bluuebunny/crossref_metadata_2025 huggingface dataset:
A combined light sheet fluorescence and differential interference contrast microscope for live imaging of multicellular specimens
Authors: BAKER R.P. , TAORMINA M.J. , JEMIELITA M. , PARTHASARATHY R.
Published: January 2015

We describe a microscope capable of both light sheet fluorescence microscopy and differential interference contrast microscopy (DICM). The two imaging modes, which to the best of our knowledge have not previously been combined, are complementary: light sheet fluorescence microscopy provides three‐dimensional imaging of fluorescently labelled components of multicellular systems with high speed, large fields of view, and low phototoxicity, whereas differential interference contrast microscopy reveals the unlabelled neighbourhood of tissues, organs, and other structures with high contrast and inherent optical sectioning. Use of a single Nomarski prism for differential interference contrast microscopy and a shared detection path for both imaging modes enables simple integration of the two techniques in one custom microscope. We provide several examples of the utility of the resulting instrument, focusing especially on the digestive tract of the larval zebrafish, revealing in this complex and heterogeneous environment anatomical features, the behaviour of commensal microbes, immune cell motions, and more.
Bootstrap Determination of the Co‐Integration Rank in VAR Models with Unrestricted Deterministic Components
Authors: Cavaliere Giuseppe , Rahbek Anders , Robert Taylor A. M.
Published: January 2015

In a recent paper, Cavaliere et al., develop bootstrap implementations of the popular likelihood‐based co‐integration rank tests and associated sequential rank determination procedures of Johansen . By using estimates of the parameters of the underlying co‐integrated VAR model obtained under the restriction of the null hypothesis, they show that consistent bootstrap inference can be obtained for processes whose deterministic component is either zero, a restricted constant or a restricted trend. In this article, we extend their bootstrap approach to allow the deterministic component to follow the practically relevant cases of either an unrestricted constant or an unrestricted trend from Johansen . A full asymptotic theory is provided for these two cases, establishing the asymptotic validity of the resulting bootstrap tests. Our results, taken together with those in Cavaliere et al., , therefore show that the bootstrap approach based on imposing the reduced rank null hypothesis is valid for all five of these deterministic settings. Monte Carlo evidence demonstrates the improvements that the proposed bootstrap methods can deliver over the corresponding asymptotic procedures.
Infinitely Divisible Distributions in Integer‐Valued Garch Models
Authors: Gonçalves E. , Mendes‐Lopes N. , Silva F.
Published: January 2015

We propose an integer‐valued stochastic process with conditional marginal distribution belonging to the class of infinitely divisible discrete probability laws. With this proposal, we introduce a wide class of models for count time series that includes the Poisson integer‐valued generalized autoregressive conditional heteroscedastic (INGARCH) model (Ferland et al., 2006) and the negative binomial and generalized Poisson INGARCH models (Zhu, 2011, 2012a). The main probabilistic analysis of this process is developed stating, in particular, first‐order and second‐order stationarity conditions. The existence of a strictly stationary and ergodic solution is established in a subclass including the Poisson and generalized Poisson INGARCH models.
Estimation in Functional Lagged Regression
Authors: Hörmann Siegfried , Kidziński Łukasz , Kokoszka Piotr
Published: January 2015

The paper introduces a functional time series (lagged) regression model. The impulse‐response coefficients in such a model are operators acting on a separable Hilbert space, which is the function space L2 in applications. A spectral approach to the estimation of these coefficients is proposed and asymptotically justified under a general nonparametric condition on the temporal dependence of the input series. Since the data are infinite‐dimensional, the estimation involves a spectral‐domain dimension‐reduction technique. Consistency of the estimators is established under general data‐dependent assumptions on the rate of the dimension‐reduction parameter. Their finite‐sample performance is evaluated by a simulation study that compares two ad hoc approaches to dimension reduction with an alternative, asymptotically justified method.
Bootstrap Inference in Regressions with Estimated Factors and Serial Correlation
Authors: Djogbenou Antoine , Gonçalves Sílvia , Perron Benoit
Published: January 2015

This article considers bootstrap inference in a factor‐augmented regression context where the errors could potentially be serially correlated. This generalizes results in Gonçalves & Perron (2014) and makes the bootstrap applicable to forecasting contexts where the forecast horizon is greater than one. We propose and justify two residual‐based approaches, a block wild bootstrap and a dependent wild bootstrap. Our simulations document improvement in coverage rates of confidence intervals for the coefficients when using block wild bootstrap or dependent wild bootstrap relative to both asymptotic theory and the wild bootstrap when serial correlation is present in the regression errors.
Using geographic profiling to locate elusive nocturnal animals: a case study with spectral tarsiers
Authors: Faulkner S. C. , Stevenson M. D. , Verity R. , Mustari A. H. , Semple S. , Tosh D. G. , Le Comber S. C.
Published: January 2015

