bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceptions of cancer of unknown primary site: a national survey of Australian medical oncologists
Authors: Karapetis Christos S. , Guccione Lisa , Tattersall Martin H. N. , Gooden Helen , Vajdic Claire M. , Lambert Sylvie , Robotin Monica , Mileshkin Linda , Schofield Penelope
Published: January 2017

Background

Despite being the sixth most common cause of cancer death in Australia, cancer of unknown primary (CUP) site remains poorly understood.

Aims

To describe practices relating to the diagnosis, investigation, classification, communication and management of CUP among medical oncologists.

Methods

We invited all members of the Medical Oncology Group of Australia to participate in a national, anonymous online survey about CUP. The survey collected data regarding diagnosis acceptance, diagnostic tests, treatment protocols and communication practices around the diagnosis of CUP.

Results

Three hundred and two oncologists were invited and 86 (28%) completed the survey. Eighty (93%) respondents were directly involved in the assessment of patients with CUP. Eighty‐five (99%) respondents were prepared to make a diagnosis of CUP if, after appropriate diagnostic tests, the primary location could not be ascertained. Eighty‐three percent would assign a primary site to obtain Pharmaceutical Benefits Schedule funding of medical therapy. Sixty‐two percent did not have a specific treatment protocol designed for CUP. The majority of oncologists used serum tumour markers and computed tomography scans in the initial work‐up, while 43% indicated they would use a positron emission tomography scan in the majority of cases. The majority would arrange mammography in female patients. Thematic analysis of responses to open‐ended questions about how CUP is described identified little consistency in the language being used.

Conclusion

The approach to diagnosis, investigation and management of CUP by medical oncologists in Australia is variable. Many preferred to estimate the primary site and treat accordingly. Pharmaceutical Benefits Schedule restrictions may encourage the practice of ‘best guessing’.
Kernel δ18O reflects changes in apical dominance and plant transpiration in tropical maize
Authors: Cabrera‐Bosquet L. , Grieder C. , Alvarez Prado S. , Sánchez C. , Araus J. L.
Published: January 2017

Modification of source–sink ratios in tropical maize through detasseling is an ancestral agronomical practice used for increasing yields under stressful conditions. However, the mechanisms behind such effect are not well understood given the difficulties to determine physiological processes such as photosynthesis and whole‐plant transpiration in the field. We have tested the potential ability of kernel δ18O to assess differences in grain yield (GY) through changes in plant transpiration caused by the modification of water availability and source–sink modification treatments, (including removal of the tassel and different numbers of leaves) in three tropical maize hybrids differing in drought tolerance. Drought‐tolerant genotypes displayed higher yields and lower kernel δ18O values than the drought‐susceptible genotype under both well‐watered (WW) and water‐stressed (WS) conditions. Detasseling caused a positive increase in GY under well‐watered (up to 8%) and water‐deficit conditions (up to 36%). Reduction in leaf area (source) through defoliation treatments caused a large impact on GY showing a trade‐off between maintaining a photosynthetic versus transpiring leaf area. Thus, while a reasonable reduction in leaf area significantly improved plant water availability (as shown by lower kernel δ18O values) and consequently GY under water deficit (up to 40%), it caused a maximum reduction of 25% in GY under well‐watered conditions. Variations in GY were significantly (p < .05) correlated with changes in δ18O under both well‐watered (r = −.67) and WS conditions (r = .75 and .82). Our results also reinforce the utility of δ18O measured in mature kernels as a powerful ecophysiological tool for assessing genotypic differences in apical dominance, transpiration and yield under both WW and WS conditions in tropical maize.
Current practices related to family presence during acute deterioration in adult emergency department patients
Authors: Youngson Megan J , Currey Judy , Considine Julie
Published: January 2017

Aims and objectives

To explore the characteristics of and interactions between clinicians, patients and family members during management of the deteriorating adult patient in the emergency department.

Background

Previous research into family presence during resuscitation has identified many positive outcomes when families are included. However, over the last three decades the epidemiology of acute clinical deterioration has changed, with a decrease in in‐hospital cardiac arrests and an increase in acute clinical deterioration. Despite the decrease in cardiac arrests, research related to family presence continues to focus on care during resuscitation rather than care during acute deterioration.

Design

Descriptive exploratory study using nonparticipatory observation.

Methods

Five clinical deterioration episodes were observed within a 50‐bed, urban, Australian emergency department. Field notes were taken using a semistructured tool to allow for thematic analysis.

Results

Presence, roles and engagement describe the interactions between clinicians, family members and patients while family are present during a patient's episode of deterioration. Presence was classified as no presence, physical presence and therapeutic presence. Clinicians and family members moved through primary, secondary and tertiary roles during patients’ deterioration episode. Engagement was observed to be superficial or deep. There was a complex interplay between presence, roles and engagement with each influencing which form the other could take.

Conclusions

Current practices of managing family during episodes of acute deterioration are complex and multifaceted. There is fluid interplay between presence, roles and engagement during a patient's episode of deterioration.

