bluuebunny/crossref_metadata_2025 huggingface dataset:
New insights into mechanisms driving carbon allocation in tropical forests
Authors: Hofhansl Florian , Schnecker Jörg , Singer Gabriel , Wanek Wolfgang
Published: September 2014

The proportion of carbon allocated to wood production is an important determinant of the carbon sink strength of global forest ecosystems. Understanding the mechanisms controlling wood production and its responses to environmental drivers is essential for parameterization of global vegetation models and to accurately predict future responses of tropical forests in terms of carbon sequestration.

Here, we synthesize data from 105 pantropical old‐growth rainforests to investigate environmental controls on the partitioning of net primary production to wood production (%WP) using structural equation modeling.

Our results reveal that %WP is governed by two independent pathways of direct and indirect environmental controls. While temperature and soil phosphorus availability indirectly affected %WP via increasing productivity, precipitation and dry season length both directly increased %WP via tradeoffs along the plant economics spectrum.

We provide new insights into the mechanisms driving %WP, allowing us to conclude that projected climate change could enhance %WP in less productive tropical forests, thus increasing carbon sequestration in montane forests, but adversely affecting lowland forests.
Hijacking of an autophagy‐like process is critical for the life cycle of a DNA virus infecting oceanic algal blooms
Authors: Schatz Daniella , Shemi Adva , Rosenwasser Shilo , Sabanay Helena , Wolf Sharon G. , Ben‐Dor Shifra , Vardi Assaf
Published: September 2014

Marine photosynthetic microorganisms are the basis of marine food webs and are responsible for nearly 50% of the global primary production. Emiliania huxleyi forms massive oceanic blooms that are routinely terminated by large double‐stranded DNA coccolithoviruses. The cellular mechanisms that govern the replication cycle of these giant viruses are largely unknown.

We used diverse techniques, including fluorescence microscopy, transmission electron microscopy, cryoelectron tomography, immunolabeling and biochemical methodologies to investigate the role of autophagy in host–virus interactions.

Hallmarks of autophagy are induced during the lytic phase of E. huxleyi viral infection, concomitant with up‐regulation of autophagy‐related genes (ATG genes). Pretreatment of the infected cells with an autophagy inhibitor causes a major reduction in the production of extracellular viral particles, without reducing viral DNA replication within the cell. The host‐encoded Atg8 protein was detected within purified virions, demonstrating the pivotal role of the autophagy‐like process in viral assembly and egress.

We show that autophagy, which is classically considered as a defense mechanism, is essential for viral propagation and for facilitating a high burst size. This cellular mechanism may have a major impact on the fate of the viral‐infected blooms, and therefore on the cycling of nutrients within the marine ecosystem.
Ontogeny of the sheathing leaf base in maize (Zea mays)
Authors: Johnston Robyn , Leiboff Samuel , Scanlon Michael J.
Published: September 2014

Leaves develop from the shoot apical meristem (SAM) via recruitment of leaf founder cells. Unlike eudicots, most monocot leaves display parallel venation and sheathing bases wherein the margins overlap the stem.

Here we utilized computed tomography (CT) imaging, localization of PIN‐FORMED1 (PIN1) auxin transport proteins, andin situhybridization of leaf developmental transcripts to analyze the ontogeny of monocot leaf morphology in maize (Zea mays).

CTimaging of whole‐mounted shoot apices illustrates the plastochron‐specific stages during initiation of the basal sheath margins from the tubular disc of insertion (DOI).PIN1 localizations identify basipetal auxin transport in theSAML1 layer at the site of leaf initiation, a process that continues reiteratively during later recruitment of lateral leaf domains. Refinement of these auxin transport domains results in multiple, parallel provascular strands within the initiating primordium. By contrast, auxin is transported from the L2 toward the L1 at the developing margins of the leaf sheath. Transcripts involved in organ boundary formation and dorsiventral patterning accumulate within theDOI, preceding the outgrowth of the overlapping margins of the sheathing leaf base.