Estimates of biodiversity, population size, population density and habitat use have important implications for management of both species and habitats, yet are based on census data that can be extremely difficult to collect. Traditional assessment techniques are often limited by time and money and by the difficulties of working in certain habitats, and species become more difficult to find as population size decreases. Particular difficulties arise when studying elusive species with cryptic behaviours. Here, we show how geographic profiling (GP) – a statistical tool originally developed in criminology to prioritize large lists of suspects in cases of serial crime – can be used to address these problems. We ask whether GP can be used to locate sleeping sites of spectral tarsiers Tarsius tarsier in Sulawesi, Southeast Asia, using as input the positions at which tarsier vocalizations were recorded in the field. This novel application of GP is potentially of value as tarsiers are cryptic and nocturnal and can easily be overlooked in habitat assessments (e.g. in dense rainforest). Our results show that GP provides a useful tool for locating sleeping sites of this species, and indeed analysis of a preliminary dataset during field work strongly suggested the presence of a sleeping tree at a previously unknown location; two sleeping trees were subsequently found within 5 m of the predicted site. We believe that GP can be successfully applied to locating the nests, dens or roosts of elusive animals such as tarsiers, potentially improving estimates of population size with important implications for management of both species and habitats.
Attitudes towards organ donor advocacy among Swedish intensive care nurses
Authors: Forsberg Anna , Lennerling Annette , Fridh Isabell , Rizell Magnus , Lovén Charlotte , Flodén Anne
Published: January 2015

Objectives

To explore the attitudes of Swedish intensive care nurses towards organ donor advocacy.

Background

The concept of organ donor advocacy is critical to nurses who care for potential donors in order to facilitate organ donation (OD).

Design

A retrospective cross‐sectional study was employed.

Methods

Inclusion criteria in this survey were to be a registered nurse and to work in a Swedish intensive care unit (ICU). Participants were identified by the Swedish association of health professionals. A number of 502 Swedish ICU nurses answered the 32‐item questionnaire Attitudes Towards Organ Donor Advocacy Scale (ATODAS), covering the five dimensions of organ donor advocacy: attitudes towards championing organ donation at a structural hospital level, or at a political and research level, attitudes towards actively and personally safeguarding the will and wishes of the potential organ donor, or by using a more professional approach and finally to safeguard the will and wishes of the relatives. Data were analysed with the SPSS version 18·0 and the results were assessed by using Student's t‐test and post hoc test, analysis of variance (ANOVA), χ2, Pearson's correlation and regression analysis.

Results

The most favoured advocacy action was safeguarding the POD's will and wishes by a professional approach, closely followed by actively and personally safeguarding the POD's will and wishes. Nurses at local hospitals reported a more positive attitude towards organ donor advocacy overall compared with nurses at larger regional or university hospitals. Important factors leading to positive attitudes were seniority, working experience, participating in conversations with relatives, caring for brain‐dead persons and private experiences from OD or organ transplantation.

Conclusions

Intensive and critical care nurses with short working experience in university hospitals showed the least positive attitude towards organ donor advocacy. This is problematic because many ODs and all transplantations are performed in university hospitals.

Relevance to clinical practice

This study emphasizes the importance of organizing the care of PODs and their relatives in a way that promotes advocacy.
Phenotyping nematode feeding sites: three‐dimensional reconstruction and volumetric measurements of giant cells induced by root‐knot nematodes in Arabidopsis
Authors: Cabrera Javier , Díaz‐Manzano Fernando E. , Barcala Marta , Arganda‐Carreras Ignacio , de Almeida‐Engler Janice , Engler Gilbert , Fenoll Carmen , Escobar Carolina
Published: January 2015

The control of plant parasitic nematodes is an increasing problem. A key process during the infection is the induction of specialized nourishing cells, called giant cells (GCs), in roots. Understanding the function of genes required for GC development is crucial to identify targets for new control strategies. We propose a standardized method for GC phenotyping in different plant genotypes, like those with modified genes essential for GC development.

The method combines images obtained by bright‐field microscopy from the complete serial sectioning of galls with TrakEM2, specialized three‐dimensional (3D) reconstruction software for biological structures.

The volumes and shapes from 162 3D models of individual GCs induced by Meloidogyne javanica in Arabidopsis were analyzed for the first time along their life cycle. A high correlation between the combined volume of all GCs within a gall and the total area occupied by all the GCs in the section/s where they show maximum expansion, and a proof of concept from two Arabidopsis transgenic lines (J0121 ≫ DTA and J0121 ≫ GFP) demonstrate the reliability of the method.

We phenotyped GCs and developed a reliable simplified method based on a two‐dimensional (2D) parameter for comparison of GCs from different Arabidopsis genotypes, which is also applicable to galls from different plant species and in different growing conditions, as thickness/transparency is not a restriction.
Effect of hot water treatment on peach volatile emission and Monilinia fructicola development
Authors: Spadoni A. , Cappellin L. , Neri F. , Algarra Alarcon A. , Romano A. , Guidarelli M. , Gasperi F. , Biasioli F. , Mari M.
Published: January 2015