Relevance to clinical practice

This study will contribute to best practice, provide a strong foundation for clinician education and present opportunities for future research.
Sexual violence in the college population: a systematic review of disclosure and campus resources and services
Authors: Halstead Valerie , Williams Jessica R , Gonzalez‐Guarda Rosa
Published: January 2017

Aims and objectives

To synthesise research examining college student sexual violence disclosure and campus sexual violence resources and services.

Background

Recently, the issue of sexual violence within the college population has garnered attention worldwide. The prevalence of sexual violence within college students is alarmingly high. Survivors often experience negative outcomes (e.g. health‐related consequences, impact on education). Efforts have been made to address this significant public health concern.

Design

Systematic review of published literature.

Methods

Studies were identified through systematic searches of PubMed, CINAHL and PsycInfo of articles published between January 2010–February 2015. A total of 672 articles were identified. After screening, 16 articles were included in this review.

Results

A lack of consistency in how sexual violence was referred to and measured was identified. Research on college student sexual violence disclosure has primarily been conducted in six areas: (1) informal disclosure, (2) formal disclosure, (3) friends’ perceptions of disclosure, (4) process/effects of disclosure on the survivor, (5) barriers to disclosure and (6) social support in the disclosure process. Research related to campus sexual violence resources and services has primarily focused on: (1) students’ knowledge, (2) students’ utilization and (3) students’ suggestions. Synthesised findings are presented.

Conclusions

Sexual violence impacts college student survivors and the campus community as a whole. To appropriately assist/address sexual violence, a thorough understanding of college student sexual violence disclosure and campus sexual violence resources/services is necessary. Suggestions for researchers, colleges and nurses are provided.

Relevance to clinical practice

Nurses who serve students, especially those at on‐campus student health centres, are opportunely placed to address sexual violence. Findings highlight the need for nurses to use consistent definitions of sexual violence when identifying survivors. Nurses should take measures to increase disclosure and promote sexual violence resources/services provided by their facility. Additional suggestions for nurses are provided.
Re‐establishment of the overlooked species Torenia godefroyi (Linderniaceae), and notes on the identity of T. lindernioides
Authors: Prasad M. G. , Roy R. K. , Sunojkumar P.
Published: January 2017

Torenia godefroyi, an Asian species overlooked since first described, has been considered as a variety of Lindernia crustacea (now treated as Torenia crustacea). However, detailed examination of fresh specimens, type and additional material clearly indicates that T. godefroyi is distinct from T. crustacea. Therefore, T. godefroyi is re‐established here as a distinct species. Furthermore, the taxonomic identity of another Asian species, Torenia lindernioides, described from India is discussed. We observe that morphological characters of T. lindernioides overlap with T. godefroyi and suggest to synonymise it under T. godefroyi. An amended description, photographs, and notes about the distribution and habitat of T. godefroyi are provided.
Foliar uptake of radiocaesium from irrigation water by paddy rice (Oryza sativa): an overlooked pathway in contaminated environments
Authors: Uematsu Shinichiro , Vandenhove Hildegarde , Sweeck Lieve , Hees May Van , Wannijn Jean , Smolders Erik
Published: January 2017

Flooded (paddy) rice (Oryza sativa) can take up ions from the irrigation water by foliar uptake via the exposed stem base. We hypothesised that the stem base uptake of radiocaesium (RCs) is a pathway for rice grown in RCs‐contaminated environments.

We developed a bi‐compartmental device which discriminates the stem base from root RCs uptake from solutions, thereby using RCs isotopes (137Cs and 134Cs) with < 2% solution leak between the compartments.

Radiocaesium uptake was linear over time (0–24 h). Radiocaesium uptake to the entire plant, expressed per dry weight of the exposed parts, was sixfold higher for the roots than for the exposed stem base. At equal RCs concentrations in both compartments, the exposed stem base and root uptake contributed almost equally to the total shoot RCs concentrations. Reducing potassium supply to the roots not only increased the root RCs uptake but also increased RCs uptake by the stem base.

This study was the first to experimentally demonstrate active and internally regulated RCs uptake by the stem base of rice. Scenario calculations for the Fukushima‐affected area predict that RCs in irrigation water could be an important source of RCs in rice as indirectly suggested from field data.
Visual perception of faces with unilateral and bilateral cleft lip and palate: An Eye‐Tracking Study
Authors: Dindaroğlu Furkan , Doğan Servet , Amado Sonia , Doğan Ege
Published: January 2017

Structured Abstract

Objectives

To test the hypotheses that there are differences between orthodontists, individuals with cleft lip and palate (CLP) and laypersons in the visual perception of faces with unilateral (UCLP) and bilateral cleft lip and palate (BCLP), the faces with UCLP and BCLP are visually perceived differently and the hierarchy of visual attention changes when viewing individuals with CLP.

Setting and Sample Population

Department of Orthodontics and Experimental Psychology at Ege University, İzmir. Sixty images (faces with a social smile and at rest) of 30 volunteers (unaffected controls, UCLP, BCLP) were viewed by 80 participants: orthodontists, individuals with CLP and laypersons.

