bluuebunny/crossref_metadata_2025 huggingface dataset:
A Study of STEM Assessments in Engineering, Science, and Mathematics for Elementary and Middle School Students
Authors: Harwell Michael , Moreno Mario , Phillips Alison , Guzey S. Selcen , Moore Tamara J. , Roehrig Gillian H.
Published: February 2015

The purpose of this study was to develop, scale, and validate assessments in engineering, science, and mathematics with grade appropriate items that were sensitive to the curriculum developed by teachers. The use of item response theory to assess item functioning was a focus of the study. The work is part of a larger project focused on increasing student learning in science, technology, engineering, and mathematics (STEM)‐related areas in grades 4–8 through an engineering design‐based, integrated approach to STEM instruction and assessment. The fact that the assessments are available to school districts at no cost, and represent psychometrically sound instruments that are sensitive to STEM‐oriented curriculum, offers schools an important tool for gauging students' understanding of engineering, science, and mathematics concepts.
Comparison of two bupivacaine delivery methods to control postoperative pain after enucleation in dogs
Authors: Chow Derek W. Y. , Wong Man Yu , Westermeyer Hans D.
Published: February 2015

Objective

To compare the efficacy of a preoperative retrobulbar injection of bupivacaine to an intraoperative splash block of bupivacaine in controlling postoperative pain following enucleation in dogs.

Animals studied

Prospective, randomized, double‐masked clinical study of 31 client owned dogs with end‐stage ophthalmic disease requiring enucleation.

Procedures

Dogs admitted for unilateral enucleation were randomly assigned to receive bupivacaine 0.5% (1 mL/kg) into the retrobulbar space either via an inferior‐temporal palpebral (ITP) injection preoperatively or an intraoperative splash block. Pain was assessed prior to pre‐anesthetic sedation and at 0, 0.25, 0.5, 1, 2, 4 6, 8, and 24 hours (H) after extubation by masked observers using a previously described subjective pain scoring system. Rescue analgesia was initiated if overall pain score was >9 or if the score in any category at any time point was >3.

Results

There were no adverse reactions. One of 15 dogs that received bupivacaine via a preoperative retrobulbarITPinjection required rescue analgesia. There was no significant difference between groups with regard to the need for rescue analgesia or pain scores at any time point or overall.

Conclusions and Clinical Relevance

Pain control using an intraoperative orbital splash administration of bupivacaine is not significantly different to a preoperative retrobulbar injection of bupivacaine.
The effect of processing method on the in vitro characteristics of red blood cell products
Authors: Hansen A. L. , Kurach J. D. R. , Turner T. R. , Jenkins C. , Busch M. P. , Norris P. J. , Dugger J. , Tomasulo P. A. , Devine D. V. , Acker J. P.
Published: February 2015

Background and Objectives

While the clinical impact of differences in red blood cell (RBC) component processing methods is unknown, there are concerns they may be confounding variables in studies such as the ongoing ‘age of blood’ investigations. Here, we compare the in vitro characteristics of red cell concentrates (RCCs) produced by several different processing methods.

Materials and Methods

Nine processing methods were examined: three apheresis methods (Alyx, MCS+ and Trima), as well as leucoreduced whole blood‐derived RCCs produced by buffy coat and whole blood filtration and non‐leucoreduced RCCs. RCCs were stored in saline–adenine–glucose–mannitol or additive solutions (AS) 1 or 3 for 42 days, with quality tested on day 5 and day 42.

Results

Many significant product differences were observed both early in and at the end of storage. Mean haemoglobin (Hb) ranged from 52 to 71 g/unit and mean Hct from 59·5 to 64·8%. Most RCC passed regulated quality control criteria according to Canadian Standards Association guidelines, although there were some failures relating to Hb content and residual WBC counts.

Conclusion

Processing method impacts RCC characteristics throughout storage; better understanding of these differences and reporting of processing method details is critical.
Sliding Contact Between a Cylindrical Punch and a Graded Half-Plane With an Arbitrary Gradient Direction
Authors: Peijian Chen , Shaohua Chen , Juan Peng
Published: February 2015

Contact behavior of a rigid cylindrical punch sliding on an elastically graded half-plane with shear modulus gradient variation in an arbitrary direction is investigated. The governing partial differential equations and the boundary conditions are achieved with the help of Fourier integral transformation. As a result, the present problem is reduced to a singular integral equation of the second kind, which can be solved numerically. Furthermore, the presently general model can be well degraded to special cases of a lateral gradient half-plane and a homogeneous one. Normal stress in the contact region is predicted with different material parameters, which is usually used to estimate the possibility of surface crack initiation. The moment that is needed to ensure stable sliding of the cylindrical punch on the contact surface is further predicted. The result in the present paper should be helpful for the design of novel graded materials with surfaces of strong abrasion resistance.
Design Exploration for Determining the Set Points of Continuous Casting Operation: An Industrial Application
Authors: Shukla Rishabh , Goyal Sharad , Singh Amarendra K. , Panchal Jitesh H. , Allen Janet K. , Mistree Farrokh
Published: February 2015