The effect of hot water treatment (HWT) to control peach brown rot was investigated. Peaches were dipped in water at 60°C for 60 s and artificially inoculated with Monilinia fructicola conidia. HWT failed to control brown rot if applied before inoculation and microscopic observations revealed a stimulatory effect on germ tube elongation of M. fructicola conidia placed immediately after HWT on the fruit surface, compared to the control. The influence of fruit volatile emission due to HWT was performed on the pathogen conidia exposed to the headspace surrounding peaches. The results showed an increase of M. fructicola conidial germination ranging from 33 to 64% for cultivars Lucie Tardibelle and Red Haven heat‐treated peaches, respectively, compared to the control. The volatile blend emitted from heat‐treated fruit was analysed by solid‐phase microextraction/gas chromatography‐mass spectrometry (SPME/GC‐MS) and proton transfer reaction‐time of flight‐mass spectrometry (PTR‐ToF‐MS). Fifty compounds were detected by SPME/GC‐MS in volatile blends of cv. Lucie Tardibelle peaches and significant differences in volatile emission were observed among heated and control fruit. Using PTR‐ToF‐MS analysis, acetaldehyde and ethanol were detected at levels 15‐ and 28‐fold higher in heated fruit compared to unheated ones, respectively. In vitro assays confirmed the stimulatory effect (60 and 15%) of acetaldehyde (0·6 μL L−1) and ethanol (0·2 μL L−1) on M. fructicola conidial germination and mycelial growth, respectively. The results showed that volatile organic compounds (VOCs) emitted from heat‐treated peaches could stimulate M. fructicola conidial germination, increasing brown rot incidence in treated peaches when the inoculation occurs immediately after HWT.
Prevalence of hepatitis C virus in mothers and their children in Malawi
Authors: Fox James M. , Newton Robert , Bedaj Marija , Keding Ada , Molyneux Elizabeth , Carpenter Lucy M. , Martin Fabiola , Mutalima Nora
Published: January 2015

Objectives

Hepatitis C virus (HCV) prevalence is poorly mapped in the East African region; with the advent of novel HCV therapies, better epidemiological data are required to target the infection. We sought to estimate HCV prevalence in healthy Malawian mothers and assess mother‐to‐child transmission (MTCT); context is provided by reviewing previously published HCV prevalence data from the region.

Methods

Using ELISA screening and confirmatory blot, serological testing of 418 healthy Malawian mothers for HCV was performed. To examine MTCT, the children of any positive women were also tested for HCV; all children had malignant disease unrelated to hepatocellular carcinoma. We compared our results to published literature on HCV prevalence in Malawi and its neighbouring countries.

Results

Three of 418 women were HCV reactive by ELISA; two were confirmed positive by immunoblot (0.5%). One child of an HCV‐infected mother was HCV seropositive. The literature review revealed HCV prevalence ranging from 0 to 7.2% in the region, being highest in Tanzania and specifically for cohorts of inpatients and HIV‐co‐infected people. The overall estimated prevalence of HCV in Malawi was 1.0% (95%CI 0.7–1.4) when all studies were included (including this one), but lower in healthy cohorts alone at 0.3% (95%CI 0.1–1.2).

Conclusions

This is the first study using confirmatory tests to examine HCV prevalence in healthy Malawian mothers; the prevalence was low. Future studies need to address the source of infection in healthy women.
Laboratory blood analysis in Strigiformes—Part II: plasma biochemistry reference intervals and agreement between the Abaxis Vetscan V2 and the Roche Cobas c501
Authors: Ammersbach Mélanie , Beaufrère Hugues , Gionet Rollick Annick , Tully Thomas
Published: January 2015

Background

Limited plasma biochemical information is available in Strigiformes. Only one study investigated the agreement between a point‐of‐care with a reference laboratory analyzer for biochemistry variables in birds.

Objectives

The objective was to report reference intervals (RI) for plasma biochemistry variables in Strigiformes, and to assess agreement between the Abaxis Vetscan V2 and Roche Cobas c501.

Methods

A prospective study was designed to assess plasma biochemistry RI for concentration of calcium, phosphorus, total protein, albumin, globulin, glucose, bilirubin, uric acid, bile acids, sodium, potassium, and chloride, and activities of AST, GGT, CK, amylase, lipase, LDH, and GLDH. In addition, the agreement between the Vetscan and the Cobas in owl species was assessed.

Results

A total of 190 individuals were sampled belonging to 12 Strigiformes species including Barn Owls, Barred Owls, Great Horned Owls, Eurasian Eagle Owls, Spectacled Owls, Eastern Screech Owls, Long‐Eared Owls, Short‐Eared Owls, Great Gray Owls, Snowy Owls, Northern Saw‐Whet Owls, and Northern Hawk‐Owls. Order‐, species‐, and method‐specific RI were determined on both analyzers. Although Vetscan data were not equivalent to the Cobas, 4 analytes (glucose, AST, CK, and total protein, with correction for bias) were within acceptable agreement, 3 analytes (uric acid, calcium, and phosphorus) were within close agreement, and the remaining analytes were in strong disagreement. Species‐specific differences were observed notably for the concentration of glucose in Barn Owls and electrolytes in Northern Saw‐Whet Owls.

Conclusions

Overall, this study suggests that the Vetscan has acceptable clinical performance in Strigiformes for some analytes and highlights discrepancies for several analytes.
Control of Wake Structure Behind a Square Cylinder by Magnetohydrodynamics
Authors: Rashidi S. , Bovand M. , Esfahani J. A. , Öztop H. F. , Masoodi R.
Published: January 2015

In this paper, a two-dimensional (2D) numerical simulation has been performed for an unsteady magnetohydrodynamics (MHD) flow around a solid square cylinder placed in a channel. Computational simulations were done for the ranges of Reynolds and Stuart numbers of 1–250 and 0–10, respectively. Finite volume method (FVM) has been used to solve the unsteady Navier–Stokes equations. The effects of streamwise magnetic field on the flow separation and suppress of the vortex shedding are studied in detail for the above ranges. Additionally, four new empirical equations for wake length and Stuart number are suggested. Finally, a comparison is performed between the cases of with and without a channel to study the effect of channel walls. The obtained results revealed that Strouhal number decreases linearly with increasing Stuart number. Also, the flow distribution pattern changes from time-dependent pattern to steady-state by increasing Stuart number.
Contribution of Collagen Fiber Undulation to Regional Biomechanical Properties Along Porcine Thoracic Aorta
Authors: Zeinali-Davarani Shahrokh , Wang Yunjie , Chow Ming-Jay , Turcotte Raphaël , Zhang Yanhang
Published: January 2015

