bluuebunny/crossref_metadata_2025 huggingface dataset:
Traps baited with pear ester and acetic acid attract both sexes of Hedya nubiferana (Lepidoptera: Tortricidae)
Authors: Jósvai J. K. , Koczor S. , Tóth M.
Published: February 2015

This study was initiated with the objective of studying field responses of the green budworm moth, Hedya nubiferana (Haworth) (Lepidoptera: Tortricidae), to pear ester [PE; ethyl (E,Z)‐2,4‐decadienoate] and acetic acid (AA) with the aim of developing a lure attractive also for females. In the overwhelming majority of tests, traps baited with the PEAA lure (the combination of both PE and AA) caught more than traps baited with either of the constituents presented alone. PEAA lures were attractive to H. nubiferana no matter whether the two compounds were provided in separate dispensers or mixed together in a single one, and a large percentage (up to 71%) of trap catch consisted of females. Traps with PEAA lures caught (females plus males) on an average 30% of the catches in traps baited with the synthetic green budworm moth sex pheromone (only males). This suggested that the new PEAA lure had a trapping performance comparable with that of pheromone traps, which latter are used by farmers today. Consequently, the PEAA lure showed potential for future practical applications as a female‐targeted lure for H. nubiferana. To our knowledge, this is the first well‐documented report on the attraction of PEAA lure for a tortricid species other than codling moth.
Action of anti‐M3 muscarinic acetylcholine receptor IgG of primary Sjögren's syndrome on the enzymatic antioxidant system in rat submandibular gland
Authors: Reina Silvia , Rodríguez Marcelo , Stranieri Graciela , Borda Enri
Published: February 2015

Background

We demonstrate that serum immunoglobulin G (IgG) directed against glandular M3 muscarinic acetylcholine receptors (M3 mAChR) and pilocarpine triggers the increment of superoxide dismutase (SOD) and catalase (CAT) and the production of nitric oxide (NO) and prostaglandin E2 (PGE2).

Methods

Enzyme‐linked immunosorbent assay (ELISA) was performed in the presence of the human M3 mAChR synthetic peptide as antigen to detect in serum of pSS patients the autoantibodies. Further, SOD and CAT specific activity and NO were determined chemically in the presence of anti‐M3 mAChR IgG and pilocarpine. The level of PGE2 generation in the presence of autoantibody and pilocarpine was determined by ELISA.

Results

An association between anti‐M3 mAChR autoantibodies and pilocarpine given the increment of the specific activity of SOD and CAT in the serum of pSS patients and in the rat submandibular gland was observed. As a result of this action, M3 synthetic peptide and atropine abrogated the stimulatory action. The L‐type calcium channel, calcium/calmodulin complex and COX‐2 inhibitors selectively blocked the increment of the specific activity of SOD and CAT in the rat submandibular gland. An increased production of NO and PGE2 by the cholinergic autoantibody and pilocarpine was also detected.

Conclusion

On the basis of these results, the increment of the specific activity of SOD and CAT in pSS patients as compared to control healthy individuals may be seen as a defensive reaction to the increment of the amount of ROS, which becoming uncontrollable, leads to irreversible cellular and tissue damage.
Evidence of ancient genome reduction in red algae (Rhodophyta)
Authors: Qiu Huan , Price Dana C. , Yang Eun Chan , Yoon Hwan Su , Bhattacharya Debashish
Published: February 2015

Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5–10 thousand genes) when compared with other free‐living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl‐phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.
Proteomic and gene expression analysis of zebrafish brain undergoing continuous light/dark stress
Authors: Purushothaman Sruthi , Saxena Sandeep , Meghah Vupalapathy , Meena Lakshmi Mula G. , Singh Sachin K. , Brahmendra Swamy Cherukuvada V. , Idris Mohammed M.
Published: February 2015

Several organisms irrespective of their complexity in structure and function have an inbuilt circadian rhythm. Zebrafish could be used as an alternate model animal in sleep research as it exhibits similar sleep–wake dynamics as mammals andDrosophila. In this study, we have analysed the adult zebrafish brain for its differential proteome and gene expression during perturbed light/dark cycle. A total of 53 and 25 proteins including sncb, peroxiredoxins andTCRalpha were identified based on two‐dimensional gel electrophoresis Fourier transform mass spectrometer/ion trap tandem mass spectrometer and differential in‐gel electrophoresisMALDI TOF MS/MSanalysis, respectively, with at least 1.5‐fold changes between the control and experimental brains. Real time‐polymerase chain reaction revealed that many circadian pathway‐associated genes, such as per1b, bmal1b, cry1b, bmal2 and nr1d2, were differentially regulated during continuous light/dark exposures. It is hypothesized that the differential regulation of these genes might lead to the discovery of potential diagnostic markers for gaining insight into the light/dark‐associated stress in humans.
Turning the Tables on Legal History: Parker's Common Law, History, and Democracy in America
Authors: Lavi Shai
Published: February 2015