To compete with other materials and/or contribute toward light-weighting of vehicles, newer grades of steel are continuously invented and experimented upon. Due to the costs and time involved in such developments, manufacture of new grades of steel at an industrial scale is difficult. We propose a method that is useful for steel manufacturers interested in producing a steel product mix with new grades of steels by predicting the required change in the operating set points of each unit operation in the manufacturing chain of products with the new grade of steel. Here, we demonstrate a method to determine the set points of one unit operation, continuous casting which is measured in terms of conflicting objectives including productivity, quality, and production costs. These parameters are sensitive to the operating set points of casting speed, superheat, mold oscillation frequency, and secondary cooling conditions. To ensure targeted performance and address the challenges of uncertainty and conflicting objectives, an integrated computational method based on surrogate models and the compromise decision support problem (cDSP) is presented. The method is used to explore the design space available for casting operations and determine operating set points to meet requirements imposed on the caster from subsequent downstream processes. This method is of value to the steel industry and enables the rapid and cost effective production of a product mix with a new grade of steel.
Analysis of Weld Formation in Multilayer Ultrasonic Metal Welding Using High-Speed Images
Authors: Shawn Lee S. , Hyung Kim Tae , Jack Hu S. , Cai Wayne W. , Abell Jeffrey A.
Published: February 2015

One of the major challenges in manufacturing automotive lithium-ion batteries and battery packs is to achieve consistent weld quality in joining multiple layers of dissimilar materials. While most fusion welding processes face difficulties in such joining, ultrasonic welding stands out as the ideal method. However, inconsistency of weld quality still exists because of limited knowledge on the weld formation through the multiple interfaces. This study aims to establish real-time phenomenological observation on the multilayer ultrasonic welding process by analyzing the vibration behavior of metal layers. Such behavior is characterized by a direct measurement of the lateral displacement of each metal layer using high-speed images. Two different weld tools are used in order to investigate the effect of tool geometry on the weld formation mechanism and the overall joint quality. A series of microscopies and bond density measurements is carried out to validate the observations and hypotheses of those phenomena in multilayer ultrasonic welding. The results of this study enhance the understanding of the ultrasonic welding process of multiple metal sheets and provide insights for optimum tool design to improve the quality of multilayer joints.
Estimating Lower Bound Limit Loads for Structures Subjected to Multiple Loads
Authors: Hari Manoj Simha C. , Adibi-Asl Reza
Published: February 2015

It is shown that the extended variational theorem of Mura et al. (1965, “Extended Theorems of Limit Analysis,” Q. Appl. Math., 23(2), pp. 171–179) can be applied to structures subjected to more than one load and be used to compute lower bound limit load multipliers. In particular, the multiplier proposed by Simha and Adibi-Asl (2011, “Lower Bound Limit Load Estimation Using a Linear Elastic Analysis,” ASME J. Pressure Vessel Technol., 134(2), p. 021207), which can be computed using an elastic stress field, is shown to be a lower bound. Furthermore, it is demonstrated that lower bound limit load for cracked structures may also be computed using a subvolume selection method. No iterations or elastic modulus adjustment are required. Several analytical and numerical examples that illustrate the procedure are presented.
Negative bias temperature instability threshold voltage shift turnaround in SiGe channel MOSFETs
Authors: Kambour Kenneth E. , Kouhestani Camron , McMarr Patrick , Hughes Harold L. , Steinke Daniel R. , Devine Roderick A. B.
Published: February 2015

Negative bias temperature instability (NBTI) has been measured at various temperatures in high-k gate insulator MOSFETs with buried Si0.65Ge0.35 channels and with regular Si surface channels. Previous studies on both surface channel Si devices and Si1−xGex buried channel devices provide evidence for net positive charge trapping as a function of electrical stressing time albeit reduced for the case of Si1−xGex compared to the Si case. In our case, for buried Si0.65Ge0.35, the authors find initial negative charge trapping followed by positive charge trapping at longer times, typically >10−1 s. The effect is accentuated at higher temperatures and yields a turnaround in the measured threshold voltage shift as a function of stress time. Closer examination of NBTI in high-k gate, Si surface devices stressed at room temperature and 90 °C suggests both electron and hole trapping may be present there although the majority effect is hole trapping.
Electromagnetic effects in high-frequency large-area capacitive discharges: A review
Authors: Liu Yong-Xin , Zhang Yu-Ru , Bogaerts Annemie , Wang You-Nian
Published: February 2015

In traditional capacitively coupled plasmas, the discharge can be described by an electrostatic model, in which the Poisson equation is employed to determine the electrostatic electric field. However, current plasma reactors are much larger and driven at a much higher frequency. If the excitation wavelength λ in the plasma becomes comparable to the electrode radius, and the plasma skin depth δ becomes comparable to the electrode spacing, the electromagnetic (EM) effects will become significant and compromise the plasma uniformity. In this regime, capacitive discharges have to be described by an EM model, i.e., the full set of Maxwell's equations should be solved to address the EM effects. This paper gives an overview of the theory, simulation and experiments that have recently been carried out to understand these effects, which cause major uniformity problems in plasma processing for microelectronics and flat panel display industries. Furthermore, some methods for improving the plasma uniformity are also described and compared.
Pore radius fine tuning of a silica matrix (MCM-41) based on the synthesis of alumina nanolayers with different thicknesses by atomic layer deposition
Authors: Zemtsova Elena G. , Arbenin Andrei Yu. , Plotnikov Alexander F. , Smirnov Vladimir M.
Published: February 2015