We suggest a model wherein sheathing bases and parallel veins are both patterned via the extended recruitment of lateral maize leaf domains from theSAM.
Physiological characterization of aluminum tolerance and accumulation in tartary and wild buckwheat
Authors: Wang Hua , Chen Rong Fu , Iwashita Takashi , Shen Ren Fang , Ma Jian Feng
Published: September 2014

Ionic aluminum (Al) is toxic for plant growth, but some plant species are able to accumulate Al at high concentrations without showing toxicity symptoms.

In order to determine whether other species in the genus Fagopyrum are able to accumulate Al like common buckwheat (Fagopyrum esculentum), we investigated the external and internal detoxification mechanisms of Al in two self‐compatible species: tartary (Fagopyrum tataricum) and wild buckwheat (Fagopyrum homotropicum).

Both tartary and wild buckwheat showed high Al tolerance comparable to common buckwheat. Furthermore, these two species also secreted oxalate rapidly from the roots in response to Al in a time‐dependent manner. Both tartary and wild buckwheat accumulated > 1 mg g−1 Al in the leaves after short‐term exposure to Al. Analysis with 27Al‐nuclear magnetic resonance (NMR) revealed that Al was present in the form of Al‐oxalate (1 : 3 ratio) in the roots and leaves, but in the form of Al‐citrate (1 : 1 ratio) in the xylem sap in both species.

These results indicate that similar to common buckwheat, both tartary and wild buckwheat detoxify Al externally and internally, respectively, by secreting oxalate from the roots and by forming the Al‐oxalate complex, which is a nonphytotoxic form. These features of Al response and accumulation may be conserved in genus Fagopyrum.
Conservation of Male Sterility 2 function during spore and pollen wall development supports an evolutionarily early recruitment of a core component in the sporopollenin biosynthetic pathway
Authors: Wallace Simon , Chater Caspar C. , Kamisugi Yasuko , Cuming Andrew C. , Wellman Charles H. , Beerling David J. , Fleming Andrew J.
Published: September 2014

The early evolution of plants required the acquisition of a number of key adaptations to overcome physiological difficulties associated with survival on land. One of these was a tough sporopollenin wall that enclosed reproductive propagules and provided protection from desiccation and UV‐B radiation. All land plants possess such walled spores (or their derived homologue, pollen).

We took a reverse genetics approach, consisting of knock‐out and complementation experiments to test the functional conservation of the sporopollenin‐associated gene MALE STERILTY 2 (which is essential for pollen wall development in Arabidopsis thaliana) in the bryophyte Physcomitrella patens.

Knock‐outs of a putative moss homologue of the A. thaliana MS2 gene, which is highly expressed in the moss sporophyte, led to spores with highly defective walls comparable to that observed in the A. thaliana ms2 mutant, and extremely compromised germination. Conversely, the moss MS2 gene could not rescue the A. thaliana ms2 phenotype.

The results presented here suggest that a core component of the biochemical and developmental pathway required for angiosperm pollen wall development was recruited early in land plant evolution but the continued increase in pollen wall complexity observed in angiosperms has been accompanied by divergence in MS2 gene function.
Protective immune responses to fungal infections
Authors: Rivera A.
Published: September 2014

The incidence of fungal infections has been on the rise over several decades. Fungal infections threaten animals, plants and humans alike and are thus of significant concern to scientists across disciplines. Over the last decade, significant advances on fungal immunology have lead to a better understanding of important mechanisms of host protection against fungi. In this article, I review recent advances of relevant mechanisms of immune‐mediated protection to fungal infections.
Transcriptomic and proteomic analyses of embryogenic tissues in Picea balfouriana treated with 6‐benzylaminopurine
Authors: Li Qingfen , Zhang Shougong , Wang Junhui
Published: September 2014