Parker's Common Law, History, and Democracy in America joins an ongoing effort to turn the tables on “law and …” by replacing the familiar question “What can history, sociology, and cultural studies tell us about law?” with a new line of inquiry asking “What can law teach us about the reach and limits of disciplinary thinking?” In his study of the reception of common law into nineteenth‐century American jurisprudence, Parker unearths a notion of time based on stability and repetition that challenges the dominant modernist and historicist approach to the writing of law and history. Parker, however, shies away from drawing the full implications of this move and it remains unclear whether, in the final analysis, he escapes the spell of legal historicism.
Response: The Politeness of History
Authors: Parker Kunal M.
Published: February 2015

In my response to the reviews of my book by Marianne Constable, Shai Lavi, and Renisa Mawani, I situate the argument of Common Law, History, and Democracy in America, 1790–1900: Legal Thought Before Modernism within a concern with contemporary forms of historical knowledge. Where contemporary historical knowledge practices subsume their objects of investigation, I adopt the temporality of the object of investigation—namely, the common law—as the structure my book. In different registers, Constable, Lavi, and Mawani urge me to take up more explicitly the foundational questioning about which they care. I welcome their readings. However, given the distinct problematic from which I start, I argue, the book is not in the first instance an argument about the ontology of history or law.
Genetic isolation between two recently diverged populations of a symbiotic fungus
Authors: Branco Sara , Gladieux Pierre , Ellison Christopher E. , Kuo Alan , LaButti Kurt , Lipzen Anna , Grigoriev Igor V. , Liao Hui‐Ling , Vilgalys Rytas , Peay Kabir G. , Taylor John W. , Bruns Thomas D.
Published: February 2015

Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind‐dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced the whole genomes of 28 individuals from coastal and montane sites in California. We detected two clearly delineated coast and mountain populations with very low divergence. Genomic divergence was restricted to few regions, including a region of extreme divergence containing a gene encoding for a membrane Na+/H+ exchanger known for enhancing salt tolerance in plants and yeast. Our results are consistent with a very recent split between the montane and coastal Su. brevipes populations, with few small genomic regions under positive selection and a pattern of dispersal and/or establishment limitation. Furthermore, we identify a putatively adaptive gene that motivates further functional analyses to link genotypes and phenotypes and shed light on the genetic basis of adaptive traits.
The effects of music therapy in endotracheal suctioning of mechanically ventilated patients
Authors: Yaman Aktaş Yeşim , Karabulut Neziha
Published: February 2015

Background

Endotracheal suctioning has been identified as a painful procedure for critically ill patients.

Aim

To determine the effect of music therapy on pain intensity, sedation level and physiological parameters during endotracheal suctioning of mechanically ventilated patients in cardiovascular surgery intensive care unit (ICU).

Design

Experimental survey.

Methods

The study was conducted between May 2010 and June 2013 in Ordu Medical Park Hospital Cardiovascular Surgery Intensive Care Unit. The study sample consisted of 66 patients (33 experimental and 33 control) who complied with the criteria of inclusion for the study. Data was collected using the ‘Patient Information Form’, ‘Critical‐Care Pain Observation Tool’, ‘Ramsay Sedation Scale’ and ‘Form of Physiological Parameters’.

Results

The mean scores of the Ramsay Sedation Scale during endotracheal aspiration were respectively 1·88 and 1·55 in the experimental and control group and the difference between the groups was statistically significant (p = 0·003). The mean score of Critical‐Care Pain Observation Tool during endotracheal suctioning in the experimental group was found to be lower statistically than those of the control group (p < 0·001). There were no significant differences before, during and 20 min after suctioning between the two groups with regard to systolic blood pressure, diastolic blood pressure, heart rate and oxygen saturation (p > 0·05).

Conclusions

The results of this study implies that music therapy can be effective practice for nurses attempting to reduce patients' pain and control sedation level in patients on mechanical ventilators during endotracheal suctioning.

Relevance to clinical practice

It is recommended that music therapy should be added to the routine nursing care for mechanically ventilated patients.
The use of the MeDALL‐chip to assess IgE sensitization: a new diagnostic tool for allergic disease?
Authors: Skrindo Ingebjørg , Lupinek Christian , Valenta Rudolf , Hovland Vegard , Pahr Sandra , Baar Alexandra , Carlsen Kai‐Håkon , Mowinckel Petter , Wickman Magnus , Melen Erik , Bousquet Jean , Anto Josep M. , Lødrup Carlsen Karin C.
Published: February 2015

Background

Allergic sensitization is frequently present in asthma and rhinitis, but the role of specific immunoglobulin E (s‐IgE) is not always clear. Multiple s‐IgE analyses may provide insight into this relationship, thus a microarray chip was developed within the EU‐funded MeDALL project. The main objective was to evaluate the performance of the MeDALL‐chip compared to ImmunoCAP and skin prick test (SPT) in detecting allergic sensitization in children and secondarily to investigate the association to asthma and allergic rhinitis.

Methods

From the ‘Environment and Childhood Asthma Study’, 265 children were investigated at 10 and 16 yr of age with clinical examination, interview, SPT, ImmunoCAP, and the MeDALL‐chip including 152 allergen components in the analysis.