The authors investigated a new approach to modify the surface of the mesoporous silica matrix MCM-41. This approach is based on manipulating the chemical composition of the porous surface layer and also on fine tuning the pore radius by applying the atomic layer deposition (ALD) technique. The synthesis of alumina nanolayers was performed on the planar and the porous matrix (MCM-41) by the ALD technique using aluminum tri-sec-butoxide and water as precursors. The authors show that one cycle on silicon, using aluminum tri-sec-butoxide and water as precursors, results in a 1–1.2 Å increase in alumina nanolayer thickness. This is comparable to the increase in thickness per cycle for other precursors such as trimethylaluminum and aluminum chloride. The authors show that the synthesis of an Al2O3 nanolayer on the pore surface of the mesoporous silica matrix MCM-41 by the ALD technique results in a regular change in the porous structure of the samples. The specific porosity (ml/g) of the MCM-41 was 0.95 and that of MCM-41 after 5 ALD cycles was 0.39. The pore diameter (nm) of MCM-41 was 3.3 and that of MCM-41 after 5 ALD cycles was 2.3.
Measurements of isocenter path characteristics of the gantry rotation axis with a smartphone application
Authors: Schiefer H. , Ingulfsen N. , Kluckert J. , Peters S. , Plasswilm L.
Published: February 2015

Purpose:

For stereotactic radiosurgery, the AAPM Report No. 54 [AAPM Task Group 42 (AAPM, 1995)] requires the overall stability of the isocenter (couch, gantry, and collimator) to be within a 1 mm radius. In reality, a rotating system has no rigid axis and thus no isocenter point which is fixed in space. As a consequence, the isocenter concept is reviewed here. It is the aim to develop a measurement method following the revised definitions.

Methods:

The mechanical isocenter is defined here by the point which rotates on the shortest path in the room coordinate system. The path is labeled as “isocenter path.” Its center of gravity is assumed to be the mechanical isocenter. Following this definition, an image‐based and radiation‐free measurement method was developed. Multiple marker pairs in a plane perpendicular to the assumed gantry rotation axis of a linear accelerator are imaged with a smartphone application from several rotation angles. Each marker pair represents an independent measuring system. The room coordinates of the isocenter path and the mechanical isocenter are calculated based on the marker coordinates. The presented measurement method is by this means strictly focused on the mechanical isocenter.

Results:

The measurement result is available virtually immediately following completion of measurement. When 12 independent measurement systems are evaluated, the standard deviations of the isocenter path points and mechanical isocenter coordinates are 0.02 and 0.002 mm, respectively.

Conclusions:

The measurement is highly accurate, time efficient, and simple to adapt. It is therefore suitable for regular checks of the mechanical isocenter characteristics of the gantry and collimator rotation axis. When the isocenter path is reproducible and its extent is in the range of the needed geometrical accuracy, it should be taken into account in the planning process. This is especially true for stereotactic treatments and radiosurgery.
Disordered Eating Behavior, Body Image, and Energy Status of Female Student Dancers
Authors: Robbeson Justine G. , Kruger Herculina Salome , Wright Hattie H.
Published: February 2015

Background:

Modern culture has stereotyped the female body as one that is continually getting thinner. Internalization of the ‘thin’ ideal is partly attributable to the inner ideal to be successful combined with the external pressure imposed by media and others. Many individuals attempt to achieve these ideals by behavior modification that imposes health risks.

Purpose:

To investigate disordered eating (DE) behavior and energy status in female student dancers.

Methods:

Volunteer dancers (n = 26) aged 19.0 (18.0; 21.0) years, matched by controls (n = 26) aged 20.0 (19.0; 21.0) years were recruited. Eating Disorder Inventory-3 (EDI-3) subscales, Three-factor Eating Questionnaire (TFEQ) Cognitive Dietary Restraint (CDR) subscale, and EDI-3 Referral Form behavioral questions assessed DE behavior. Energy status was assessed with a food record and Actiheart monitor.

Results:

Dancers achieved significantly higher scores than controls in all questionnaires, namely: EDI-3 Drive for Thinness [12.0 (3.0; 19.0) vs. 4.5 (2.0; 9.0), p = .023], EDI-3 Body Dissatisfaction [16.0 (10.0; 25.0) vs. 6.5 (3.0; 14.0), p = .004], and TFEQ-CDR [9.0 (2.0; 15.0) vs. 3.0 (3.0; 7.0), p = .032]; dancers used excessive exercise to lose weight (19.2% vs. 0%, c2 = 5.53, p = .019), and had lower energy availability (24% vs. 8%, p < .05) than controls. The average energy balance (EB) was negative for both groups [dancers: EB = -3896 (-5236; -1222) vs. controls: EB = -2639 (-4744; -789) kJ/day].

Conclusions:

Female dancers are at risk for DE behavior and many have suboptimal energy status which may be related to their quest to achieve a more desirable appearance; education on healthy weight management practices is needed.
The Effect of Calcium or Calcium and Vitamin D Supplementation on Bone Mineral Density in Healthy Males: A Systematic Review and Meta-Analysis
Authors: Silk Leslie N. , Greene David A. , Baker Michael K.
Published: February 2015

