain binding to the various types of Fc receptors and provide an overview of the astonishing diversity of effector functions that are mediated through Fc-FcR interactions on myeloid cells. Lastly, we discuss the impact of FcR-mediated interactions in the context of IgG-mediated inflammation, autoimmunity, susceptibility to infection, and responsiveness to antibody-based therapeutics.
Regulation of Immunity to Tuberculosis
Authors: Brighenti Susanna , Ordway Diane J.
Published: January 2017

Immunity againstMycobacterium tuberculosisrequires a balance between adaptive immune responses to constrain bacterial replication and the prevention of potentially damaging immune activation. Regulatory T (Treg) cells express the transcription factor Foxp3+ and constitute an essential counterbalance of inflammatory Th1 responses and are required to maintain immune homeostasis. The first reports describing the presence of Foxp3-expressing CD4+ Treg cells in tuberculosis (TB) emerged in 2006. Different Treg cell subsets, most likely specialized for different tissues and microenvironments, have been shown to expand in both human TB and animal models of TB. Recently, additional functional roles for Treg cells have been demonstrated during different stages and spectrums of TB disease. Foxp3+ regulatory cells can quickly expand during early infection and impede the onset of cellular immunity and persist during chronic TB infection. Increased frequencies of Treg cells have been associated with a detrimental outcome of active TB, and may be dependent on theM. tuberculosisstrain, animal model, local environment, and the stage of infection. Some investigations also suggest that Treg cells are required together with effector T cell responses to obtain reduced pathology and sterilizing immunity. In this review, we will first provide an overview of the regulatory cells and mechanisms that control immune homeostasis. Then, we will review what is known about the phenotype and function of Treg cells from studies in human TB and experimental animal models of TB. We will discuss the potential role of Treg cells in the progression of TB disease and the relevance of this knowledge for future efforts to prevent, modulate, and treat TB.
The Minimal Unit of Infection:Mycobacterium tuberculosisin the Macrophage
Authors: VanderVen Brian C. , Huang Lu , Rohde Kyle H. , Russell David G.
Published: January 2017

The interaction betweenMycobacterium tuberculosisand its host cell is highly complex and extremely intimate. Were it not for the disease, one might regard this interaction at the cellular level as an almost symbiotic one. The metabolic activity and physiology of both cells are shaped by this coexistence. We believe that where this appreciation has greatest significance is in the field of drug discovery. Evolution rewards efficiency, and recent data from many groups discussed in this review indicate thatM. tuberculosishas evolved to utilize the environmental cues within its host to control large genetic programs or regulons. But these regulons may represent chinks in the bacterium’s armor because they include off-target effects, such as the constraint of the metabolic plasticity ofM. tuberculosis. A prime example is how the presence of cholesterol within the host cell appears to limit the ability ofM. tuberculosisto fully utilize or assimilate other carbon sources. And that is the reason for the title of this review. We believe firmly that, to understand the physiology ofM. tuberculosisand to identify new drug targets, it is imperative that the bacterium be interrogated within the context of its host cell. The constraints induced by the environmental cues present within the host cell need to be preserved and exploited. TheM. tuberculosis-infected macrophage truly is the “minimal unit of infection.”
Tuberculosis and Pregnancy—Maternal, Fetal, and Neonatal Considerations
Authors: Gould Jane M. , Aronoff Stephen C.
Published: January 2017

The issue of tuberculosis during pregnancy is not simply a historical inquiry but rather an increasingly familiar clinical problem facing industrial nations as well as the developing countries of the world. This review focuses on the maternal aspects of tuberculous infection, as well as transmission to the fetus and newborn.
Bromodomains in Protozoan Parasites: Evolution, Function, and Opportunities for Drug Development
Authors: Jeffers Victoria , Yang Chunlin , Huang Sherri , Sullivan William J.
Published: January 2017

Parasitic infections remain one of the most pressing global health concerns of our day, affecting billions of people and producing unsustainable economic burdens. The rise of drug-resistant parasites has created an urgent need to study their biology in hopes of uncovering new potential drug targets. It has been established that disrupting gene expression by interfering with lysine acetylation is detrimental to survival of apicomplexan (
Toxoplasma gondii
and
Plasmodium
spp.) and kinetoplastid (
Leishmania
spp. and
Trypanosoma
spp.) parasites. As “readers” of lysine acetylation, bromodomain proteins have emerged as key gene expression regulators and a promising new class of drug target. Here we review recent studies that demonstrate the essential roles played by bromodomain-containing proteins in parasite viability, invasion, and stage switching and present work showing the efficacy of bromodomain inhibitors as novel antiparasitic agents. In addition, we performed a phylogenetic analysis of bromodomain proteins in representative pathogens, some of which possess unique features that may be specific to parasite processes and useful in future drug development.
Pathogenicity Determinants of the Human Malaria Parasite Plasmodium falciparum Have Ancient Origins
Authors: Brazier Andrew J. , Avril Marion , Bernabeu Maria , Benjamin Maxwell , Smith Joseph D.
Published: January 2017

Cytoadhesion of
P. falciparum
-infected erythrocytes in the microcirculation is a major virulence determinant.
P. falciparum
is descended from a subgenus of parasites that also infect chimpanzees and gorillas and exhibits strict host species specificity. Despite their high genetic similarity to
P. falciparum
, it is unknown whether ape parasites encode adhesion properties similar to those of
P. falciparum
or are as virulent in their natural hosts. Consequently, it has been unclear when virulent adhesion traits arose in
P. falciparum
and how long they have been present in the parasite population. It is also unknown whether cytoadhesive interactions pose a barrier to cross-species transmission. We show that parasite domains from the chimpanzee malaria parasite
P. reichenowi
bind human receptors with specificity similar to that of
P. falciparum
. Our findings suggest that parasite adhesion traits associated with both mild and severe malaria have much earlier origins than previously appreciated and have important implications for virulence evolution in a major human pathogen.
Host Range Restriction of Insect-Specific Flaviviruses Occurs at Several Levels of the Viral Life Cycle
Authors: Junglen Sandra , Korries Marvin , Grasse Wolfgang , Wieseler Janett , Kopp Anne , Hermanns Kyra , León-Juárez Moises , Drosten Christian , Kümmerer Beate Mareike
Published: January 2017

Most viruses of the genus
Flavivirus
, e.g., YFV and dengue virus, are mosquito borne and transmitted to vertebrates during blood feeding of mosquitoes. Within the last decade, an increasing number of viruses with a host range exclusively restricted to insects in close relationship to the vertebrate-pathogenic flaviviruses were discovered in mosquitoes. To identify barriers that could block the arboviral vertebrate tropism, we set out to identify the steps at which the ISF replication cycle fails in vertebrates. Our studies revealed blocks at several levels, suggesting that flavivirus host range expansion from insects to vertebrates was a complex process that involved overcoming multiple barriers.
Intracranial infection caused by minor skin contusion associated with previous craniotomy
Authors: Mashiko Ryota , Taguchi Shijima , Tobita Tadamichi , Shibata Yasushi
Published: January 2017

Minor damage to the scalp may lead to intracranial infection. Moreover, the postoperative state of the scalp, skull and meninges is especially noteworthy with respect to invasion of pathogens into the skull. Therefore, a detailed medical history should be obtained from patients with even minor scalp injuries to avoid intracranial infection. We herein report a case of intracranial infection caused by a minor scalp injury associated with previous craniotomy, which was missed at first.