Results

Allergic sensitization at 10 yr was more frequently detected using the MeDALL‐chip (38.1%) compared to the ImmunoCAP (32.8%) (p = 0.034) and SPT (25.5%) (p < 0.001), but no significant difference was seen at 16 yr (MeDALL‐chip 49.8%, ImmunoCAP 48.6%, SPT 45.8%). The MeDALL‐chip did not differ significantly from the ImmunoCAP or SPT in terms of detecting allergic sensitization in subjects with rhinitis or asthma at 10 or 16 yr.

Conclusion

The prevalence of allergic sensitization increased by all three diagnostic tests from 10 to 16 yr was similar by SPT and ImmunoCAP and significantly higher with the MeDALL‐chip at 10 yr. All three tests were comparable for identification of allergic sensitization among children with current rhinitis or asthma.
Freshwater occurrence of the extinct dolphinParapontoporia(Cetacea:Lipotidae) from the upperPliocene nonmarineTulareFormation ofCalifornia
Authors: Boessenecker Robert W. , Poust Ashley W.
Published: February 2015

The diminutive, extinct longirostrine dolphinParapontoporiais one of the most abundantly represented lateNeogene odontocetes from the easternNorthPacific and is widely known from numerous marine strata of lateMiocene andPliocene age inCalifornia,BajaCalifornia and possibly Japan.Parapontoporiahas been identified as the sister taxon of the recently extinctChinese river dolphin (Lipotes vexillifer); unlikeLipotes, which exclusively inhabited freshwater, the depositional context ofParapontoporiasuggests it was marine. A newly identified petrosal ofParapontoporiasp. was preserved alongside terrestrial vertebrates in the nonmarineTulareFormation (upperPliocene toPleistocene, 2.2–0.6 Ma),California, which was deposited under lacustrine and fluviodeltaic conditions. Abundantly preserved freshwater molluscs and rare marine taxa suggest predominantly freshwater settings with intermittent periods of estuarine conditions. This occurrence ofParapontoporiaindicates its presence in theSanJoaquin basin after the retreat of the inland sea and suggests that this extinct odontocete may have been freshwater tolerant and an inhabitant of marine and freshwater settings, heralding the exclusively freshwater existence of its Recent sister taxonLipotes vexillifer.
Biologic Response Modifiers and Pediatric Psoriasis
Authors: Bellodi Schmidt Fernanda , Shah Kara N.
Published: February 2015

The efficacy and safety of biologic response modifiers such as etanercept, adalimumab, infliximab, and ustekinumab have been demonstrated in the treatment of psoriasis in adults, but none are currently approved for the treatment of psoriasis in children in the United States, and only etanercept is approved for the treatment of psoriasis in children in the European Union. Through case reports, case series, and a large clinical trial of the use of etanercept, the literature supports the use of these agents to treat psoriasis in children. Data on the use of the tumor necrosis factor‐α antagonists etanercept, adalimumab, and infliximab in the treatment of other inflammatory diseases in children—namely Crohn's disease, juvenile arthritis, and uveitis—support their safety profile in children.
Lulwoana sp., a dark septate endophyte in roots of Posidonia oceanica (L.) Delile seagrass
Authors: Torta L. , Lo Piccolo S. , Piazza G. , Burruano S. , Colombo P. , Ottonello D. , Perrone R. , Di Maida G. , Pirrotta M. , Tomasello A. , Calvo S.
Published: February 2015

Posidonia oceanica is the most common, widespread and important monocotyledon seagrass in the Mediterranean Basin, and hosts a large biodiversity of species, including microorganisms with key roles in the marine environment. In this study, we ascertain the presence of a fungal endophyte in the roots of P. oceanica growing on different substrata (rock, sand and matte) in two Sicilian marine meadows. Staining techniques on root fragments and sections, in combination with microscope observations, were used to visualise the fungal presence and determine the percentage of fungal colonisation (FC) in this tissue. In root fragments, statistical analysis of the FC showed a higher mean in roots anchored on rock than on matte and sand. In root sections, an inter‐ and intracellular septate mycelium, producing intracellular microsclerotia, was detected from the rhizodermis to the vascular cylinder. Using isolation techniques, we obtained, from both sampling sites, sterile, slow‐growing fungal colonies, dark in colour, with septate mycelium, belonging to the dark septate endophytes (DSEs). DNA sequencing of the internal transcribed spacer (ITS) region identified these colonies as Lulwoana sp. To our knowledge, this is the first report of Lulwoana sp. as DSE in roots of P. oceanica. Moreover, the highest fungal colonisation, detected in P. oceanica roots growing on rock, suggests that the presence of the DSE may help the host in several ways, particularly in capturing mineral nutrients through lytic activity.
Physical activity in patients with idiopathic pulmonary fibrosis
Authors: Nakayama Masayuki , Bando Masashi , Araki Koji , Sekine Toshie , Kurosaki Fumio , Sawata Tetsuro , Nakazawa Shoko , Mato Naoko , Yamasawa Hideaki , Sugiyama Yukihiko
Published: February 2015

Background and objective

Physical activity is an important parameter in patients with chronic obstructive pulmonary disease, but has not been studied in detail in patients with interstitial lung disease. This study aimed to evaluate physical activity in patients with idiopathic pulmonary fibrosis (IPF).