Materials and Methods

Eye fixations on four areas of interest were quantified: eyes, nose, upper lip and lower lip–chin. Time to first fixation, fixation before, fixation count and fixation duration parameters were analysed.

Results

Orthodontists fixated on the upper‐lip area more often than laypersons or individuals with CLP (F2.144=8.47, P=.00, η²=.19 in faces at rest). The upper‐lip area received more fixations (F2.144=21.93, P=.00, η²=.23) and longer fixation durations (F2.144=28.86, P=.00, η²=.27) from all participants who gazed on faces with UCLP and a social smile.

Conclusion

The hypotheses of the study were supported. Orthodontists and laypersons focused more attention on the upper lip and eyes in the resting position, respectively. The upper‐lip area of the BCLP images captured more attention at rest.
Molecular mechanisms and ecological function of far‐red light signalling
Authors: Sheerin David J. , Hiltbrunner Andreas
Published: January 2017

Land plants possess the ability to sense and respond to far‐red light (700–760 nm), which serves as an important environmental cue. Due to the nature of far‐red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far‐red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far‐red light through phyA and the physiological responses to this light quality. Light‐activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red‐light responses, phyA is transported from the cytoplasm to the nucleus in far‐red light by the shuttle proteins FAR‐RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1‐LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far‐red light; current hypotheses are discussed.
Ischemic stroke in Kawasaki disease
Authors: Prangwatanagul Wasana , Limsuwan Alisa
Published: January 2017

Pediatric stroke is considered to be rare. Stroke resulting from cerebral vasculitis is also uncommon in young children. With the increasing prevalence of Kawasaki disease (KD) diagnosis, this acquired vasculitis has been reported with various clinical presentations including neurological symptoms. Herein we describe the case of a KD patient presenting with stroke. A 15‐month‐old boy was referred due to stroke that occurred on the fifth day of febrile illness. He was initially admitted to another hospital due to fever and diarrhea. He was discharged and re‐admitted 2 days afterward due to left hemiplegia. During the 10 days of the second hospitalization, he had a presumptive diagnosis of encephalomeningitis. Upon referral to the present hospital, he was found to have right middle cerebral artery branch stenosis and fusiform aneurysms of the coronary arteries. Retrospectively, the patient had the full clinical criteria for KD diagnosis. Therefore, stroke could be considered as one of the uncommon clinical manifestations of KD.
No‐tillage with half‐amount residue retention enhances microbial functional diversity, enzyme activity and glomalin‐related soil protein content within soil aggregates
Authors: Dai Jue , Hu Junli , Zhu Anning , Lin Xiangui
Published: January 2017

A 3‐year field tillage and residue management experiment established in North China was used to analyse topsoil (0–15 cm) aggregation, and microbial functional diversity, enzyme activity and glomalin‐related soil protein (GRSP) content within aggregates. Compared with conventional tillage (CT), no‐tillage (NT) alone significantly (P < 0.05) increased organic C contents in 50–250 and <2 μm aggregates and decreased the proportion of C accumulated by 2–50 μm aggregates and microbial functional diversity indices in <2 μm aggregates. Regardless of tillage practice, both half‐amount (C50) and full (C100) residue retention tended to increase organic C and GRSP contents, or dehydrogenase and invertase activities, in certain aggregates. Under CT, a poorer performance of C50 than C100 was observed in maintaining Shannon index (H′) and Simpson index (D) in >250 and <2 μm aggregates, and also McIntosh index (U) in <2 μm aggregates, owing to insufficient residue and possible decreases in the distribution of decomposer micro‐organisms. Under NT, however, C50 was more effective than C100 in maintaining/elevating H′, D and U in all soil aggregates except for 50–250 μm, suggesting that surplus residue may induce worse soil conditions, decreasing heterotrophic microbial activities. Thus, NT with half‐amount residue retention improved soil physical–chemical–biological properties and could be a useful management practice in North China.
Linearizing Structures
Authors: Bachrach Asaf , Katzir Roni
Published: January 2017

The linearization of unboundedly many syntactic structures given a finite number of ordering instructions poses a compositionality problem similar to the semantic problem of determining the meanings of unboundedly many structures. We discuss this challenge and use various constructions such as Right‐Node Raising that have been argued to involve multidominance—and that combine a remarkable productivity across and inside languages with a sensitivity to linear order—to tease apart different theories of linearization. We use data from such constructions, including new data provided in the paper, to argue in favor of a specific view of linearization first proposed in Bachrach & Katzir, one in which linearization compatibility requirements are computed very locally, at every node in the structure.
Description of the novel KIR2DL1*034 allele Identified from a southern Chinese Han individual
Authors: Chen R. , Zhang G.‐B. , Deng Z.‐H.
Published: January 2017

The novel KIR2DL1*034 allele differs from the closest allele KIR2DL1*00302 by a single missense mutation.
A review of maternal alloimmunisation to Rh D in Northern Ireland
Authors: McCauley C. J. , Morris K. , Maguire K.
Published: January 2017

Objectives

To estimate the current incidence of maternal sensitisation to Rhesus (Rh) D in Northern Ireland, examine adherence to recommendations for administration of anti‐D immunoglobulin and identify potential causes for all cases of anti‐D alloimmunisation sensitisation from January 2010 to September 2015.