The cytokinin 6‐benzylaminopurine (6‐BAP) influences the embryogenic capacity of the tissues of Picea balfouriana during long subculture (after 3 months). Tissues that proliferate in 3.6 and 5 µM 6‐BAP exhibit the highest and lowest embryogenic capacity, respectively, generating 113 ± 6 and 23 ± 3 mature embryos per 100 mg of tissue. In this study, a comparative transcriptomic and proteomic approach was applied to characterize the genes and proteins that are differentially expressed among tissues under the influence of different levels of 6‐BAP. A total of 51 375 unigenes and 2617 proteins were obtained after quality filtering. There were 2770 transcripts for proteins found among these unigenes. Gene ontology (GO) analysis of the differentially expressed unigenes and proteins showed that they were involved in cell and binding activity and were enriched in ribosome and glutathione metabolism pathways. Ribosomal proteins, glutathione S‐transferase proteins, germin‐like proteins and calmodulin‐independent protein kinases were up‐regulated in the embryogenic tissues with the highest embryogenic ability (treated with 3.6 µM 6‐BAP), which was validated via quantitative real‐time polymerase chain reaction (qRT‐PCR) analysis, and these proteins might serve as molecular markers of embryogenic ability. Data are available via Sequence Read Archive (SRA) and ProteomeXchange with identifier SRP042246 and PXD001022, respectively.
Skeletal muscle water and electrolytes following prolonged dehydrating exercise
Authors: Mora‐Rodríguez R. , Fernández‐Elías V. E. , Hamouti N. , Ortega J. F.
Published: September 2014

We studied if dehydrating exercise would reduce muscle water (H2Omuscle) and affect muscle electrolyte concentrations. Vastus lateralis muscle biopsies were collected prior, immediately after, and 1 and 4 h after prolonged dehydrating exercise (150 min at 33 ± 1 °C, 25% ± 2% humidity) on nine endurance‐trained cyclists (VO2max = 54.4 ± 1.05 mL/kg/min). Plasma volume (PV) changes and fluid shifts between compartments (Cl− method) were measured. Exercise dehydrated subjects 4.7% ± 0.3% of body mass by losing 2.75 ± 0.15 L of water and reducing PV 18.4% ± 1% below pre‐exercise values (P < 0.05). Right after exercise H2Omuscle remained at pre‐exercise values (i.e., 398 ± 6 mL/100 g dw muscle−1) but declined 13% ± 2% (342 ± 12 mL/100 g dw muscle−1; P < 0.05) after 1 h of supine rest. At that time, PV recovered toward pre‐exercise levels. The Cl− method corroborated the shift of fluid between extracellular and intracellular compartments. After 4 h of recovery, PV returned to pre‐exercise values; however, H2Omuscle remained reduced at the same level. Muscle Na+ and K+ increased (P < 0.05) in response to the H2Omuscle reductions. Our findings suggest that active skeletal muscle does not show a net loss of H2O during prolonged dehydrating exercise. However, during the first hour of recovery H2Omuscle decreases seemly to restore PV and thus cardiovascular stability.
Class (Non)Voting in Switzerland 1971‐2011: Ruptures and Continuities in a Changing Political Landscape
Authors: Rennwald Line
Published: September 2014

Abstract

This article deals with the evolution of class voting in Switzerland from 1971 to 2011. It shows that class cleavage (working class versus owners/employers) has weakened in Switzerland. The existence of a large right‐wing party with strong support among the working class contributes to blurring the traditional class divisions in voting. However, the analysis indicates that class cleavage has not completely disappeared. The centre‐right parties display much continuity in their class basis over time, thus contributing to the persistence of class cleavage. Besides taking into account the diversity of the right‐wing parties, the article also offers a new perspective by including nonvoting. Class differences in turnout are important in Switzerland, but the findings suggest that the most important change over time concerns party choice and not turnout.
The detection of blood group phenotypes using paper diagnostics
Authors: Then W. L. , Li M. , McLiesh H. , Shen W. , Garnier G.
Published: September 2014

Background and Objectives

Paper biodiagnostics for blood typing are novel, cheap, fast and easy to use. Agglutinated red blood cells cannot travel through the porous structure of paper, indicating a positive antibody–antigen interaction has occurred. Conversely, non‐agglutinated blood can disperse and wick through the paper structure with the ease to indicate a negative result. This principle has been demonstrated to detect blood group phenotypes: ABO and RhD. However, typing for red blood cell antigens such as Rh, Kell, Duffy and Kidd has not yet been explored on paper.