As major extracellular matrix components, elastin, and collagen play crucial roles in regulating the mechanical properties of the aortic wall and, thus, the normal cardiovascular function. The mechanical properties of aorta, known to vary with age and multitude of diseases as well as the proximity to the heart, have been attributed to the variations in the content and architecture of wall constituents. This study is focused on the role of layer-specific collagen undulation in the variation of mechanical properties along the porcine descending thoracic aorta. Planar biaxial tensile tests are performed to characterize the hyperelastic anisotropic mechanical behavior of tissues dissected from four locations along the thoracic aorta. Multiphoton microscopy is used to image the associated regional microstructure. Exponential-based and recruitment-based constitutive models are used to account for the observed mechanical behavior while considering the aortic wall as a composite of two layers with independent properties. An elevated stiffness is observed in distal regions compared to proximal regions of thoracic aorta, consistent with sharper and earlier collagen recruitment estimated for medial and adventitial layers in the models. Multiphoton images further support our prediction that higher stiffness in distal regions is associated with less undulation in collagen fibers. Recruitment-based models further reveal that regardless of the location, collagen in the media is recruited from the onset of stretching, whereas adventitial collagen starts to engage with a delay. A parameter sensitivity analysis is performed to discriminate between the models in terms of the confidence in the estimated model parameters.
Computational Analysis of Fluid Flow Within a Device for Applying Biaxial Strain to Cultured Cells
Authors: Lee Jason , Baker Aaron B.
Published: January 2015

In vitro systems for applying mechanical strain to cultured cells are commonly used to investigate cellular mechanotransduction pathways in a variety of cell types. These systems often apply mechanical forces to a flexible membrane on which cells are cultured. A consequence of the motion of the membrane in these systems is the generation of flow and the unintended application of shear stress to the cells. We recently described a flexible system for applying mechanical strain to cultured cells, which uses a linear motor to drive a piston array to create biaxial strain within multiwell culture plates. To better understand the fluidic stresses generated by this system and other systems of this type, we created a computational fluid dynamics model to simulate the flow during the mechanical loading cycle. Alterations in the frequency or maximal strain magnitude led to a linear increase in the average fluid velocity within the well and a nonlinear increase in the shear stress at the culture surface over the ranges tested (0.5–2.0 Hz and 1–10% maximal strain). For all cases, the applied shear stresses were relatively low and on the order of millipascal with a dynamic waveform having a primary and secondary peak in the shear stress over a single mechanical strain cycle. These findings should be considered when interpreting experimental results using these devices, particularly in the case when the cell type used is sensitive to low magnitude, oscillatory shear stresses.
Periodization and Physical Performance in Elite Female Soccer Players
Authors: Mara Jocelyn K. , Thompson Kevin G. , Pumpa Kate L. , Ball Nick B.
Published: January 2015

Purpose:

To investigate the variation in training demands, physical performance, and player well-being across a women’s soccer season.

Methods:

Seventeen elite female players wore GPS tracking devices during every training session (N = 90) throughout 1 national-league season. Intermittent high-speed-running capacity and 5-, 15-, and 25-m-sprint testing were conducted at the beginning of preseason, end of preseason, midseason, and end of season. In addition, subjective well-being measures were selfreported daily by players over the course of the season.

Results:

Time over 5 m was lowest at the end of preseason (mean 1.148 s, SE 0.017 s) but then progressively deteriorated to the end of the season (P < .001). Sprint performance over 15 m improved by 2.8% (P = .013) after preseason training, while 25-m-sprint performance peaked at midseason, with a 3.1% (P = .05) improvement from the start of preseason, before declining at the end of season (P = .023). Training demands varied between phases, with total distance and high-speed distance greatest during preseason before decreasing (P < .001) during the early- and late-season phases. Endurance capacity and well-being measures did not change across training phases.

Conclusions:

Monitoring training demands and subsequent physical performance in elite female soccer players allow coaches to ensure that training periodization goals are being met and related positive training adaptations are being elicited.
Gross Efficiency During Flat and Uphill Cycling in Field Conditions
Authors: Nimmerichter Alfred , Prinz Bernhard , Haselsberger Kevin , Novak Nina , Simon Dieter , Hopker James G.
Published: January 2015

Purpose:

While a number of studies have investigated gross efficiency (GE) in laboratory conditions, few studies have analyzed it in field conditions. Therefore, the aim of this study was to analyze the effect of gradient and cadence on GE in field conditions.

Methods:

Thirteen trained cyclists (mean ± SD age 23.3 ± 4.1 y, stature 177.0 ± 5.5 cm, body mass 69.0 ± 7.2 kg, maximal oxygen uptake [V̇O2max] 68.4 ± 5.1 mL ∙ min–1 ∙ kg–1) completed an incremental graded exercise test to determine ventilatory threshold (VT) and 4 field trials of 6 min duration at 90% of VT on flat (1.1%) and uphill terrain (5.1%) with 2 different cadences (60 and 90 rpm). V̇O2 was measured with a portable gas analyzer and power output was controlled with a mobile power crank that was mounted on a 26-in mountain bike.