Background

Post‐partum anti‐D immunoglobulin administered to Rh D‐negative women and routine antenatal anti‐D prophylaxis have greatly reduced the incidence of haemolytic disease of the fetus and newborn due to immune anti‐D. Despite these measures, anti‐D alloimmunisation sensitisation continues to occur, albeit much less frequently than in the past.

Methods/Materials

This was a retrospective review of new sensitisations to Rh D detected in antenatal records between January 2010 and September 2015 in Northern Ireland. A review of patient notes and laboratory data was carried out to examine adherence to standards and identify potential causes of sensitisation.

Results

A total of 67 new sensitisations to Rh D were identified over a 69‐month period, and the sensitisation rate for the full calendar years 2010–2014 was 0·310%. Only 4% of cases appear to have been preventable, with two cases involving failure to adhere to guidelines.

Conclusion

A total 96% of sensitisations occurred despite full compliance with guidelines. In a large proportion, sensitisation occurred following delivery (51%). A change in practice in Northern Ireland is under consideration to increase the dose of anti‐D immunoglobulin given following delivery from 500 to 1500 U in an attempt to reduce these sensitisations.
Task‐sharing with nurses to enhance access to HIV treatment in Côte d'Ivoire
Authors: McNairy Margaret L. , Bashi Jules B. , Chung Hannah , Wemin Louise , Lorng Marie‐Nicole Akpro , Brou Hermann , Nioble Cyprien , Lokossue A. , Abo Kouame , Achi Delphine , Ouattara Kiyali , Sess Daniel , Sanogo Pongathie Adama , Ekra Alexandre , Ettiegne‐Traore Virginie , Diabate Conombo J. , Abrams Elaine J. , El‐Sadr Wafaa M.
Published: January 2017

Objective

We report the first national programme in Côte d'Ivoire to evaluate the feasibility of nurse‐led HIV care as a model of task‐sharing with nurses to increase coverage and decentralisation of HIV services.

Methods

Twenty‐six public HIV facilities implemented either a nurse‐with‐onsite‐physician or a nurse‐with‐visiting‐physician model of HIV task‐sharing. Routinely collected patient data were reviewed to analyse patient characteristics of those enrolling in care and initiating antiretroviral therapy (ART). Retention, loss to programme and death were compared across facility‐level characteristics.

Results

A total of 1224 patients enrolled in HIV care, with 666 initiating ART, from January 2012 to May 2013 (median follow‐up 13 months). The majority (94%) were adults ≥15 years. Fourteen facilities provided ART initiation for the first time during the pilot period; 20 facilities were primary level. Nurse‐led care with a visiting physician was provided in 14 of the primary‐level facilities. Nurse‐led ART care with an onsite physician was provided in all secondary‐level facilities and six of the primary‐level facilities. During the pilot, 567 (85%) of patients were retained, 28 (4.2%) died, 47 (7.1%) were lost to follow‐up, and 24 (3.6%) transferred. Five deaths (10.9%) were recorded among children as compared to 23 deaths (3.7%) among adults (P = 0.037). There were no differences in retention by model of nurse‐led ART care.

Conclusion

Task‐sharing of HIV care and ART initiation with nurses in Côte d'Ivoire is feasible. This pilot illustrates two models of nurse‐led HIV care and has informed national policy on nurse‐led HIV care in Côte d'Ivoire.
A formula for certain Shalika germs of ramified unitary groups
Authors: Tsai Cheng-Chiang
Published: January 2017

In this article, for nilpotent orbits of ramified quasi-split unitary groups with two Jordan blocks, we give closed formulas for their Shalika germs at certain equi-valued elements with half-integral depth previously studied by Hales. Associated with these elements are hyperelliptic curves defined over the residue field, and the numbers we obtain can be expressed in terms of Frobenius eigenvalues on the first$\ell$-adic cohomology of the curves, generalizing previous result of Hales on stable subregular Shalika germs. These Shalika germ formulas imply new results on stability and endoscopic transfer of nilpotent orbital integrals of ramified unitary groups. We also describe how the same numbers appear in the local character expansions of specific supercuspidal representations and consequently dimensions of degenerate Whittaker models.
Barrier tuning of atomic layer deposited Ta2O5 and Al2O3 in double dielectric diodes
Authors: Nemr Noureddine Ibrahim , Sedghi Naser , Mitrovic Ivona Z. , Hall Steve
Published: January 2017

The performance of ultrathin atomic layer deposited dielectrics of low (Al2O3) and high (Ta2O5) electron affinity (χ) is investigated in metal-insulator-(insulator)-metal [MI(I)M] diodes. The conduction mechanisms in 4 nm thick atomic layer deposited Al2O3 and Ta2O5 single barrier MIM diodes are first studied to show the dominance of tunneling and thermally activated Poole–Frenkel emission, respectively, in these oxides. Varying the layer thickness of Ta2O5 with a 1 nm thick layer of Al2O3 shows evidence for resonant tunneling in double barrier MIIM structures and is correlated with the simulated bound states in the quantum well formed between the two dielectrics. These findings demonstrate experimental work on barrier tuning of resonant tunneling diodes with sufficient rectifying capability at a turn-on voltage as low as 0.32 V enabling their potential use in terahertz applications.
Economical rotatable holder for magnetotransport measurements
Authors: Narasimham Avyaya J. , Pennock Daniel , Potter Graham J. , Taylor Brian , LaBella Vincent P.
Published: January 2017