Methods

Physical activity was monitored in 31 stable IPF patients using an accelerometer for 1 month. The following factors reflecting physical activity were measured: the number of steps, walking distance, the time spent at magnitude of movement (MM) 1–6, physical activity‐related energy expenditure (PAEE) and total energy expenditure. We also measured the following clinical parameters: the modified Medical Research Council (MRC) scale, Krebs von den Lungen‐6 (KL‐6), pulmonary function parameters, 6‐min walk test (6MWT) results and high‐resolution computed tomography (HRCT) findings of the chest. We determined the relationship between these parameters and physical activity.

Results

We recorded 24 days of physical activity data. The time spent at MM < 1 was more than 10 h per day, whereas that at MM > 1 was approximately 1 h per day. The modified MRC scale, serum KL‐6 levels, 6MWT distance, and the extent of honeycomb and reticular abnormality on HRCT were associated with several facets of physical activity. In particular, lower KL‐6 levels were correlated with higher physical activity based on the number of steps, walking distance, the time spent at MM 1–4 and PAEE.

Conclusions

The modified MRC scale, 6MWT distance, extent of fibrosis on HRCT and serum KL‐6 levels are strongly associated with physical activity.
Availability and price of malaria rapid diagnostic tests in the public and private health sectors in 2011: results from 10 nationally representative cross‐sectional retail surveys
Authors: Poyer Stephen , Shewchuk Tanya , Tougher Sarah , Ye Yazoume ,   The ACTwatch Group, Mann Andrea G. , Willey Barbara A. , Thomson Rebecca , Amuasi John H. , Ren Ruilin , Wamukoya Marilyn , Taylor Mark , Nguah Samuel Blay , Mberu Blessing , Kalolella Admirabilis , Juma Elizabeth , Festo Charles , Johanes Boniface , Diap Graciela , Bruxvoort Katia , Ansong Daniel , Hanson Kara , Arnold Fred , Goodman Catherine
Published: February 2015

Objectives

To describe the state of the public and private malaria diagnostics market shortly after WHO updated its guidelines for testing all suspected malaria cases prior to treatment.

Methods

Ten nationally representative cross‐sectional cluster surveys were conducted in 2011 among public and private health facilities, community health workers and retail outlets (pharmacies and drug shops) in nine countries (Tanzania mainland and Zanzibar surveyed separately). Eligible outlets had antimalarials in stock on the day of interview or had stocked antimalarials in the past 3 months.

Results

Three thousand four hundred and thirty‐nine rapid diagnostic test (RDT) products from 39 manufacturers were audited among 12 197 outlets interviewed. Availability was typically highest in public health facilities, although availability in these facilities varied greatly across countries, from 15% in Nigeria to >90% in Madagascar and Cambodia. Private for‐profit sector availability was 46% in Cambodia, 20% in Zambia, but low in other countries. Median retail prices for RDTs in the private for‐profit sector ranged from $0.00 in Madagascar to $3.13 in Zambia. The reported number of RDTs used in the 7 days before the survey in public health facilities ranged from 3 (Benin) to 50 (Zambia).

Conclusions

Eighteen months after WHO updated its case management guidelines, RDT availability remained poor in the private sector in sub‐Saharan Africa. Given the ongoing importance of the private sector as a source of fever treatment, the goal of universal diagnosis will not be achievable under current circumstances. These results constitute national baselines against which progress in scaling‐up diagnostic tests can be assessed.
Discovering Gaps in Internationalization Competences of SMEs–a Comparative Case Study of Austrian SMEs
Authors: Anzengruber Johanna
Published: February 2015

This article adds to the debate on internationalization competences of SMEs. After an examination of the most influential papers, we systematically discuss the role of individual and organizational competence gaps before and during the internationalization phase. In more detail, we raise the question what kinds of competences gaps hinder SMEs to go international and what competence gaps arise during the internationalization. This is done using a comparative case study design with competence gap data from twenty-four SMEs in China and Austria. Our research reveals severe differences in competence gaps among those SMEs who have internationalized and those who will internationalize theirs businesses. Indeed, we found out that while internationalized SMEs perceive organizational competence gaps as higher as individual ones – exactly the opposite is found at the SMEs working exclusively in their home markets. We conclude by proposing a systematic, continuous, and task-oriented allocation of the competence development efforts.
Characterization and Optimization of a Tensioned Metastable Fluid Nuclear Particle Sensor Using Laser-Based Profilometry
Authors: Hagen Alexander R. , Grimes Thomas F. , Archambault Brian C. , Harris Trevor N. , Taleyarkhan Rusi P.
Published: February 2015