Materials and Methods

Two paper testing methods – an elution and a direct flow‐through method – were investigated to detect red blood cell antigens excluding the ABO system and RhD. Antigens explored include the following: C, c, E, e, K, k, Fya, Fyb, Jka, Jkb, M, N, S and s, P1, Lea and Leb. The variables tested include the following: reaction time and reagent concentration. The importance of antibody type/structure for successful agglutination on paper was confirmed.

Results

Some blood group phenotypes showed less agglutination due to weaker antibody–antigen interactions. Most blood groups with antibodies available as IgM, such as C, c, E, e, K and k, and Jka and Jkb, and P1, were successful using both methods. However, other blood groups, especially those with antibodies only available as polyclonal antibodies, were unsuccessful and require further scrutiny.

Conclusion

Paper can be used as an alternative blood grouping diagnostic tool for selected blood group phenotypes.
New perspectives on the origin of hypertension; the role of the hypothalamic melanocortin system
Authors: Samuelsson Anne‐Maj
Published: September 2014

New Findings

What is the topic of this review?

The growing epidemic of obesity has attracted increasing interest in the effect of obesity in pregnancy on the developing child. Independent associations have been reported between maternal obesity and hypertension in the offspring. This review focuses on novel advances in our comprehension of sympathetically mediated hypertension.

What advances does it highlight?

Our recent studies have unravelled important mechanisms of leptin and the melanocortin system in the early origins of hypertension. Offspring of obese dams have a heightened arterial pressure response to leptin, which is normalized by central administration of melanocortin receptor antagonist. The central melanocortin system may contribute to the elevated arterial pressure in juvenile offspring secondary to maternal obesity.

Maternal obesity is a major public health problem. Pregnant obese women have increased risk of adverse outcomes for mother and child. Recent observational studies from mother–child cohort studies suggest that obesity during pregnancy is a risk factor for the development of cardiovascular diseases in the child later in life. We have previously shown that maternal obesity in rodents leads to sympathetically mediated hypertension in the juvenile offspring prior to obesity. This was associated with an exaggerated leptin surge in early postnatal life. Increased leptin during this critical period of development is likely to contribute to the onset of hypertension by altered leptin sensitivity and dysregulation of the normal neurotrophic action of leptin. Unpublished evidence also suggests that the central melanocortin system, including melanocortin 4 receptors, plays a key role in early origins of hypertension in offspring of obese rat dams. This review focuses on the role of the central leptin–melanocortin signalling pathways in the early origins of hypertension. The overall aim is to understand the central leptin–melanocortin system, with its multiple intracellular signalling pathways which differentially and independently regulate appetite, renal sympathetic nerve activity and blood pressure.
Solid Particle Erosion Downstream of an Orifice
Authors: Nemitallah M. A. , Ben-Mansour R. , Habib M. A. , Ahmed W. H. , Toor I. H. , Gasem Z. M. , Badr H. M.
Published: September 2014

The paper deals with solid particle erosion downstream of a sharp-edged orifice commonly found in many chemical processing industries. The orifice is installed in a pipe that is long enough to ensure fully developed turbulent flow in both upstream and downstream directions. Both the k-ε model and the Lagrangian particle-tracking technique were used for predicting solid particle trajectories. Gambit 2.2 was used to construct the computational grid and the commercial Fluent 12.1 code was used to perform the calculations. The available erosion correlations were used for determination of erosion characteristics considering carbon steel and aluminum pipes. The investigation was carried out for a flow restricting orifice of fixed geometry and pipe flow velocities in the range 1–4 m/s using solid particle of diameters 50–500 μm. The results indicated two critical erosion regions downstream of the orifice: the first is in the immediate neighborhood of the orifice plate and the second is in the flow reattachment zone. The results showed also a strong dependence of erosion on both particle size and flow velocity.
Neighborhood Deprivation and Physical Activity Facilities—No Support for the Deprivation Amplification Hypothesis
Authors: Schneider Sven , D’Agostino Adriana , Weyers Simone , Diehl Katharina , Gruber Johannes
Published: September 2014

Background:

The “deprivation amplification” hypothesis states that individuals who are already socially disadvantaged experience a further contextual disadvantage regarding their access to health relevant facilities. This hypothesis is investigated for the first time for Germany, led by the question as to whether deprived neighborhoods experience worse access to physical activity facilities than affluent ones. We differentiate between facilities for children and adolescents vs. for adults, and between free vs. fee-based facilities.