A low cost rotatable holder is designed and fabricated for the Quantum Design VersaLab that enables rotation of the device over 90° without the need for rewiring. This allows the magnetic field to be oriented from in plane to perpendicular to plane for the devices, enabling angle dependent measurements. Several measurements are performed to test performance against the standard sample mounting puck that comes with the system. In addition, anomalous Hall measurements are performed on Si|SiO2|Ta (5 nm)|CoFeB (1 nm)|MgO (1.6 nm)|Ta (Cap) devices with the field perpendicular and parallel to the plane of the sample to demonstrate rotation.
The symmetry and coupling properties of solutions in general anisotropic multilayer waveguides
Authors: Hernando Quintanilla F. , Lowe M. J. S. , Craster R. V.
Published: January 2017

Multilayered plate and shell structures play an important role in many engineering settings where, for instance, coated pipes are commonplace such as in the petrochemical, aerospace, and power generation industries. There are numerous demands, and indeed requirements, on nondestructive evaluation (NDE) to detect defects or to measure material properties using guided waves; to choose the most suitable inspection approach, it is essential to know the properties of the guided wave solutions for any given multilayered system and this requires dispersion curves computed reliably, robustly, and accurately. Here, the circumstances are elucidated, and possible layer combinations, under which guided wave solutions, in multilayered systems composed of generally anisotropic layers in flat and cylindrical geometries, have specific properties of coupling and parity; the partial wave decomposition of the wave field is utilised to unravel the behaviour. A classification into five families is introduced and the authors claim that this is the fundamental way to approach generally anisotropic waveguides. This coupling and parity provides information to be used in the design of more efficient and robust dispersion curve tracing algorithms. A critical benefit is that the analysis enables the separation of solutions into categories for which dispersion curves do not cross; this allows the curves to be calculated simply and without ambiguity.
Temporal characterization of experimental recorder attack transients
Authors: Ernoult A. , Fabre B.
Published: January 2017

Through the comparison of notes produced on two recorders by one novice and two experienced players in musical contexts, this study identifies the temporal aspects of the attack transients which are controlled by the player and those which are imposed by the dynamic response of the instrument. The rise times of mouth pressure used by the novice player are longer than the ones produced by the experienced players, which are the shortest ones preserving the control of the jet velocity rise times. For shortest rise times, the jet development is limited by the inertia of the channel. The onset time of the acoustic oscillation is divided in two parts: the time needed to initiate the oscillation and the duration of the growth. The times of growth are similar for the novice and the experienced players, which is linked to the similarity of the gain characterizing the linear behavior of the instrument. The times needed to initiate the oscillation show the most pronounced difference between the two types of players; it is much longer for a novice player. This difference is interpreted in terms of the initial input of energy in the system which is larger for the experienced players.
Signal competition in optical coherence tomography and its relevance for cochlear vibrometry
Authors: Lin Nathan C. , Hendon Christine P. , Olson Elizabeth S.
Published: January 2017

The usual technique for measuring vibration within the cochlear partition is heterodyne interferometry. Recently, spectral domain phase microscopy (SDPM) was introduced and offers improvements over standard heterodyne interferometry. In particular, it has a penetration depth of several mm due to working in the infrared range, has narrow and steep optical sectioning due to using a wideband light source, and is able to measure from several cochlear layers simultaneously. However, SDPM is susceptible to systematic error due to “phase leakage,” in which the signal from one layer competes with the signal from other layers. Here, phase leakage is explored in vibration measurements in the cochlea and a model structure. The similarity between phase leakage and signal competition in heterodyne interferometry is demonstrated both experimentally and theoretically. Due to phase leakage, erroneous vibration amplitudes can be reported in regions of low reflectivity that are near structures of high reflectivity. When vibration amplitudes are greater than ∼0.1 of the light source wavelength, phase leakage can cause reported vibration waveforms to be distorted. To aid in the screening of phase leakage in experimental results, the error is plotted and discussed as a function of the important parameters of signal strength and vibration amplitude.
Mixed results from cancer replications unsettle field
Authors: Kaiser Jocelyn
Published: January 2017

Only two confirmations in first five results.
How do gut microbes help herbivores? Counting the ways
Authors: Pennisi Elizabeth
Published: January 2017

Symbiotic bacteria lend talents that range from recycling nitrogen to taming plant toxins.
Protein structure determination using metagenome sequence data
Authors: Ovchinnikov Sergey , Park Hahnbeom , Varghese Neha , Huang Po-Ssu , Pavlopoulos Georgios A. , Kim David E. , Kamisetty Hetunandan , Kyrpides Nikos C. , Baker David
Published: January 2017

Filling in the protein fold picture

Fewer than a third of the 14,849 known protein families have at least one member with an experimentally determined structure. This leaves more than 5000 protein families with no structural information. Protein modeling using residue-residue contacts inferred from evolutionary data has been successful in modeling unknown structures, but it requires large numbers of aligned sequences. Ovchinnikov
et al.
augmented such sequence alignments with metagenome sequence data (see the Perspective by Söding). They determined the number of sequences required to allow modeling, developed criteria for model quality, and, where possible, improved modeling by matching predicted contacts to known structures. Their method predicted quality structural models for 614 protein families, of which about 140 represent newly discovered protein folds.