Results:

GE was significantly affected by cadence (20.6% ± 1.7% vs 18.1% ± 1.3% at 60 and 90 rpm, respectively; P < .001) and terrain (20.0% ± 1.5% vs 18.7% ± 1.7% at flat and uphill cycling, respectively; P = .029). The end-exercise V̇O2 was 2536 ± 352 and 2594 ± 329 mL/min for flat and uphill cycling, respectively (P = .489). There was a significant difference in end-exercise V̇O2 between 60 (2352 ± 193 mL/min) and 90 rpm (2778 ± 431 mL/min) (P < .001).

Conclusions:

These findings support previous laboratory-based studies demonstrating reductions in GE with increasing cadence and gradient that might be attributed to changes in muscle-activity pattern.
Postoperative Rehabilitation After Hip Resurfacing: A Systematic Review
Authors: Cheatham Scott , Mokha Monique , Lee Matt
Published: January 2015

Context:

Hip-resurfacing arthroplasty (HRA) has become a popular procedure in the treatment of hip-joint arthritis in individuals under the age of 65 y. Although the body of literature examining operative procedures has grown, there is a lack of consistent reporting of the effectiveness of an HRA postoperative rehabilitation program. To date, no systematic reviews have evaluated the available evidence on postoperative rehabilitation programs.

Objective:

To evaluate the available evidence on postoperative rehabilitation programs after HRA.

Evidence Acquisition:

A systematic review was conducted according to the PRISMA guidelines. A search of PubMed, CINAHL, SPORTDiscus, ProQuest, and Google Scholar was conducted in April 2014 using the following keywords alone and in combination: postoperative, postsurgical, rehabilitation, physical therapy, programs, hip resurfacing, arthroplasty, and metal-on-metal. The grading of studies was conducted using the PEDro and Oxford Centre for Evidence-Based Medicine scales.

Evidence Synthesis:

The authors identified 648 citations, 4 of which met the inclusion criteria. The qualifying studies yielded 1 randomized control trial, 2 case reports, and 1 case series, for a total of 90 patients. Patients were mostly male (n = 86), had a mean age of 48 ± 5.47 y, and had been physically active before HRA. Postoperative rehabilitation programs varied in length (range 8–24 wk) and consisted of at least 3 phases. The methodology to assess program effects varied, but all 4 studies did measure a combination of function, pain, and quality of life using written questionnaires, with follow-up ranging from 9 mo to 1 y. The most common questionnaire was the Harris Hip Score.

Conclusion:

This review found postoperative rehabilitation programs after HRA to be underinvestigated. Limited results indicate that postoperative rehabilitation programs may be effective in improving gait (stride length, velocity, and cadence), hip range of motion, and pain and function, as measured by questionnaires, but not hip strength.
Tissue-based map of the human proteome
Authors: Uhlén Mathias , Fagerberg Linn , Hallström Björn M. , Lindskog Cecilia , Oksvold Per , Mardinoglu Adil , Sivertsson Åsa , Kampf Caroline , Sjöstedt Evelina , Asplund Anna , Olsson IngMarie , Edlund Karolina , Lundberg Emma , Navani Sanjay , Szigyarto Cristina Al-Khalili , Odeberg Jacob , Djureinovic Dijana , Takanen Jenny Ottosson , Hober Sophia , Alm Tove , Edqvist Per-Henrik , Berling Holger , Tegel Hanna , Mulder Jan , Rockberg Johan , Nilsson Peter , Schwenk Jochen M. , Hamsten Marica , von Feilitzen Kalle , Forsberg Mattias , Persson Lukas , Johansson Fredric , Zwahlen Martin , von Heijne Gunnar , Nielsen Jens , Pontén Fredrik
Published: January 2015

Protein expression across human tissues

Sequencing the human genome gave new insights into human biology and disease. However, the ultimate goal is to understand the dynamic expression of each of the approximately 20,000 protein-coding genes and the function of each protein. Uhlén
et al.
now present a map of protein expression across 32 human tissues. They not only measured expression at an RNA level, but also used antibody profiling to precisely localize the corresponding proteins. An interactive website allows exploration of expression patterns across the human body.

Science
, this issue
10.1126/science.1260419
Human-like hand use in
Australopithecus africanus
Authors: Skinner Matthew M. , Stephens Nicholas B. , Tsegai Zewdi J. , Foote Alexandra C. , Nguyen N. Huynh , Gross Thomas , Pahr Dieter H. , Hublin Jean-Jacques , Kivell Tracy L.
Published: January 2015

Getting a grip

The evolution of the hand—particularly the opposable thumb—was key to the success of early humans. Without a precise grip, involving forceful opposition of thumb with fingers, tool technology could not have emerged. Skinner
et al.
analyzed the internal bone structure of Pliocene
Australopithecus
hands, dated at 3.2 million years old. Internal bone structure reveals the patterns and directions of forces operating on the hand, providing clues to the kinds of activities performed. Modern human-like hand postures consistent with the habitual use of tools appeared about half a million years earlier than the first archaeological evidence of stone tools.