Methods:

We identified all physical activity facilities by traversing each neighborhood by foot or bicycle in the framework of a systematic audit. Number, location, and type of facilities were recorded and visualized. The investigation area encompassed 18 social areas in a major German city with 92,000 inhabitants and an area of 12.0 km2.

Results:

A lower socioeconomic area status was related to a higher availability of physical activity facilities for children and adolescents (7.11/1000 minors in deprived social areas versus 4.46/1000 minors in affluent social areas; P < .05). For adults, the pattern was similar but not significant (P ≥ .05). These results were also shown in analyses in which only free facilities were taken into consideration.

Conclusions:

Our study cannot support the “deprivation amplification” hypothesis regarding the availability of physical activity facilities.
Emerging Viral Diseases: Confronting Threats with New Technologies
Authors: Marston Hilary D. , Folkers Gregory K. , Morens David M. , Fauci Anthony S.
Published: September 2014

Emerging viral diseases continue to threaten human health, but recent scientific advances are better positioning us to treat them and to detect and control the causative pathogens.
The Ubiquitinase Pathway Takes Center Stage in Viral Myocarditis
Authors: Drum Chester L.
Published: September 2014

Targeted degradation of a viral protease by the cardiac myocyte ubiquitinase system keeps viral replication and cardiac damage at bay.
The Capsid Binder Vapendavir and the Novel Protease Inhibitor SG85 Inhibit Enterovirus 71 Replication
Authors: Tijsma Aloys , Franco David , Tucker Simon , Hilgenfeld Rolf , Froeyen Mathy , Leyssen Pieter , Neyts Johan
Published: September 2014

Antivirals against enterovirus 71 (EV71) are urgently needed. We demonstrate that the novel enteroviral protease inhibitor (PI) SG85 and capsid binder (CB) vapendavir efficiently inhibit the
in vitro
replication of 21 EV71 strains/isolates that are representative of the different genogroups A, B, and C. The PI rupintrivir, the CB pirodavir, and the host-targeting compound enviroxime, which were included as reference compounds, also inhibited the replication of all isolates. Remarkably, the CB compound pleconaril was devoid of any anti-EV71 activity. An
in silico
docking study revealed that pleconaril—unlike vapendavir and pirodavir—lacks essential binding interactions with the viral capsid. Vapendavir and SG85 (or analogues) should be further explored for the treatment of EV71 infections. The data presented here may serve as a reference when developing yet-novel inhibitors.
Role of
Pfmdr1
in
In Vitro
Plasmodium falciparum Susceptibility to Chloroquine, Quinine, Monodesethylamodiaquine, Mefloquine, Lumefantrine, and Dihydroartemisinin
Authors: Wurtz Nathalie , Fall Bécaye , Pascual Aurélie , Fall Mansour , Baret Eric , Camara Cheikhou , Nakoulima Aminata , Diatta Bakary , Fall Khadidiatou Ba , Mbaye Pape Saliou , Diémé Yaya , Bercion Raymond , Wade Boubacar , Pradines Bruno
Published: September 2014