Science
, this issue p.
294
; see also p.
248
Mechanistic basis for a molecular triage reaction
Authors: Shao Sichen , Rodrigo-Brenni Monica C. , Kivlen Maryann H. , Hegde Ramanujan S.
Published: January 2017

Deciding a protein's fate

Protein synthesis inside cells is finely balanced with protein degradation to maintain homeostasis. Shao
et al.
show how differential affinities and binding kinetics of three chaperones regulate the fate of tail-anchored (TA) membrane proteins. The chaperone SGTA binds to TA proteins and quickly transfers them to the targeting factor TRC40 through the C-terminal domain of the quality-control module BAG6. Proteins that dissociate from SGTA can either rebind or, at a slower rate, be bound by the C-terminal domain of BAG6. The latter puts them on a path to degradation. This hierarchy means that biosynthesis has the higher priority, but excess free TA proteins are degraded.

Science
, this issue p.
298
A peptide hormone required for Casparian strip diffusion barrier formation in
Arabidopsis
roots
Authors: Nakayama Takuya , Shinohara Hidefumi , Tanaka Mina , Baba Koki , Ogawa-Ohnishi Mari , Matsubayashi Yoshikatsu
Published: January 2017

Keeping roots water-tight

The Casparian strip provides a waterproofing function to plant roots, protecting them against unregulated influxes of water and minerals. The integrity of the Casparian strip depends on a receptor-like kinase. Doblas
et al.
and Nakayama
et al.
now identify the peptide ligands in the core of the root (the stele) that help regulate Casparian strip formation. The receptor is expressed on the outward-facing surface of the root endodermal cells that surround the stele. When the endodermal layer is sealed by the Casparian strip, the peptide ligands cannot reach their receptors. When the endodermal layer is breached, whether by damage or during development, the peptides reach their receptors and activate signaling that encourages lignin deposition, shoring up the strips.

Science
, this issue p.
280
, p.
284
Scaling carbon nanotube complementary transistors to 5-nm gate lengths
Authors: Qiu Chenguang , Zhang Zhiyong , Xiao Mengmeng , Yang Yingjun , Zhong Donglai , Peng Lian-Mao
Published: January 2017

Moving transistors downscale

One option for extending the performance of complementary metal-oxide semiconductor (CMOS) devices based on silicon technology is to use semiconducting carbon nanotubes as the gates. Qiu
et al.
fabricated top-gated carbon nanotube field-effect transistors with a gate length of 5 nm. Thin graphene contacts helped maintain electrostatic control. A scaling trend study revealed that, compared with silicon CMOS devices, the nanotube-based devices operated much faster and at much lower supply voltage, and they approached the limit of one electron per switching operation.

Science
, this issue p.
271
Transformation of bulk alloys to oxide nanowires
Authors: Lei Danni , Benson Jim , Magasinski Alexandre , Berdichevsky Gene , Yushin Gleb
Published: January 2017

Alcohols remove lithium to make nanowires

Many existing routes for making metal and metal oxide nanowires are complex, require harsh solvents, or are not easily scaled up. Lei
et al.
developed an extraction process to remove lithium from aluminum or magnesium alloys by using alcohol solvents. The resulting highly reactive Al or Mg atoms formed alkoxide nanowires, which could be converted into oxides by high-temperature treatment. The authors used this approach to produce Al
2
O
3
separators that enhanced the safety of lithium batteries.

Science
, this issue p.
267
Draft Genome Sequences of Three Aeromonas hydrophila Isolates from Catfish and Tilapia
Authors: Tekedar Hasan C. , Kumru Salih , Kalindamar Safak , Karsi Attila , Waldbieser Geoffrey C. , Sonstegard Tad , Schroeder Steven G. , Liles Mark R. , Griffin Matt J. , Lawrence Mark L.
Published: January 2017

Aeromonas hydrophila
is a Gram-negative bacterium that is particularly adapted to freshwater environments and can cause severe infections in fish and humans. Here, we report the draft genomes of three
A. hydrophila
catfish and tilapia isolates.
Rapid Aminoglycoside NP Test for Rapid Detection of Multiple Aminoglycoside Resistance in Enterobacteriaceae
Authors: Nordmann Patrice , Jayol Aurélie , Dobias Jan , Poirel Laurent
Published: January 2017