State-of-the-art neutron detectors lack capabilities required by the fields of homeland security, health physics, and even for direct in-core nuclear power monitoring. A new system being developed at Purdue’s Metastable Fluid and Advanced Research Laboratory in conjunction with S/A Labs, LLC provides capabilities that the state-of-the-art lacks, and simultaneously with beta (β) and gamma (γ) blindness, high (>90% intrinsic) efficiency for neutron/alpha spectroscopy and directionality, simple detection mechanism, and lowered electronic component dependence. This system, the tensioned metastable fluid detector (TMFD), provides these capabilities despite its vastly reduced cost and complexity compared with equivalent present day systems. Fluids may be placed at pressures lower than perfect vacuum (i.e., negative), resulting in tensioned metastable states. These states may be induced by tensioning fluids just as one would tension solids. The TMFD works by cavitation nucleation of bubbles resulting from energy deposited by charged ions or laser photon pile-up heating of fluid molecules, which are placed under sufficiently tensioned (negative) pressure states of metastability. The charged ions may be created from neutron scattering or from energetic charged particles such as alphas, alpha recoils, and fission fragments. A methodology has been created to profile the pressures in these chambers by laser-induced cavitation (LIC) for verification of a multiphysics simulation of the chambers. The methodology and simulation together have led to large efficiency gains in the current acoustically tensioned metastable fluid detector (ATMFD) system. This paper describes in detail the LIC methodology and provides background on the simulation it validates.
Measured Biaxial Residual Stress Maps in a Stainless Steel Weld
Authors: Olson Mitchell D. , Hill Michael R. , Patel Vipul I. , Muránsky Ondrej , Sisneros Thomas
Published: February 2015

This paper describes a sequence of residual stress measurements made to determine a two-dimensional map of biaxial residual stress in a stainless steel weld. A long stainless steel (316L) plate with an eight-pass groove weld (308L filler) was used. The biaxial stress measurements follow a recently developed approach, comprising a combination of contour method and slitting measurements, with a computation to determine the effects of out-of-plane stress on a thin slice. The measured longitudinal stress is highly tensile in the weld- and heat-affected zone, with a maximum around 450 MPa, and compressive stress toward the transverse edges around −250 MPa. The total transverse stress has a banded profile in the weld with highly tensile stress at the bottom of the plate (y = 0) of 400 MPa, rapidly changing to compressive stress (at y = 5 mm) of −200 MPa, then tensile stress at the weld root (y = 17 mm) and in the weld around 200 MPa, followed by compressive stress at the top of the weld at around −150 MPa. The results of the biaxial map compare well with the results of neutron diffraction measurements and output from a computational weld simulation.
Cardiac amyloidosis with gastrointestinal involvement: a case report.
Authors: Tantau Alina , Avram Ioan , Cozma Angela , Sampelean Dorel
Published: February 2015

Familial amyloidosis is a rare type of amyloidosis, difficult to diagnose. We present the case of a woman with chronic heart failure. Low ejection fraction and concentric left ventricle hypertrophy with granular sparkling were seen by echocardiography and cardiac magnetic resonance imaging. Based on myocardial biopsy and genetic tests, the diagnosis of transthyretin familial amyloidosis, secondary to the Glu54Gln gene mutation, was made. The presentation contains the diagnostic algorithm used in the case of our patient, including clinical, biochemical, imaging, histological and genetic examinations, for the purpose of a complete diagnosis.
Systems integration for global sustainability
Authors: Liu Jianguo , Mooney Harold , Hull Vanessa , Davis Steven J. , Gaskell Joanne , Hertel Thomas , Lubchenco Jane , Seto Karen C. , Gleick Peter , Kremen Claire , Li Shuxin
Published: February 2015

Seeking systems-based solutions

Without sustainable solutions, the world's most pressing environmental concerns will continue to persist or worsen. Achieving the goal of sustainability involves so many factors—from economics to ecology—that investigating one or even a handful of variables at a time often overlooks major parts of the problem. Liu
et al.
review systems-based approaches that are beginning to provide tenable ways to assess sustainability. Further integrating coupled human and natural components of a problem across multiple dimensions, including how one solution can create unintended consequences elsewhere, is essential for developing effective policies that seek global sustainability.

Science
, this issue
10.1126/science.1258832
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Authors: Taylor Tiffany B. , Mulley Geraldine , Dills Alexander H. , Alsohim Abdullah S. , McGuffin Liam J. , Studholme David J. , Silby Mark W. , Brockhurst Michael A. , Johnson Louise J. , Jackson Robert W.
Published: February 2015

Losing and then regaining flagella

The ability to adapt to changes in the function of gene regulators, as opposed to structural genes, is a crucial aspect of evolutionary change. Taylor
et al.
mutated a central regulator for the formation of flagella in the bacterium
Pseudomonas fluorescens
. They then put the mutated flagella-free bacteria under strong selection pressure to regain mobility. The mutated bacteria regained the lost flagella, and motility, within 4 days. Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis. The mutations increased the levels of the co-opted regulator, then altered its specificity for the flagella pathway.

Science
, this issue p.
1014
Cycles of species replacement emerge from locally induced maternal effects on offspring behavior in a passerine bird
Authors: Duckworth Renée A. , Belloni Virginia , Anderson Samantha R.
Published: February 2015

Mother knows best

Dynamic natural environments are challenging places to start life. In many species, however, the environment the mother lives in can actually shape the environment in which her offspring grow. Such maternal effects facilitate the exchange of important environmental information across generations. Duckworth
et al.
show that a mother's physiological responses to her environment can convey more complex information than we thought (see the Perspective by Dantzer). Female western bluebirds deposit more androgens in their eggs when competition for nest sites increases. This results in more-aggressive male chicks that are more likely to move on and colonize new, less crowded habitats.