The involvement of
Pfmdr1
(
Plasmodium falciparum
multidrug resistance 1) polymorphisms in antimalarial drug resistance is still debated. Here, we evaluate the association between polymorphisms in
Pfmdr1
(N86Y, Y184F, S1034C, N1042D, and D1246Y) and
Pfcrt
(K76T) and
in vitro
responses to chloroquine (CQ), mefloquine (MQ), lumefantrine (LMF), quinine (QN), monodesethylamodiaquine (MDAQ), and dihydroartemisinin (DHA) in 174
Plasmodium falciparum
isolates from Dakar, Senegal. The
Pfmdr1
86Y mutation was identified in 14.9% of the samples, and the 184F mutation was identified in 71.8% of the isolates. No 1034C, 1042N, or 1246Y mutations were detected. The
Pfmdr1
86Y mutation was significantly associated with increased susceptibility to MDAQ (
P
= 0.0023), LMF (
P
= 0.0001), DHA (
P
= 0.0387), and MQ (
P
= 0.00002). The N86Y mutation was not associated with CQ (
P
= 0.214) or QN (
P
= 0.287) responses. The
Pfmdr1
184F mutation was not associated with various susceptibility responses to the 6 antimalarial drugs (
P
= 0.168 for CQ, 0.778 for MDAQ, 0.324 for LMF, 0.961 for DHA, 0.084 for QN, and 0.298 for MQ). The
Pfmdr1
86Y-Y184 haplotype was significantly associated with increased susceptibility to MDAQ (
P
= 0.0136), LMF (
P
= 0.0019), and MQ (
P
= 0.0001). The additional
Pfmdr1
86Y mutation increased significantly the
in vitro
susceptibility to MDAQ (
P
< 0.0001), LMF (
P
< 0.0001), MQ (
P
< 0.0001), and QN (
P
= 0.0026) in wild-type
Pfcrt
K76 parasites. The additional
Pfmdr1
86Y mutation significantly increased the
in vitro
susceptibility to CQ (
P
= 0.0179) in
Pfcrt
76T CQ-resistant parasites.
Effective Control of Salmonella Infections by Employing Combinations of Recombinant Antimicrobial Human β-Defensins hBD-1 and hBD-2
Authors: Maiti Soumitra , Patro Sunita , Purohit Sukumar , Jain Sumeet , Senapati Shantibhusan , Dey Nrisingha
Published: September 2014

We successfully produced two human β-defensins (hBD-1 and hBD-2) in bacteria as functional peptides and tested their antibacterial activities against
Salmonella enterica
serovar Typhi,
Escherichia coli
, and
Staphylococcus aureus
employing both spectroscopic and viable CFU count methods. Purified peptides showed approximately 50% inhibition of the bacterial population when used individually and up to 90% when used in combination. The 50% lethal doses (LD
50
) of hBD-1 against
S.
Typhi,
E. coli
, and
S. aureus
were 0.36, 0.40, and 0.69 μg/μl, respectively, while those for hBD-2 against the same bacteria were 0.38, 0.36, and 0.66 μg/μl, respectively. Moreover, we observed that bacterium-derived antimicrobial peptides were also effective in increasing survival time and decreasing bacterial loads in the peritoneal fluid, liver, and spleen of a mouse intraperitoneally infected with
S.
Typhi. The 1:1 hBD-1/hBD-2 combination showed maximum effectiveness in challenging the
Salmonella
infection
in vitro
and
in vivo
. We also observed less tissue damage and sepsis formation in the livers of infected mice after treatment with hBD-1 and hBD-2 peptides individually or in combination. Based on these findings, we conclude that bacterium-derived recombinant β-defensins (hBD-1 and hBD-2) are promising antimicrobial peptide (AMP)-based substances for the development of new therapeutics against typhoid fever.
Switching from Posaconazole Suspension to Tablets Increases Serum Drug Levels in Leukemia Patients without Clinically Relevant Hepatotoxicity
Authors: Jung Dong Sik , Tverdek Frank P. , Kontoyiannis Dimitrios P.
Published: September 2014

We evaluated posaconazole serum concentrations and hepatotoxicity in 12 leukemia patients who transitioned from posaconazole suspension to tablets. Patients who switched to tablets had significantly increased posaconazole concentrations (median: suspension, 748 ng/ml; tablet, 1,910 ng/ml;
P
< 0.01) without clinically relevant hepatotoxicity.
A CRISPR with Roles in Myxococcus xanthus Development and Exopolysaccharide Production
Authors: Wallace Regina A. , Black Wesley P. , Yang Xianshuang , Yang Zhaomin
Published: September 2014