Research examining the preventative effects of calcium and vitamin D supplementation has focused on children and females, leaving the effects on male bone mineral density (BMD) largely unexplored. Thus, the aim of this systematic review and meta-analysis is to examine the efficacy of calcium supplementation, with or without vitamin D for improving BMD in healthy males. Medline, EMBASE, SPORTDiscus, Academic Search Complete, CINHAHL Plus and PubMed databases were searched for studies including healthy males which provided participants calcium supplementation with or without vitamin D and used changes to BMD as the primary outcome measure. Between trial standardized mean differences of percentage change from baseline in BMD of femoral neck, lumbar spine, total body and total hip sites were calculated. Nine studies were included in the systematic review with six references totaling 867 participants contributing to the meta-analysis. Significant pooled effects size (ES) for comparison between supplementation and control groups were found at all sites included in the meta-analysis. The largest effect was found in total body (ES = 0.644; 95% CI = 0.406–0.883; p < .001), followed by total hip (ES = 0.483, 95% CI= 0.255–0.711, p < .001), femoral neck (ES = 0.402, 95% CI = 0.233–0.570, p = .000) and lumbar spine (ES = 0.306, 95% CI = 0.173–0.440, p < .001). Limited evidence appears to support the use of calcium and vitamin D supplementation for improving BMD in older males. There is a need for high quality randomized controlled trials, especially in younger and middle-aged male cohorts and athletic populations to determine whether supplementation provides a preventative benefit.
The Effect of Neurodegeneration on Visuomotor Behavior in Alzheimer’s Disease and Parkinson’s Disease
Authors: de Boer Casper , van der Steen Johannes , Mattace-Raso Francesco , Boon Agnita J.W. , Pel Johan J.M.
Published: February 2015

The early stages of neurodegenerative disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) involve deterioration of specific (visuo)motor functions. The aim of the current study was to investigate differences in visuomotor behavior between age-matched groups of 17 patients with AD, 17 patients with PD, and 20 healthy control subjects across three eye-hand-coordination tasks of different cognitive complexity. In two of three tasks, timing and execution parameters of eyes and hand significantly differed between groups. Timing and execution parameters of the eyes and hands could potentially give a quantitative description of disease specific deficits in the spatial and temporal domains and may serve as a tool to monitor disease progression in AD and PD populations.
Sensory Interactions for Head and Trunk Control in Space in Young and Older Adults During Normal and Narrow-Base Walking
Authors: Zhang Fang , Deshpande Nandini
Published: February 2015

Fifteen young (20–30 years old) and 15 older (>65 years old) healthy participants were recruited to investigate age-related differences in head and trunk control under suboptimal vestibular conditions (galvanic vestibular stimulation, or GVS) and vision conditions during normal and narrow-based walking. Head-roll velocity decreased in the blurred-vision condition and marginally increased with GVS in older but not in young participants. Head pitch increased, whereas head-roll velocity decreased in narrow-base walking. Trunk pitch, trunk-pitch velocity, and gait speed increased with GVS, whereas trunk-pitch velocity and gait speed decreased in narrow-base walking. Marginally increased head-roll velocity in the older participants possibly suggests decreased integrative ability of the central nervous system in elderly people. The changes in head control during narrow-base walking may be an attempt to simplify the interpretation of the vestibular signal and increase otolith sensitivity. The complexity of controlling the trunk in the mediolateral direction was suggested by different strategies used for trunk control in different conditions.
Amorphous intergranular phases control the properties of rodent tooth enamel
Authors: Gordon Lyle M. , Cohen Michael J. , MacRenaris Keith W. , Pasteris Jill D. , Seda Takele , Joester Derk
Published: February 2015

Key trace minerals greatly strengthen teeth

The outer layers of teeth are made up of nanowires of enamel that are prone to decay. Gordon
et al.
analyzed the composition of tooth enamel from a variety of rodents at the nanometer scale (see the Perspective by Politi). In regular and pigmented enamel, which contain different trace elements at varying boundary regions, two intergranular phases—magnesium amorphous calcium phosphate or a mixed-phase iron oxide—control the rates of enamel demineralization. This suggests that there may be alternative options to fluoridation for strengthening teeth against decay.

Science
, this issue p.
746
; see also p.
712
Structural basis for RNA replication by the hepatitis C virus polymerase
Authors: Appleby Todd C. , Perry Jason K. , Murakami Eisuke , Barauskas Ona , Feng Joy , Cho Aesop , Fox David , Wetmore Diana R. , McGrath Mary E. , Ray Adrian S. , Sofia Michael J. , Swaminathan S. , Edwards Thomas E.
Published: February 2015

A view of the HCV polymerase at work

More than 3% of the world's population is infected with hepatitis C virus (HCV), a predisposing factor for life-threatening liver diseases such as cirrhosis and cancer. HCV encodes a polymerase called NS5B that catalyzes replication of the viral RNA genome. Drugs inhibiting NS5B have shown impressive antiviral activity in recent clinical trials. Appleby
et al.
(see the Perspective by Bressanelli) reveal the inner workings of HCV RNA replication by analyzing crystal structures of stalled NS5B polymerase ternary complexes during the initiation and elongation of RNA synthesis. They also define the way in which sofosbuvir, a drug with potent clinical efficacy, interacts with the NS5B active site.

Science
, this issue p.
771
; see also p.
715
Plastic waste inputs from land into the ocean
Authors: Jambeck Jenna R. , Geyer Roland , Wilcox Chris , Siegler Theodore R. , Perryman Miriam , Andrady Anthony , Narayan Ramani , Law Kara Lavender
Published: February 2015

Dumping lots of plastics into our oceans

Considerable progress has been made in determining the amount and location of plastic debris in our seas, but how much plastic actually enters them in the first place is more uncertain. Jambeck
et al.
combine available data on solid waste with a model that uses population density and economic status to estimate the amount of land-based plastic waste entering the ocean. Unless waste management practices are improved, the flux of plastics to the oceans could increase by an order of magnitude within the next decade.