Science
, this issue p.
875
; see also p.
822
Structural basis for Notch1 engagement of Delta-like 4
Authors: Luca Vincent C. , Jude Kevin M. , Pierce Nathan W. , Nachury Maxence V. , Fischer Suzanne , Garcia K. Christopher
Published: February 2015

An interaction that guides cell fate

Notch signaling is important in cell fate determination in mammals. Signaling is initiated when the extracellular domain of the transmembrane Notch protein on one cell binds to a surface ligand on another cell. Luca
et al.
report the crystal structure of the interacting regions of Notch and the Delta-like ligand DLL-4. The Notch protein is modified by O-linked glycan addition, and this is required for signaling. The structure shows two interaction interfaces. A glycan anchors the less conserved interface, which potentially provides a flexible way of regulating Notch interactions during development.

Science
, this issue p.
847
Leadership Training for Early Career Researchers
Authors: Clayton Julie
Published: February 2015

A decade ago, the "sink or swim" culture was widespread in research. But academic institutions across the United States and Europe are now investing resources in helping young researchers gain the skills they need for climbing the career ladder. Top on the list are leadership skills, whether for conflict management, handling finances, or negotiating intellectual property rights in an international consortium, these are highly rated assets that can help researchers advance to senior roles. Here's a look at some of the most established leadership programs that hold alumni who are leaping ahead as a result of the training.
Plumes on Europa tease NASA mission planners
Authors: Hand Eric
Published: February 2015

Astrobiologists covet chance to sample subterranean ocean, but plumes may come and go.
Research at Kew overhauled for leaner times
Authors: Stokstad Erik
Published: February 2015

World-leading collection focuses on its strengths following critical reviews and budget cuts.
The computer connection
The Innovators How a Group of Hackers, Geniuses, and Geeks Created the Digital Revolution
Walter Isaacson
Simon and Schuster, 2014. 559 pp.
Authors: Greenbaum Dov , Gerstein Mark
Published: February 2015

A closer look at the collaborations that fueled the digital revolution
Using ancient protein kinases to unravel a modern cancer drug’s mechanism
Authors: Wilson C. , Agafonov R. V. , Hoemberger M. , Kutter S. , Zorba A. , Halpin J. , Buosi V. , Otten R. , Waterman D. , Theobald D. L. , Kern D.
Published: February 2015

Evolution of dynamics affects function

The drug Gleevac inhibits Abl kinases and is used to treat multiple cancers. The closely related Src kinases also play a role in cancer but are not inhibited effectively by Gleevac. Nevertheless, Gleevac-bound structures of Src and Abl are nearly identical. Based on this structural information and protein sequence data, Wilson
et al.
reconstructed the common ancestor of Src and Abl. Mutations that affected conformational dynamics caused Gleevac affinity to be gained on the evolutionary trajectory toward Abl and lost on the trajectory toward Src.

Science
, this issue p.
882
The meaning of microbes
Philosophy of Microbiology
Maureen A. O'Malley
Cambridge University Press, 2014. 279 pp.
Authors: Woolfson Adrian
Published: February 2015

Microorganisms may offer unique insights into the nature and evolution of life
Delineating Ebola entry
Authors: Falzarano Darryl , Feldmann Heinz
Published: February 2015

A specific calcium channel is required for Ebola virus to infect a cell

[Also see Report by

Sakurai
et al.

]
Decreasing
pfmdr1
Copy Number Suggests that Plasmodium falciparum in Western Cambodia Is Regaining
In Vitro
Susceptibility to Mefloquine
Authors: Lim Pharath , Dek Dalin , Try Vorleak , Sreng Sokunthea , Suon Seila , Fairhurst Rick M.
Published: February 2015

Dihydroartemisinin-piperaquine is the current frontline artemisinin combination therapy (ACT) for
Plasmodium falciparum
malaria in Cambodia but is now failing in several western provinces. To investigate artesunate plus mefloquine (AS+MQ) as a replacement ACT, we measured the prevalence of multiple
pfmdr1
copies—a molecular marker for MQ resistance—in 844
P. falciparum
clinical isolates collected in 2008 to 2013. The
pfmdr1
copy number is decreasing in Western Cambodia, suggesting that
P. falciparum
is regaining
in vitro
susceptibility to MQ.
The Transforming Growth Factor β1/Interleukin-31 Pathway Is Upregulated in Patients with Hepatitis B Virus-Related Acute-on-Chronic Liver Failure and Is Associated with Disease Severity and Survival
Authors: Yu Xueping , Guo Ruyi , Ming Desong , Deng Yong , Su Milong , Lin Chengzu , Li Julan , Lin Zhenzhong , Su Zhijun
Published: February 2015