Science
, this issue p.
395
Japan's nuclear renaissance dogged by waste challenge
Authors: Normile Dennis
Published: January 2015

Nuclear reprocessing is years late; repository is in limbo.
The insurgent
Authors: Grimm David
Published: January 2015

Animal rights activist Justin Goodman is using science's own tools to combat animal research.
Overcoming challenges in cellular analysis: Multiparameter analysis of rare cells
Authors: Cossarizza Andrea , Cousins David
Published: January 2015

There are a variety of challenges when studying rare cell types, primarily due to their very low abundance against a high background of other cells. Identifying ways to study these cell types and better understand their roles in different human diseases is important to advance basic biomedical research—especially elucidating and characterizing disease mechanisms and targets—as well as in medical diagnostics and therapeutics. With multiparameter capabilities and a very high analysis rate, flow cytometry is one of the technologies often utilized to analyze rare cells. During this webinar, the application of this technology to the isolation and analysis of rare cells will be discussed, with a focus on innate lymphoid cells (ILCs), circulating antigen-specific lymphocytes, and innate-like cells (such as natural killer T cells and circulating endothelial cells).
Time variability and heterogeneity in the coma of 67P/Churyumov-Gerasimenko
Authors: Hässig M. , Altwegg K. , Balsiger H. , Bar-Nun A. , Berthelier J. J. , Bieler A. , Bochsler P. , Briois C. , Calmonte U. , Combi M. , De Keyser J. , Eberhardt P. , Fiethe B. , Fuselier S. A. , Galand M. , Gasc S. , Gombosi T. I. , Hansen K. C. , Jäckel A. , Keller H. U. , Kopp E. , Korth A. , Kührt E. , Le Roy L. , Mall U. , Marty B. , Mousis O. , Neefs E. , Owen T. , Rème H. , Rubin M. , Sémon T. , Tornow C. , Tzou C.-Y. , Waite J. H. , Wurz P.
Published: January 2015

Comets contain the best-preserved material from the beginning of our planetary system. Their nuclei and comae composition reveal clues about physical and chemical conditions during the early solar system when comets formed. ROSINA (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) onboard the Rosetta spacecraft has measured the coma composition of comet 67P/Churyumov-Gerasimenko with well-sampled time resolution per rotation. Measurements were made over many comet rotation periods and a wide range of latitudes. These measurements show large fluctuations in composition in a heterogeneous coma that has diurnal and possibly seasonal variations in the major outgassing species: water, carbon monoxide, and carbon dioxide. These results indicate a complex coma-nucleus relationship where seasonal variations may be driven by temperature differences just below the comet surface.
The morphological diversity of comet 67P/Churyumov-Gerasimenko
Authors: Thomas Nicolas , Sierks Holger , Barbieri Cesare , Lamy Philippe L. , Rodrigo Rafael , Rickman Hans , Koschny Detlef , Keller Horst Uwe , Agarwal Jessica , A'Hearn Michael F. , Angrilli Francesco , Auger Anne-Therese , Barucci M. Antonella , Bertaux Jean-Loup , Bertini Ivano , Besse Sebastien , Bodewits Dennis , Cremonese Gabriele , Da Deppo Vania , Davidsson Björn , De Cecco Mariolino , Debei Stefano , El-Maarry Mohamed Ramy , Ferri Francesca , Fornasier Sonia , Fulle Marco , Giacomini Lorenza , Groussin Olivier , Gutierrez Pedro J. , Güttler Carsten , Hviid Stubbe F. , Ip Wing-Huen , Jorda Laurent , Knollenberg Jörg , Kramm J.-Rainer , Kührt Ekkehard , Küppers Michael , La Forgia Fiorangela , Lara Luisa M. , Lazzarin Monica , Moreno Josè J. Lopez , Magrin Sara , Marchi Simone , Marzari Francesco , Massironi Matteo , Michalik Harald , Moissl Richard , Mottola Stefano , Naletto Giampiero , Oklay Nilda , Pajola Maurizio , Pommerol Antoine , Preusker Frank , Sabau Lola , Scholten Frank , Snodgrass Colin , Tubiana Cecilia , Vincent Jean-Baptiste , Wenzel Klaus-Peter
Published: January 2015

Images of comet 67P/Churyumov-Gerasimenko acquired by the OSIRIS (Optical, Spectroscopic and Infrared Remote Imaging System) imaging system onboard the European Space Agency’s Rosetta spacecraft at scales of better than 0.8 meter per pixel show a wide variety of different structures and textures. The data show the importance of airfall, surface dust transport, mass wasting, and insolation weathering for cometary surface evolution, and they offer some support for subsurface fluidization models and mass loss through the ejection of large chunks of material.
Streptococcus gallolyticus subsp. pasteurianus Infection in Twin Infants
Authors: Hede Sannya Vidyadhar , Olarte Liset , Chandramohan Lakshmi , Kaplan Sheldon L. , Hulten Kristina G.
Published: January 2015

Streptococcus gallolyticus
subsp.
pasteurianus
, previously known as
Streptococcus bovis
biotype II.2, is an uncommon pathogen in neonates. Nevertheless, it can cause severe neonatal sepsis and meningitis often clinically indistinguishable from those caused by group B streptococci and has been associated with considerable morbidity. We report the first known cases of
S. gallolyticus
subsp.
pasteurianus
infection in twin infants.
Detection and Discrimination of Classical and Atypical L-Type Bovine Spongiform Encephalopathy by Real-Time Quaking-Induced Conversion
Authors: Orrú Christina D. , Favole Alessandra , Corona Cristiano , Mazza Maria , Manca Matteo , Groveman Bradley R. , Hughson Andrew G. , Acutis Pier Luigi , Caramelli Maria , Zanusso Gianluigi , Casalone Cristina , Caughey Byron
Published: January 2015