Science
, this issue p.
768
An arboreal docodont from the Jurassic and mammaliaform ecological diversification
Authors: Meng Qing-Jin , Ji Qiang , Zhang Yu-Guang , Liu Di , Grossnickle David M. , Luo Zhe-Xi
Published: February 2015

Taking advantage of new neighborhoods

Mammals are one of the most morphologically diverse organisms, with adaptation to unique ecological conditions creating a wide array of forms, from mice to whales. Two new basal mammals from the mid-Jurassic period suggest that this diversification was well under way millions of years earlier than previously thought. Luo
et al.
describe a burrowing species with limb and digit modifications similar to those of current burrowers and identify the likely genes and developmental pathways involved. Meng
et al.
describe an arboreal species with modifications for climbing and that possessed teeth clearly adapted for a herbivorous diet, including the consumption of sap.

Science
, this issue p.
760
, p.
764
A data-intensive approach to mechanistic elucidation applied to chiral anion catalysis
Authors: Milo Anat , Neel Andrew J. , Toste F. Dean , Sigman Matthew S.
Published: February 2015

Optimizing a catalyst many ways at once

Optimization strategies are often likened to hikes in a hilly landscape. If your goal is to get to the top of the highest hill, and you only take steps toward higher ground, you might never find a peak on a route that requires a preliminary descent. So it is in chemistry, where optimizing each structural feature of a catalyst consecutively might gloss over subtle tradeoffs that in combination offer the best performance. Milo
et al.
use multidimensional analysis techniques to generate a predictive model of how selectivity depends on multiple characteristics of the catalyst and substrate in a C-N bond-forming reaction (see the Perspective by Lu). They then apply this model to improve the catalyst globally.

Science
, this issue p.
737
; see also p.
719
Structural insight into tight junction disassembly by
Clostridium perfringens
enterotoxin
Authors: Saitoh Yasunori , Suzuki Hiroshi , Tani Kazutoshi , Nishikawa Kouki , Irie Katsumasa , Ogura Yuki , Tamura Atsushi , Tsukita Sachiko , Fujiyoshi Yoshinori
Published: February 2015

How a toxin makes epithelial sheets leaky

The entire human body and its many compartments are shielded from their external environments by the barrier function of epithelial cell sheets. The paracellular barrier function of tight junctions (TJs) is critical for maintaining homeostasis in any multicellular organism, especially in the skin and internal organs and at the blood-brain barrier. One of the major components of TJs is a family of adhesive membrane proteins known as claudins. Several members of the claudin family are receptors for the bacterial toxin
Clostridium perfringens
enterotoxin. This toxin often causes food-borne illness both in humans and animals. Saitoh
et al.
crystallized a complex between the toxin and a claudin that reveals just how the toxin damages epithelial barriers (see the Perspective by Artursson and Knight).

Science
, this issue p.
775
; see also p.
716
Agricultural researchers rattled by demands for documents
Authors: Kloor Keith
Published: February 2015

Group opposed to GM foods asks a dozen scientists to hand over letters, e-mails in probe of academic-industry ties.
Captive pandas succumb to killer virus
Authors: Hvistendahl Mara
Published: February 2015

Deaths at breeding center in China have put scientists on edge.
Greasing the Wheels of Lipidomics
Authors: Dove Alan
Published: February 2015

Lipids have traditionally been among the hardest biomolecules
to study, but new technologies and techniques are gradually
revealing more of the lipidome.
Comment on “Using ecological thresholds to evaluate the costs and benefits of set-asides in a biodiversity hotspot”
Authors: Finney Christopher
Published: February 2015

Banks-Leite
et al
. (Reports, 29 August 2014, p. 1041) conclude that a large-scale program to restore the Brazilian Atlantic Forest using payments for environmental services (PES) is economically feasible. They do not analyze transaction costs, which are quantified infrequently and incompletely in the literature. Transaction costs can exceed 20% of total project costs and should be included in future research.
Randomize evaluations to improve health care delivery
Authors: Finkelstein Amy , Taubman Sarah
Published: February 2015

Administrative data and experimental designs lead the way
Botanical brilliance
Plant Behaviour and Intelligence
Anthony Trewavas
Oxford University Press, 2014. 303 pp.
Authors: Zink Andrew G. , He Zheng-Hui
Published: February 2015

Are plants decision-makers or elaborate fakers?
Just add water dimers
Authors: Okumura Mitchio
Published: February 2015

Fast reaction with water dimers may limit the impact of the simplest Criegee intermediate on atmospheric chemistry

[Also see Report by

Chao
et al.

]
Kickstarting a viral RNA polymerase
Authors: Bressanelli Stéphane
Published: February 2015

Hepatitis C virus RNA–dependent RNA polymerase primes synthesis of its RNA genome with an inbuilt proteinaceous primer

[Also see Report by

Appleby
et al.