The Gram-negative soil bacterium
Myxococcus xanthus
utilizes its social (S) gliding motility to move on surfaces during its vegetative and developmental cycles. It is known that S motility requires the type IV pilus (T4P) and the exopolysaccharide (EPS) to function. The T4P is the S motility motor, and it powers cell movement by retraction. As the key regulator of the S motor, EPS is proposed to be the anchor and trigger for T4P retraction. The production of EPS is regulated in turn by the T4P in
M. xanthus
, and T4P
−
mutants are S
−
and EPS
−
. In this study, a Δ
pilA
strain (T4P
−
and EPS
−
) was mutagenized by a transposon and screened for EPS
+
mutants. A
pilA
suppressor isolated as such harbored an insertion in the 3rd clustered regularly interspaced short palindromic repeat (CRISPR3) in
M. xanthus
. Evidence indicates that this transposon insertion, designated CRISPR3*, is a gain-of-function (GOF) mutation. Moreover, CRISPR3* eliminated developmental aggregation in both the wild-type and the
pilA
mutant backgrounds. Upstream of CRISPR3 are genes encoding the repeat-associated mysterious proteins (RAMPs). These RAMP genes are indispensable for CRISPR3* to affect development and EPS in
M. xanthus
. Analysis by reverse transcription (RT)-PCR suggested that CRISPR3* led to an increase in the processing of the RNA transcribed from CRISPR3. We propose that certain CRISPR3 transcripts, once expressed and processed, target genes critical for
M. xanthus
fruiting body development and EPS production in a RAMP-dependent manner.
Assembling Flagella in Salmonella Mutant Strains Producing a Type III Export Apparatus without FliO
Authors: Barker Clive S. , Meshcheryakova Irina V. , Inoue Tomoharu , Samatey Fadel A.
Published: September 2014

The type III export apparatus of the
Salmonella
flagellum consists of six transmembrane proteins (FlhA, FlhB, FliO, FliP, FliQ, and FliR) and three soluble proteins (FliH, FliI, and FliJ). Deletion of the
fliO
gene creates a mutant strain that is poorly motile; however, suppressor mutations in the
fliP
gene can partially rescue motility. To further understand the mechanism of suppression of a
fliO
deletion mutation, we isolated new suppressor mutant strains with partially rescued motility. Whole-genome sequence analysis of these strains found a missense mutation that localized to the
clpP
gene [
clpP
(
V20F
)], which encodes the ClpP subunit of the ClpXP protease, and a synonymous mutation that localized to the
fliA
gene [
fliA
(+
36T
→
C
)], which encodes the flagellar sigma factor, σ
28
. Combining these suppressor mutations with mutations in the
fliP
gene additively rescued motility and biosynthesis of the flagella in
fliO
deletion mutant strains. Motility was also rescued by an
flgM
deletion mutation or by plasmids carrying either the
flhDC
or
fliA
gene. The
fliA
(+
36T
→
C
) mutation increased mRNA translation of a
fliA
′-
lacZ
gene fusion, and immunoblot analysis revealed that the mutation increased levels of σ
28
. Quantitative real-time reverse transcriptase PCR showed that either the
clpP
(
V20F
) or
fliA
(+
36T
→
C
) mutation rescued expression of class 3 flagellar and chemotaxis genes; still, the suppressor mutations in the
fliP
gene had a greater effect on bypassing the loss of
fliO
function. This suggests that the function of FliO is closely associated with regulation of FliP during assembly of the flagellum.
Disposal of fetal tissue following elective abortion: what women think
Authors: Myers Amanda J , Lohr Patricia A , Pfeffer Naomi
Published: September 2014

Background and methodology

UK regulations on managing fetal tissue after pregnancy loss, including abortion, are underscored by the concept of ‘sensitive disposal’. This involves offering women burial or cremation and, when disposal is by the health care provider, separating fetal tissue from other clinical waste before incineration. We interviewed 23 women who had undergone one or more abortions about their understanding, attitudes and experiences of fetal tissue disposal and ‘sensitive disposal’. Transcripts were analysed for representative themes.

Results

Prior to the abortion, most participants did not give consideration to disposal methods because their focus was on ending the pregnancy. Appropriate disposal by health professionals was assumed but some women undergoing early medical abortion reported anxiety about how to manage disposal at home. The term ‘sensitive disposal’ was unfamiliar to most respondents. Participants generally favoured separation of fetal tissue from other clinical waste and approved of incineration as a means of destruction. Ceremonial disposal was approved of following the loss of a wanted pregnancy but not following elective abortion. Most wanted the opportunity to access information about disposal but did not favour being asked or required to make decisions about disposal.