The rapid aminoglycoside NP (Nordmann/Poirel) test was developed to rapidly identify multiple aminoglycoside (AG) resistance in
Enterobacteriaceae
. It is based on the detection of the glucose metabolism related to enterobacterial growth in the presence of a defined concentration of amikacin plus gentamicin. Formation of acid metabolites was evidenced by a color change (orange to yellow) of the red phenol pH indicator. The rapid aminoglycoside NP test was evaluated by using bacterial colonies of 18 AG-resistant isolates producing 16S rRNA methylases, 20 AG-resistant isolates expressing AG-modifying enzymes (acetyl-, adenyl-, and phosphotransferases), and 10 isolates susceptible to AG. Its sensitivity and specificity were 100% and 97%, respectively, compared to the broth dilution method, which was taken as the gold standard for determining aminoglycoside resistance. The test is inexpensive, rapid (<2 h), and implementable worldwide.
Molecular and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Characterization of Clinically Significant Melanized Fungi in India
Authors: Singh Ashutosh , Singh Pradeep Kumar , Kumar Anil , Chander Jagdish , Khanna Geetika , Roy Pradip , Meis Jacques F. , Chowdhary Anuradha
Published: January 2017

Melanized or black fungi are a heterogeneous group of fungi causing cutaneous to systemic diseases with high mortality. These fungi are rarely reported as agents of human infections, primarily due to difficulties in their classical identification. In this study, we examined, using molecular methods and matrix-assisted laser desorption ioniazation–time of flight mass spectrometry (MALDI-TOF MS), the diversity of melanized fungi (MF) isolated from patients in 19 medical centers in India. Overall, during a 4-year period, 718 (5.3%) clinical specimens yielded MF. Of these, 72 (10%) isolates had clinical significance and were identified primarily by sequencing the internal transcribed spacer and large subunit (LSU) regions. MF represented 21 genera comprising 29 species, the majority of them belonging to the orders Pleosporales (50%) and Chaetothyriales (22%). Among the 29 fungal species identified in this study, only 6 (20%) species were identified by the MALDI-TOF MS due to the limited commercial database of Bruker Daltonics for MF. However, a 100% identification rate of 20 additional species identified in this study was obtained by constructing an in-house database using 24- to 96-h-old liquid cultures. Further, the CLSI broth microdilution method revealed low MICs for posaconazole (≤1 μg/ml) and voriconazole (≤2 μg/ml) in 96% and 95% of isolates, respectively. Skin/subcutaneous and sino-nasal and pulmonary phaeohyphomycosis due to MF were diagnosed in 21.4% (
n
= 15) and 28.5% (
n
= 20) of cases. Also, 10% of patients had central nervous system involvement (
n
= 7), and 3 cases of fungal osteomyelitis due to
Cladophialophora bantiana
and
Corynespora
spp. were observed.
Herpes Simplex Virus 1 UL24 Abrogates the DNA Sensing Signal Pathway by Inhibiting NF-κB Activation
Authors: Xu Haiyan , Su Chenhe , Pearson Angela , Mody Christopher H. , Zheng Chunfu
Published: January 2017

Cyclic GMP-AMP synthase (cGAS) is a newly identified DNA sensor that recognizes foreign DNA, including the genome of herpes simplex virus 1 (HSV-1). Upon binding of viral DNA, cGAS produces cyclic GMP-AMP, which interacts with and activates stimulator of interferon genes (STING) to trigger the transcription of antiviral genes such as type I interferons (IFNs), and the production of inflammatory cytokines. HSV-1 UL24 is widely conserved among members of the herpesviruses family and is essential for efficient viral replication. In this study, we found that ectopically expressed UL24 could inhibit cGAS-STING-mediated promoter activation of IFN-β and interleukin-6 (IL-6), and UL24 also inhibited interferon-stimulatory DNA-mediated IFN-β and IL-6 production during HSV-1 infection. Furthermore, UL24 selectively blocked nuclear factor κB (NF-κB) but not IFN-regulatory factor 3 promoter activation. Coimmunoprecipitation analysis demonstrated that UL24 bound to the endogenous NF-κB subunits p65 and p50 in HSV-1-infected cells, and UL24 was also found to bind the Rel homology domains (RHDs) of these subunits. Furthermore, UL24 reduced the tumor necrosis factor alpha (TNF-α)-mediated nuclear translocation of p65 and p50. Finally, mutational analysis revealed that the region spanning amino acids (aa) 74 to 134 of UL24 [UL24(74–134)] is responsible for inhibiting cGAS-STING-mediated NF-κB promoter activity. For the first time, UL24 was shown to play an important role in immune evasion during HSV-1 infection.