]
Clinical Application of Whole-Genome Sequencing To Inform Treatment for Multidrug-Resistant Tuberculosis Cases
Authors: Witney Adam A. , Gould Katherine A. , Arnold Amber , Coleman David , Delgado Rachel , Dhillon Jasvir , Pond Marcus J. , Pope Cassie F. , Planche Tim D. , Stoker Neil G. , Cosgrove Catherine A. , Butcher Philip D. , Harrison Thomas S. , Hinds Jason
Published: February 2015

The treatment of drug-resistant tuberculosis cases is challenging, as drug options are limited, and the existing diagnostics are inadequate. Whole-genome sequencing (WGS) has been used in a clinical setting to investigate six cases of suspected extensively drug-resistant
Mycobacterium tuberculosis
(XDR-TB) encountered at a London teaching hospital between 2008 and 2014. Sixteen isolates from six suspected XDR-TB cases were sequenced; five cases were analyzed in a clinically relevant time frame, with one case sequenced retrospectively. WGS identified mutations in the
M. tuberculosis
genes associated with antibiotic resistance that are likely to be responsible for the phenotypic resistance. Thus, an evidence base was developed to inform the clinical decisions made around antibiotic treatment over prolonged periods. All strains in this study belonged to the East Asian (Beijing) lineage, and the strain relatedness was consistent with the expectations from the case histories, confirming one contact transmission event. We demonstrate that WGS data can be produced in a clinically relevant time scale some weeks before drug sensitivity testing (DST) data are available, and they actively help clinical decision-making through the assessment of whether an isolate (i) has a particular resistance mutation where there are absent or contradictory DST results, (ii) has no further resistance markers and therefore is unlikely to be XDR, or (iii) is identical to an isolate of known resistance (i.e., a likely transmission event). A small number of discrepancies between the genotypic predictions and phenotypic DST results are discussed in the wider context of the interpretation and reporting of WGS results.
Mycobacterium tuberculosis Lineage 7 Strains Are Associated with Prolonged Patient Delay in Seeking Treatment for Pulmonary Tuberculosis in Amhara Region, Ethiopia
Authors: Yimer Solomon A. , Norheim Gunnstein , Namouchi Amine , Zegeye Ephrem D. , Kinander Wibeke , Tønjum Tone , Bekele Shiferaw , Mannsåker Turid , Bjune Gunnar , Aseffa Abraham , Holm-Hansen Carol
Published: February 2015

Recent genotyping studies of
Mycobacterium tuberculosis
in Ethiopia have reported the identification of a new phylogenetically distinct
M. tuberculosis
lineage, lineage 7. We therefore investigated the genetic diversity and association of specific
M. tuberculosis
lineages with sociodemographic and clinical parameters among pulmonary TB patients in the Amhara Region, Ethiopia. DNA was isolated from
M. tuberculosis-
positive sputum specimens (
n
= 240) and analyzed by PCR and 24-locus mycobacterial interspersed repetitive unit–variable-number tandem-repeat (MIRU-VNTR) analysis and spoligotyping. Bioinformatic analysis assigned the
M. tuberculosis
genotypes to global lineages, and associations between patient characteristics and genotype were evaluated using logistic regression analysis. The study revealed a high diversity of modern and premodern
M. tuberculosis
lineages, among which approximately 25% were not previously reported. Among the
M. tuberculosis
strains (
n
= 138) assigned to seven subgroups, the largest cluster belonged to the lineage Central Asian (CAS) (
n
= 60; 26.0%), the second largest to lineage 7 (
n
= 36; 15.6%), and the third largest to the lineage Haarlem (
n
= 35; 15.2%). Four sublineages were new in the MIRU-VNTRplus database, designated NW-ETH3, NW-ETH1, NW-ETH2, and NW-ETH4, which included 24 (10.4%), 18 (7.8%), 8 (3.5%), and 5 (2.2%) isolates, respectively. Notably, patient delay in seeking treatment was significantly longer among patients infected with lineage 7 strains (Mann-Whitney test,
P
< 0.008) than in patients infected with CAS strains (adjusted odds ratio [AOR], 4.7; 95% confidence interval [CI], 1.6 to 13.5). Lineage 7 strains also grew more slowly than other
M. tuberculosis
strains. Cases of Haarlem (OR, 2.8; 95% CI, 1.2 to 6.6) and NW-ETH3 (OR, 2.8; 95% CI, 1.0 to 7.3) infection appeared in defined clusters. Intensified active case finding and contact tracing activities in the study region are needed to expedite diagnosis and treatment of TB.
Impact of Intermittent Preventive Treatment in Pregnancy with Azithromycin-Containing Regimens on Maternal Nasopharyngeal Carriage and Antibiotic Sensitivity of Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus: a Cross-Sectional Survey at Delivery
Authors: Unger Holger W. , Aho Celestine , Ome-Kaius Maria , Wangnapi Regina A. , Umbers Alexandra J. , Jack Wanda , Lafana Alice , Michael Audrey , Hanieh Sarah , Siba Peter , Mueller Ivo , Greenhill Andrew R. , Rogerson Stephen J.
Published: February 2015