Statutory surveillance of bovine spongiform encephalopathy (BSE) indicates that cattle are susceptible to both classical BSE (C-BSE) and atypical forms of BSE. Atypical forms of BSE appear to be sporadic and thus may never be eradicated. A major challenge for prion surveillance is the lack of sufficiently practical and sensitive tests for routine BSE detection and strain discrimination. The real-time quaking-induced conversion (RT-QuIC) test, which is based on prion-seeded fibrillization of recombinant prion protein (rPrPSen), is known to be highly specific and sensitive for the detection of multiple human and animal prion diseases but not BSE. Here, we tested brain tissue from cattle affected by C-BSE and atypical L-type bovine spongiform encephalopathy (L-type BSE or L-BSE) with the RT-QuIC assay and found that both BSE forms can be detected and distinguished using particular rPrPSensubstrates. Specifically, L-BSE was detected using multiple rPrPSensubstrates, while C-BSE was much more selective. This substrate-based approach suggests a diagnostic strategy for specific, sensitive, and rapid detection and discrimination of at least some BSE forms.
Detection of Mycobacterium tuberculosis by EasyNAT Diagnostic Kit in Sputum Samples from Tanzania
Authors: Mhimbira Francis A. , Bholla Maira , Sasamalo Mohamed , Mukurasi William , Hella Jerry J. , Jugheli Levan , Reither Klaus
Published: January 2015

The EasyNAT assay was evaluated for the detection of tuberculosis in sputum smears from presumptive pulmonary tuberculosis (TB) patients in an African high-TB and high-HIV setting. The sensitivity of the EasyNAT assay was 66.7%, and the specificity and positive predictive value were 100% for the culture-positive patients. The sensitivity was only 10% in the smear-negative and culture-positive patients.
Foot Infection by Clostridium sordellii: Case Report and Review of 15 Cases in France
Authors: Bouvet Philippe , Sautereau Jean , Le Coustumier Alain , Mory Francine , Bouchier Christiane , Popoff Michel-R.
Published: January 2015

We report a case of foot infection by
Clostridium sordellii
and review 15 human infections registered at a Reference Center in France during the period 1998 to 2011. All strains were found nontoxigenic, lacking the lethal toxin gene coding for TcsL. Like
Clostridium septicum
, several
C. sordellii
infections were associated with intestinal neoplasms.
Influenza Viruses with Receptor-Binding N1 Neuraminidases Occur Sporadically in Several Lineages and Show No Attenuation in Cell Culture or Mice
Authors: Hooper Kathryn A. , Crowe James E. , Bloom Jesse D.
Published: January 2015

In nearly all characterized influenza viruses, hemagglutinin (HA) is the receptor-binding protein while neuraminidase (NA) is a receptor-cleaving protein that aids in viral release. However, in recent years, several groups have described point mutations that confer receptor-binding activity on NA, albeit in laboratory rather than natural settings. One of these mutations, D151G, appears to arise in the NA of recent human H3N2 viruses upon passage in tissue culture. We inadvertently isolated the second of these mutations, G147R, in the NA of the lab-adapted A/WSN/33 (H1N1) strain while we were passaging a heavily engineered virus in the lab. G147R also occurs at low frequencies in the reported sequences of viruses from three different lineages: human 2009 pandemic H1N1 (pdmH1N1), human seasonal H1N1, and chicken H5N1. Here we reconstructed a representative G147R NA from each of these lineages and found that all of the proteins have acquired the ability to bind an unknown cellular receptor while retaining substantial sialidase activity. We then reconstructed a virus with the HA and NA of a reported G147R pdmH1N1 variant and found no attenuation of viral replication in cell culture or change in pathogenesis in mice. Furthermore, the G147R virus had modestly enhanced resistance to neutralization by the Fab of an antibody against the receptor-binding pocket of HA, although it remained completely sensitive to the full-length IgG. Overall, our results suggest that circulating N1 viruses occasionally may acquire the G147R NA receptor-binding mutation without impairment of replicative capacity.

IMPORTANCE
Influenza viruses have two main proteins on their surface: one (hemagglutinin) binds incoming viruses to cells, while the other (neuraminidase) helps release newly formed viruses from these same cells. Here we characterize unusual mutant neuraminidases that have acquired the ability to bind to cells. We show that the mutation that allows neuraminidase to bind cells has no apparent adverse effect on viral replication but does make the virus modestly more resistant to a fragment of an antibody that blocks the normal hemagglutinin-mediated mode of viral attachment. Our results suggest that viruses with receptor-binding neuraminidases may occur at low levels in circulating influenza virus lineages.
Structure of the Extracellular Domain of Matrix Protein 2 of Influenza A Virus in Complex with a Protective Monoclonal Antibody
Authors: Cho Ki Joon , Schepens Bert , Seok Jong Hyeon , Kim Sella , Roose Kenny , Lee Ji-Hye , Gallardo Rodrigo , Van Hamme Evelien , Schymkowitz Joost , Rousseau Frederic , Fiers Walter , Saelens Xavier , Kim Kyung Hyun
Published: January 2015

The extracellular domain of influenza A virus matrix protein 2 (M2e) is conserved and is being evaluated as a quasiuniversal influenza A vaccine candidate. We describe the crystal structure at 1.6 Å resolution of M2e in complex with the Fab fragment of an M2e-specific monoclonal antibody that protects against influenza A virus challenge. This antibody binds M2 expressed on the surfaces of cells infected with influenza A virus. Five out of six complementary determining regions interact with M2e, and three highly conserved M2e residues are critical for this interaction. In this complex, M2e adopts a compact U-shaped conformation stabilized in the center by the highly conserved tryptophan residue in M2e. This is the first description of the three-dimensional structure of M2e.