The transforming growth factor β1/interleukin-31 (TGF-β1/IL-31) pathway plays an important role in the process of cell injury and inflammation. The purpose of this work was to explore the role of the TGF-β1/IL-31 pathway in the cytopathic process of hepatitis B virus (HBV)-related acute-on-chronic liver failure (ACLF). The quantitative serum levels of TGF-β1, IL-9, IL-10, IL-17, IL-22, IL-23, IL-31, IL-33, and IL-35 were analyzed among chronic hepatitis B (CHB) patients (n= 17), ACLF patients (n= 18), and normal control (NC) subjects (n= 18). Disease severity in patients with ACLF was assessed using the model for end-stage liver disease (MELD) and Child-Pugh scores. Serum TGF-β1 levels were strongly positively correlated with IL-31 in all subjects, and both of them were positively correlated with IL-17, IL-22, and IL-33. In CHB and ACLF patients, serum levels of TGF-β1 and IL-31 were both increased significantly compared with those in NC subjects and positively correlated with total bilirubin (TBil) and alpha-fetoprotein (AFP) levels. ACLF patients showed the highest levels of TGF-β1 and IL-31, which were positively correlated with Child-Pugh scores. Furthermore, the recovery from the liver injury in CHB was accompanied by decreased TGF-β1 and IL-31 levels. More importantly, serum levels of TGF-β1 and IL-31 were markedly upregulated in ACLF nonsurvivors, and IL-31 displayed the highest sensitivity and specificity (85.7% and 100.0%, respectively) in predicting nonsurvival of ACLF patients. Increasing activity of the TGF-β1/IL-31 pathway is well correlated with the extent of liver injury, disease severity, and nonsurvival of ACLF patients, while reducing activity is detected along the recovery from liver injury in CHB, suggesting its potential role in the pathogenesis of liver injury during chronic HBV infection.
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Siphophage Shivani
Authors: Piya Denish , Xie Yicheng , Hernandez Morales Adriana C. , Kuty Everett Gabriel F.
Published: February 2015

Here, we describe the complete genome sequence of siphophage Shivani, a T5-like constituent phage in the therapeutic phage cocktail IntestiPhage developed for bacterial gastroenteritis. Shivani was isolated against a foodborne pathogen,
Salmonella enterica
, which is one of the leading causes of gastroenteritis.
Draft Genome Sequence of Pantoea sp. Strain MBLJ3, Isolated in a Laboratory Environmental Control Study
Authors: Zhang Jing , Hung Guo-Chiuan , Lei Haiyan , Li Tianwei , Li Bingjie , Tsai Shien , Lo Shyh-Ching
Published: February 2015

This report describes the draft genome sequence of a newly isolated strain, Pantoea sp. MBLJ3. The genome is 4.8 Mb in size, with a G+C content of 54.27%, and it contains 4,522 protein-coding sequences, 69 tRNA genes, and 5 rRNA genes.
Induction of Caspase-11 by Aspartyl Proteinases of Candida albicans and Implication in Promoting Inflammatory Response
Authors: Gabrielli Elena , Pericolini Eva , Luciano Eugenio , Sabbatini Samuele , Roselletti Elena , Perito Stefano , Kasper Lydia , Hube Bernhard , Vecchiarelli Anna
Published: February 2015

We recently demonstrated that the secreted aspartyl proteinases (Saps), Sap2 and Sap6, of
Candida albicans
have the potential to induce the canonical activation of the NLRP3 inflammasome, leading to the secretion of interleukin-1β (IL-1β) and IL-18 via caspase-1 activation. We also observed that the activation of caspase-1 is partially independent from the NLRP3 activation pathway. In this study, we examined whether Sap2 and Sap6 are also able to activate the noncanonical inflammasome pathway in murine macrophages. Our data show that both Sap2 and Sap6 can activate caspase-11 through type I interferon (IFN) production. Caspase-11 cooperates to activate caspase-1, with a subsequent increase of IL-1β secretion. Endocytosis and internalization of Saps are required for the induction of type I IFN production, which is essential for induction of noncanonical inflammasome activation. Our study indicates a sophisticated interplay between caspase-1 and caspase-11 that connects the canonical and noncanonical pathways of inflammasome activation in response to
C. albicans
Saps.
Anti-APOBEC3G Activity of HIV-1 Vif Protein Is Attenuated in Elite Controllers
Authors: Kikuchi Tadashi , Iwabu Yukie , Tada Takuya , Kawana-Tachikawa Ai , Koga Michiko , Hosoya Noriaki , Nomura Shigeru , Brumme Zabrina L. , Jessen Heiko , Pereyra Florencia , Trocha Alicja , Walker Bruce D. , Iwamoto Aikichi , Tokunaga Kenzo , Miura Toshiyuki
Published: February 2015