Sulfadoxine-pyrimethamine (SP) plus azithromycin (AZ) (SPAZ) has the potential for intermittent preventive treatment of malaria in pregnancy (IPTp), but its use could increase circulation of antibiotic-resistant bacteria associated with severe pediatric infections. We evaluated the effect of monthly SPAZ-IPTp compared to a single course of SP plus chloroquine (SPCQ) on maternal nasopharyngeal carriage and antibiotic susceptibility of
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Staphylococcus aureus
at delivery among 854 women participating in a randomized controlled trial in Papua New Guinea. Serotyping was performed, and antibiotic susceptibility was evaluated by disk diffusion and Etest. Potential risk factors for carriage were examined. Nasopharyngeal carriage at delivery of
S. pneumoniae
(SPAZ, 7.2% [30/418], versus SPCQ, 19.3% [84/436];
P
< 0.001) and
H. influenzae
(2.9% [12/418] versus 6.0% [26/436],
P
= 0.028), but not
S. aureus
, was significantly reduced among women who had received SPAZ-IPTp. The number of macrolide-resistant pneumococcal isolates was small but increased in the SPAZ group (13.3% [4/30], versus SPCQ, 2.2% [2/91];
P
= 0.033). The proportions of isolates with serotypes covered by the 13-valent pneumococcal conjugate vaccine were similar (SPAZ, 10.3% [3/29], versus SPCQ, 17.6% [16/91];
P
= 0.352). Although macrolide-resistant isolates were rare, they were more commonly detected in women who had received SPAZ-IPTp, despite the significant reduction of maternal carriage of
S. pneumoniae
and
H. influenzae
observed in this group. Future studies on SPAZ-IPTp should evaluate carriage and persistence of macrolide-resistant
S. pneumoniae
and other pathogenic bacteria in both mothers and infants and assess the clinical significance of their circulation.
A Signal-to-Cutoff Ratio in the Abbott Architect HIV Ag/Ab Combo Assay That Predicts Subsequent Confirmation of HIV-1 Infection in a Low-Prevalence Setting
Authors: Jensen Tomas Ostergaard , Robertson Peter , Whybin Ross , Chambers Ian , Lahra Monica , Rawlinson William , Post Jeffrey John
Published: February 2015

A rapid diagnosis is considered important in HIV care. In 138,911 testing episodes with the Abbott Architect HIV Ag/Ab Combo assay (3,705 reactive samples), a signal-to-cutoff ratio of >151.17 had a positive predictive value of 100% and a sensitivity of 67.4% for the detection of subsequently confirmed HIV infection. We suggest that results higher than this signal-to-cutoff ratio threshold may be reported to clinicians before the completion of confirmatory testing.
Triatoma Virus Recombinant VP4 Protein Induces Membrane Permeability through Dynamic Pores
Authors: Sánchez-Eugenia Rubén , Goikolea Julen , Gil-Cartón David , Sánchez-Magraner Lissete , Guérin Diego M. A.
Published: February 2015

In naked viruses, membrane breaching is a key step that must be performed for genome transfer into the target cells. Despite its importance, the mechanisms behind this process remain poorly understood. The small protein VP4, encoded by the genomes of most viruses of the order
Picornavirales
, has been shown to be involved in membrane alterations. Here we analyzed the permeabilization activity of the natively nonmyristoylated VP4 protein from triatoma virus (TrV), a virus belonging to the
Dicistroviridae
family within the
Picornavirales
order. The VP4 protein was produced as a C-terminal maltose binding protein (MBP) fusion to achieve its successful expression. This recombinant VP4 protein is able to produce membrane permeabilization in model membranes in a membrane composition-dependent manner. The induced permeability was also influenced by the pH, being greater at higher pH values. We demonstrate that the permeabilization activity elicited by the protein occurs through discrete pores that are inserted on the membrane. Sizing experiments using fluorescent dextrans, cryo-electron microscopy imaging, and other, additional techniques showed that recombinant VP4 forms heterogeneous proteolipidic pores rather than common proteinaceous channels. These results suggest that the VP4 protein may be involved in the membrane alterations required for genome transfer or cell entry steps during dicistrovirus infection.

IMPORTANCE
During viral infection, viruses need to overcome the membrane barrier in order to enter the cell and replicate their genome. In nonenveloped viruses membrane fusion is not possible, and hence, other mechanisms are implemented. Among other proteins, like the capsid-forming proteins and the proteins required for viral replication, several viruses of the order
Picornaviridae
contain a small protein called VP4 that has been shown to be involved in membrane alterations. Here we show that the triatoma virus VP4 protein is able to produce membrane permeabilization in model membranes by the formation of heterogeneous dynamic pores. These pores formed by VP4 may be involved in the genome transfer or cell entry steps during viral infection.
A Mutant H3N2 Influenza Virus Uses an Alternative Activation Mechanism in TMPRSS2 Knockout Mice by Loss of an Oligosaccharide in the Hemagglutinin Stalk Region
Authors: Sakai Kouji , Sekizuka Tsuyoshi , Ami Yasushi , Nakajima Noriko , Kitazawa Minori , Sato Yuko , Nakajima Katsuhiro , Anraku Masaki , Kubota Toru , Komase Katsuhiro , Takehara Kazuaki , Hasegawa Hideki , Odagiri Takato , Tashiro Masato , Kuroda Makoto , Takeda Makoto
Published: February 2015

The host protease TMPRSS2 plays an essential role in proteolytic activation of the influenza A virus (IAV) hemagglutinin (HA) protein possessing a monobasic cleavage site. However, after passages in TMPRSS2 knockout mice, an H3N2 subtype IAV began to undergo cleavage activation of HA, showing high virulence in the mice due to the loss of an oligosaccharide at position 8 in the HA stalk region. Thus, the H3N2 IAV acquired cleavability by an alternative HA activation mechanism/protease(s).
A Mutant Tat Protein Inhibits HIV-1 Reverse Transcription by Targeting the Reverse Transcription Complex
Authors: Lin Min-Hsuan , Apolloni Ann , Cutillas Vincent , Sivakumaran Haran , Martin Sally , Li Dongsheng , Wei Ting , Wang Rui , Jin Hongping , Spann Kirsten , Harrich David
Published: February 2015