IMPORTANCE
M2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported
in vivo
escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2.
Identification of PB2 Mutations Responsible for the Efficient Replication of H5N1 Influenza Viruses in Human Lung Epithelial Cells
Authors: Yamaji Reina , Yamada Shinya , Le Mai Q. , Li Chengjun , Chen Hualan , Qurnianingsih Ema , Nidom Chairul A. , Ito Mutsumi , Sakai-Tagawa Yuko , Kawaoka Yoshihiro
Published: January 2015

Highly pathogenic H5N1 avian influenza viruses have caused outbreaks among poultry worldwide, resulting in sporadic infections in humans with approximately 60% mortality. However, efficient transmission of H5N1 viruses among humans has yet to occur, suggesting that further adaptation of H5N1 viruses to humans is required for their efficient transmission among humans. The viral determinants for efficient replication in humans are currently poorly understood. Here, we report that the polymerase PB2 protein of an H5N1 influenza virus isolated from a human in Vietnam (A/Vietnam/UT36285/2010, virus 36285) increased the growth ability of an avian H5N1 virus (A/wild bird/Anhui/82/2005, virus Wb/AH82) in human lung epithelial A549 cells (however, the reassortant virus did not replicate more efficiently than human 36285 virus). Furthermore, we demonstrate that the amino acid residues at positions 249, 309, and 339 of the PB2 protein from this human isolate were responsible for its efficient replication in A549 cells. PB2 residues 249G and 339M, which are found in the human H5N1 virus, are rare in H5N1 viruses from both human and avian sources. Interestingly, PB2-249G is found in over 30% of human seasonal H3N2 viruses, which suggests that H5N1 viruses may replicate well in human cells when they acquire this mutation. Our data are of value to H5N1 virus surveillance.

IMPORTANCE
Highly pathogenic H5N1 avian influenza viruses must acquire mutations to overcome the species barrier between avian species and humans. When H5N1 viruses replicate in human respiratory cells, they can acquire amino acid mutations that allow them to adapt to humans through continuous selective pressure. Several amino acid mutations have been shown to be advantageous for virus adaptation to mammalian hosts. Here, we found that amino acid changes at positions 249, 309, and 339 of PB2 contribute to efficient replication of avian H5N1 viruses in human lung cells. These findings are beneficial for evaluating the pandemic risk of circulating avian viruses and for further functional analysis of PB2.
Evolution of the Bunyamwera Virus Polymerase To Accommodate Deletions within Genomic Untranslated Region Sequences
Authors: Mazel-Sanchez Béryl , Elliott Richard M.
Published: January 2015

The untranslated regions (UTR) present at the ends of bunyavirus genome segments are required for essential steps in the virus life cycle and provide signals for encapsidation by nucleocapsid protein and the promoters for RNA transcription and replication as well as for mRNA transcription termination. For the prototype bunyavirus, Bunyamwera virus (BUNV), only the terminal 11 nucleotides (nt) of the segments are identical. Thereafter, the UTRs are highly variable both in length and in sequence. Furthermore, apart from the conserved termini, the UTRs of different viruses are highly variable. We previously generated recombinant BUNV carrying the minimal UTRs on all three segments that were attenuated for growth in cell culture. Following serial passage of these viruses, the viruses acquired increased fitness, and amino acid changes were observed to accumulate in the viral polymerase (L protein) of most mutant viruses, with the vast majority of the amino acid changes occurring in the C-terminal region. The function of this domain within L remains unknown, but by using a minigenome assay we showed that it might be involved in UTR recognition. Moreover, we identified an amino acid mutation within the polymerase that, when introduced into an otherwise wild-type BUNV, resulted in a virus with a temperature-sensitive phenotype. Viruses carrying temperature-sensitive mutations are good candidates for the design of live attenuated vaccines. We suggest that a combination of stable deletions of the UTRs together with the introduction of temperature-sensitive mutations in both the nucleocapsid and the polymerase could be used to design live attenuated vaccines against serious pathogens within the family
Bunyaviridae
.

IMPORTANCE
Virus growth in tissue culture can be attenuated by introduction of mutations in both coding and noncoding sequences. We generated attenuated Bunyamwera viruses by deleting sequences within both the 3′ and 5′ untranslated regions (UTR) on each genome segment and showed that the viruses regained fitness following serial passage in cell culture. The fitter viruses had acquired amino acid changes predominantly in the C-terminal domain of the viral polymerase (L protein), and by using minigenome assays we showed that the mutant polymerases were better adapted to recognizing the mutant UTRs. We suggest that deletions within the UTRs should be incorporated along with other specific mutations, including deletion of the major virulence gene encoding the NSs protein and introduction of temperature-sensitive mutations, in the design of attenuated bunyaviruses that could have potential as vaccines.