HIV-1-infected individuals who control viremia to below the limit of detection without antiviral therapy have been termed elite controllers (EC). Functional attenuation of some HIV-1 proteins has been reported in EC. The HIV-1 accessory protein Vif (virion infectivity factor) enhances viral infectivity through anti-retroviral factor apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G (APOBEC3G) degradation; however, little is known regarding Vif function in EC. Here, the anti-APOBEC3G activities of clonal, plasma HIV RNA-derived Vif sequences from 46 EC, 46 noncontrollers (NC), and 44 individuals with acute infection (AI) were compared. Vesicular stomatitis virus glycoprotein (VSV-G)-pseudotyped viruses were generated by cotransfecting 293T cells with expression plasmids encoding patient-derived Vif, human APOBEC3G, VSV-G, and a
vif
/
env
-deficient
luciferase
-reporter HIV-1 proviral DNA clone. Viral stocks were used to infect 293T cells, and Vif anti-APOBEC3G activity was quantified in terms of luciferase signal. On average, the anti-APOBEC3G activities of EC-derived Vif sequences (median log
10
relative light units [RLU], 4.54 [interquartile range {IQR}, 4.30 to 4.66]) were significantly lower than those of sequences derived from NC (4.75 [4.60 to 4.92],
P
< 0.0001) and AI (4.74 [4.62 to 4.94],
P
< 0.0001). Reduced Vif activities were not associated with particular HLA class I alleles expressed by the host. Vif functional motifs were highly conserved in all patient groups. No single viral polymorphism could explain the reduced anti-APOBEC3G activity of EC-derived Vif, suggesting that various combinations of minor polymorphisms may underlie these effects. These results further support the idea of relative attenuation of viral protein function in EC-derived HIV sequences.

IMPORTANCE
HIV-1 elite controllers (EC) are rare individuals who are able to control plasma viremia to undetectable levels without antiretroviral therapy. Understanding the pathogenesis and mechanisms underpinning this rare phenotype may provide important insights for HIV vaccine design. The EC phenotype is associated with beneficial host immunogenetic factors (such as HLA-B*57) as well as with functions of attenuated viral proteins (e.g., Gag, Pol, and Nef). In this study, we demonstrated that HIV-1 Vif sequences isolated from EC display relative impairments in their ability to counteract the APOBEC3G host restriction factor compared to Vif sequences from normal progressors and acutely infected individuals. This result extends the growing body of evidence demonstrating attenuated HIV-1 protein function in EC and, in particular, supports the idea of the relevance of viral factors in contributing to this rare HIV-1 phenotype.
Integrated Microfluidic Card with TaqMan Probes and High-Resolution Melt Analysis To Detect Tuberculosis Drug Resistance Mutations across 10 Genes
Authors: Pholwat Suporn , Liu Jie , Stroup Suzanne , Gratz Jean , Banu Sayera , Rahman S. M. Mazidur , Ferdous Sara Sabrina , Foongladda Suporn , Boonlert Duangjai , Ogarkov Oleg , Zhdanova Svetlana , Kibiki Gibson , Heysell Scott , Houpt Eric
Published: February 2015

Genotypic methods for drug susceptibility testing of
Mycobacterium tuberculosis
are desirable to speed the diagnosis and proper therapy of tuberculosis (TB). However, the numbers of genes and polymorphisms implicated in resistance have proliferated, challenging diagnostic design. We developed a microfluidic TaqMan array card (TAC) that utilizes both sequence-specific probes and high-resolution melt analysis (HRM), providing two layers of detection of mutations. Twenty-seven primer pairs and 40 probes were designed to interrogate 3,200 base pairs of critical regions of the
inhA
,
katG
,
rpoB
,
embB
,
rpsL
,
rrs
,
eis
,
gyrA
,
gyrB
, and
pncA
genes. The method was evaluated on 230 clinical M. tuberculosis isolates from around the world, and it yielded 96.1% accuracy (2,431/2,530) in comparison to that of Sanger sequencing and 87% accuracy in comparison to that of the slow culture-based susceptibility testing. This TAC-HRM method integrates assays for 10 genes to yield fast, comprehensive, and accurate drug susceptibility results for the 9 major antibiotics used to treat TB and could be deployed to improve treatment outcomes.

IMPORTANCE
Multidrug-resistant tuberculosis threatens global tuberculosis control efforts. Optimal therapy utilizes susceptibility test results to guide individualized treatment regimens; however, the susceptibility testing methods in use are technically difficult and slow. We developed an integrated TaqMan array card method with high-resolution melt analysis that interrogates 10 genes to yield a fast, comprehensive, and accurate drug susceptibility result for the 9 major antituberculosis antibiotics.
Sewage Reflects the Microbiomes of Human Populations
Authors: Newton Ryan J. , McLellan Sandra L. , Dila Deborah K. , Vineis Joseph H. , Morrison Hilary G. , Eren A. Murat , Sogin Mitchell L.
Published: February 2015

Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either:
Bacteroidaceae
,
Prevotellaceae
, or
Lachnospiraceae/Ruminococcaceae
. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome.

IMPORTANCE
The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics.
CT pleurogram for diagnosing an occult diaphragmatic tear
Authors: Govindarajan Arunkumar , Sarawagi Radha , Prakash Manikka Lakshmanan , Govindarajalou Ramkumar
Published: February 2015

A 27-year-old man road traffic accident victim, in his initial CT, showed fractures in left lower ribs, pleural effusion and splenic and pancreatic lacerations. The left pleural effusion, drained with an intercostal tube, did not show any significant reduction in size and pleural fluid amylase was abnormally high. A diaphragmatic tear was suspected. Contrast was injected through the intercostal tube and a CT was performed, which revealed a small diaphragmatic tear and communication of the pleural space with peritoneum and the pancreatic laceration site.