Previously, we reported that a mutant of Tat referred to as Nullbasic inhibits HIV-1 reverse transcription although the mechanism of action is unknown. Here we show that Nullbasic is a reverse transcriptase (RT) binding protein that targets the reverse transcription complex rather than directly inhibiting RT activity. An interaction between Nullbasic and RT was observed by using coimmunoprecipitation and pulldown assays, and a direct interaction was measured by using a biolayer interferometry assay. Mixtures of recombinant 6×His-RT and Nullbasic-FLAG-V5-6×His at molar ratios of up to 1:20,000 did not inhibit RT activity in standard homopolymer primer template assays. An analysis of virus made by cells that coexpressed Nullbasic showed that Nullbasic copurified with virus particles, indicating that it was a virion protein. In addition, analysis of reverse transcription complexes (RTCs) isolated from cells infected with wild type or Nullbasic-treated HIV-1 showed that Nullbasic reduced the levels of viral DNA in RTC fractions. In addition, a shift in the distribution of viral DNA and CAp24 to less-dense non-RTC fractions was observed, indicating that RTC activity from Nullbasic-treated virus was impaired. Further analysis showed that viral cores isolated from Nullbasic-treated HIV undergo increased disassembly
in vitro
compared to untreated HIV-1. To our knowledge, this is the first description of an antiviral protein that inhibits reverse transcription by targeting the RTC and affecting core stability.

IMPORTANCE
HIV-1 infection is treated by using combinations of antiretroviral drugs that target independent steps of virus replication. A newly described antiviral protein called Nullbasic can also inhibit a combination of different steps in virus replication (transcription, reverse transcription, and Rev-mediated viral mRNA transport), although the precise mechanism of action is unknown. This study shows that Nullbasic can inhibit reverse transcription by binding to the viral enzyme called reverse transcriptase, which results in accelerated uncoating of the viral core and instability of the viral apparatus called the reverse transcription complex (RTC). This unique antiviral activity may inform development of other RTC inhibitors, as well as providing a unique investigative tool for dissecting the RTC cellular composition.
The Acetyltransferase Tip60 Is a Critical Regulator of the Differentiation-Dependent Amplification of Human Papillomaviruses
Authors: Hong Shiyuan , Dutta Anindya , Laimins Laimonis A.
Published: February 2015

The life cycle of human papillomaviruses (HPVs) is dependent upon differentiation of the infected host epithelial cell as well as activation of the ataxia telangiectasia mutated (ATM) DNA repair pathway that in normal cells acts to repair double-strand DNA breaks. In normal cells, following DNA damage the acetyltransferase Tip60 must acetylate ATM proteins prior to their full activation by autophosphorylation. E6 proteins have been shown to induce the degradation of Tip60, suggesting that Tip60 action may not be required for activation of the ATM pathway in HPV-positive cells. We investigated what role, if any, Tip60 plays in regulating the differentiation-dependent HPV life cycle. Our study indicates that Tip60 levels and activity are increased in cells that stably maintain complete HPV genomes as episomes, while low levels are seen in cells that express only HPV E6 and E7 proteins. Knockdown of Tip60 with short hairpin RNAs in cells that maintain HPV episomes blocked ATM induction and differentiation-dependent genome amplification, demonstrating the critical role of Tip60 in the viral life cycle. The JAK/STAT transcription factor STAT-5 has previously been shown to regulate the phosphorylation of ATM. Our studies demonstrate that STAT-5 regulates Tip60 activation and this occurs in part by targeting glycogen synthase kinase 3β (GSK3β). Inhibition of either STAT-5, Tip60, or GSK3β blocked differentiation-dependent genome amplification. Taken together, our findings identify Tip60 to be an important regulator of HPV genome amplification whose activity during the viral life cycle is controlled by STAT-5 and the kinase GSK3β.

IMPORTANCE
Human papillomaviruses (HPVs) are the etiological agents of cervical and other anogenital cancers. HPVs regulate their differentiation-dependent life cycle by activation of DNA damage pathways. This study demonstrates that HPVs regulate the ATM DNA damage pathway through the action of the acetyltransferase Tip60. Furthermore, the innate immune regulator STAT-5 and the kinase GSK3β mediate the activation of Tip60 in HPV-positive cells. This study identifies critical regulators of the HPV life cycle.
Human Papillomavirus Carcinogenesis: an Identity Crisis in the Retinoblastoma Tumor Suppressor Pathway
Authors: Munger Karl , Jones D. Leanne
Published: February 2015

Viruses are obligate intracellular parasites and need to reprogram host cells to establish long-term persistent infection and/or to produce viral progeny. Cellular changes initiated by the virus trigger cellular defense responses to cripple viral replication, and viruses have evolved countermeasures to neutralize them. Established models have suggested that human papillomaviruses target the retinoblastoma (RB1) and TP53 tumor suppressor networks to usurp cellular replication, which drives carcinogenesis. More recent studies, however, suggest that modulating the activity of the Polycomb family of transcriptional repressors and the resulting changes in epigenetic regulation are proximal steps in the rewiring of cellular signaling circuits. Consequently, RB1 inactivation evolved to tolerate the resulting cellular alterations. Therefore, epigenetic reprograming results in cellular “addictions” to pathways for survival. Inhibition of such a pathway could cause “synthetic lethality” in adapted cells while not markedly affecting normal cells and could prove to be an effective therapeutic approach.