IMPORTANCE
NF-κB is a critical component of the innate immune response and is strongly induced downstream of most pattern recognition receptors (PRRs), leading to the production of IFN-β as well as a number of inflammatory chemokines and interleukins. To establish persistent infection, viruses have evolved various mechanisms to counteract the host NF-κB pathway. In the present study, for the first time, HSV-1 UL24 was demonstrated to inhibit the activation of NF-κB in the DNA sensing signal pathway via binding to the RHDs of the NF-κB subunits p65 and p50 and abolishing their nuclear translocation.
Rhinovirus C, Asthma, and Cell Surface Expression of Virus Receptor CDHR3
Authors: Palmenberg Ann C.
Published: January 2017

Human rhinoviruses (RVs) of the A, B, and C species are defined agents of the common cold. But more than that, RV-A and RV-C are the dominant causes of hospitalization category infections in young children, especially those with asthma. The use of cadherin-related family member 3 (CDHR3) by RV-C as its cellular receptor creates a direct phenotypic link between human genetics (G versus A alleles cause Cys529 versus Tyr529 protein variants) and the efficiency with which RV-C can infect cells. With a lower cell surface display density, the human-specific Cys529 variant apparently confers partial protection from the severest virus-induced asthma episodes. Selective pressure favoring the Cys529 codon may have coemerged with the evolution of RV-C and helped shape modern human genomes against the virus-susceptible, albeit ancestral Tyr529.
Glycosylation of the Hemagglutinin Protein of H5N1 Influenza Virus Increases Its Virulence in Mice by Exacerbating the Host Immune Response
Authors: Zhao Dongming , Liang Libin , Wang Shuai , Nakao Tomomi , Li Yanbing , Liu Liling , Guan Yuntao , Fukuyama Satoshi , Bu Zhigao , Kawaoka Yoshihiro , Chen Hualan
Published: January 2017

The highly pathogenic avian influenza (HPAI) H5N1 viruses continue to circulate in nature and threaten public health. Although several viral determinants and host factors that influence the virulence of HPAI H5N1 viruses in mammals have been identified, the detailed molecular mechanism remains poorly defined and requires further clarification. In our previous studies, we characterized two naturally isolated HPAI H5N1 viruses that had similar viral genomes but differed substantially in their lethality in mice. In this study, we explored the molecular determinants and potential mechanism for this difference in virulence. By using reverse genetics, we found that a single amino acid at position 158 of the hemagglutinin (HA) protein substantially affected the systemic replication and pathogenicity of these H5N1 influenza viruses in mice. We further found that the G158N mutation introduced an N-linked glycosylation at positions 158 to 160 of the HA protein and that this N-linked glycosylation enhanced viral productivity in infected mammalian cells and induced stronger host immune and inflammatory responses to viral infection. These findings further our understanding of the determinants of pathogenicity of H5N1 viruses in mammals.

IMPORTANCE
Highly pathogenic avian influenza (HPAI) H5N1 viruses continue to evolve in nature and threaten human health. Key mutations in the virus hemagglutinin (HA) protein or reassortment with other pandemic viruses endow HPAI H5N1 viruses with the potential for aerosol transmissibility in mammals. A thorough understanding of the pathogenic mechanisms of these viruses will help us to develop more effective control strategies; however, such mechanisms and virulent determinants for H5N1 influenza viruses have not been fully elucidated. In this study, we identified glycosylation at positions 158 to 160 of the HA protein of two naturally occurring H5N1 viruses as an important virulence determinant. This glycosylation event enhanced viral productivity, exacerbated the host response, and thereby contributed to the high pathogenicity of H5N1 virus in mice.
The Measles Virus Receptor SLAMF1 Can Mediate Particle Endocytosis
Authors: Gonçalves-Carneiro Daniel , McKeating Jane A. , Bailey Dalan
Published: January 2017

The signaling lymphocyte activation molecule F1 (SLAMF1) is both a microbial sensor and entry receptor for measles virus (MeV). Herein, we describe a new role for SLAMF1 to mediate MeV endocytosis that is in contrast with the alternative, and generally accepted, model that MeV genome enters cells only after fusion at the cell surface. We demonstrated that MeV engagement of SLAMF1 induces dramatic but transient morphological changes, most prominently in the formation of membrane blebs, which were shown to colocalize with incoming viral particles, and rearrangement of the actin cytoskeleton in infected cells. MeV infection was dependent on these dynamic cytoskeletal changes as well as fluid uptake through a macropinocytosis-like pathway as chemical inhibition of these processes inhibited entry. Moreover, we identified a role for the RhoA-ROCK-myosin II signaling axis in this MeV internalization process, highlighting a novel role for this recently characterized pathway in virus entry. Our study shows that MeV can hijack a microbial sensor normally involved in bacterial phagocytosis to drive endocytosis using a complex pathway that shares features with canonical viral macropinocytosis, phagocytosis, and mechanotransduction. This uptake pathway is specific to SLAMF1-positive cells and occurs within 60 min of viral attachment. Measles virus remains a significant cause of mortality in human populations, and this research sheds new light on the very first steps of infection of this important pathogen.

IMPORTANCE
Measles is a significant disease in humans and is estimated to have killed over 200 million people since records began. According to current World Health Organization statistics, it still kills over 100,000 people a year, mostly children in the developing world. The causative agent, measles virus, is a small enveloped RNA virus that infects a broad range of cells during infection. In particular, immune cells are infected via interactions between glycoproteins found on the surface of the virus and SLAMF1, the immune cell receptor. In this study, we have investigated the steps governing entry of measles virus into SLAMF1-positive cells and identified endocytic uptake of viral particles. This research will impact our understanding of morbillivirus-related immunosuppression as well as the application of measles virus as an oncolytic therapeutic.