Discussion and conclusions

Knowledge about the management of fetal tissue after abortion or the concept of ‘sensitive disposal’ was limited among the women we interviewed. Current guidelines appear discordant with the views of women terminating an unwanted pregnancy. Further research is needed to better inform policy on this issue.
A subclass of starlike functions associated with left-half of the lemniscate of Bernoulli
Authors: Mendiratta Rajni , Nagpal Sumit , Ravichandran V.
Published: September 2014

Let [Formula: see text] denote the class of all analytic functions f in the open unit disk with the normalizations f(0) = f′(0) - 1 = 0 such that zf′(z)/f(z) lies in the interior of the left-half of the shifted lemniscate of Bernoulli [Formula: see text]. In this paper, we investigate the geometric properties of functions in this class and compute the [Formula: see text]-radius for functions belonging to several interesting classes.
Boundedness and blow-up of solutions for a nonlinear elliptic system
Authors: Covei Dragos-Patru
Published: September 2014

The main objective in this paper is to obtain the existence results for bounded and unbounded solutions of some quasilinear elliptic systems. Related results as obtained here have been established recently in [C. O. Alves and A. R. F. de Holanda, Existence of blow-up solutions for a class of elliptic systems, Differ. Integral Eqs.26(1/2) (2013) 105–118]. Also, we present some references to give the connection between these types of problems with probability and stochastic processes, hoping that these are interesting for the audience of analysts likely to read this paper.
FATIGUE LIFE AND CRACK GROWTH BEHAVIOR IN ANNEALED AND NORMALIZED 0.83% CARBON STEEL
Authors: MAKABE CHOBIN , YAMAZAKI SHINYA , MIYAZAKI TATSUJIRO , FUJIKAWA MASAKI
Published: September 2014

The variations of fatigue limit and fatigue life of a plain specimen of annealed and normalized 0.83% carbon steel were investigated. This material is used for cutting tools and the original microstructure includes a spherical microstructure. After heat treatment under some conditions, the microstructure changed to a lamellar microstructure. However, the fatigue lives of the plain specimens of this material showed almost the same tendency even after heat treatment under some conditions. In those cases, the initial crack length in the fatigue process is related to the size of the crystal structure and related to the distribution of ferrite. In the present study, the relationship between the distribution of hardness and the fatigue limit was investigated. Also, it was discussed that the fatigue limit of heat-treated 0.83% carbon steel could be evaluated by a relationship in which the parameters are the hardness and initial crack length. Finally, the tendencies of fatigue life of heat-treated 0.83% carbon steel were discussed based on the observations of crack growth behavior.
The power-law attributes of stratigraphic layering and their possible significance
Authors: Bailey Robin J.
Published: September 2014

Conventional stratigraphic logging is biased towards human-scale units and is correspondingly suspect as a basis for statistical analysis of spatial layering relationships. AR analysis uses lithological sample series to define layers in terms of the ‘first returns’ of each sample value, yielding objective layer thickness inventories (LTI) covering several orders of magnitude. Bilogarithmic LTI plots, relating the return thicknesses to their numerical frequency in the section, reveal power-law relationships with non-integer exponents. Over two orders of magnitude, the geometric layering relationships are thus shown to be self-similar (fractal). The power-law exponents also relate to Hurst exponents that describe the variability in the data series and the negative long range dependence in the sampled records.

Kilometre-scale gamma ray logs of continental, paralic, shallow marine and pelagic facies yield similar power-law exponents, regardless of the interpreted processes and rates of accumulation. This suggests that a ‘universal’ power law describes the self-similar layering of the stratigraphic record. This is inferred to mean that the power-law behaviours are the outcome of the threshold interactions between a sediment-transporting fluid and its bed. They suggest that the erosional operations that generate the record are characterized by self-organized criticality and involve a strange attractor.
Barriers and bridges: early human dispersals in equatorial SE Asia
Authors: Wurster Christopher M. , Bird Michael I.
Published: September 2014

Past environments of equatorial SE Asia must have played a critical role in determining the timing and trajectory of early human dispersal into and through the region. However, very few reliable terrestrial records are available with which to contextualize human dispersal events. This circumstance, coupled with a sparse archaeological record and the likelihood that much of the archaeological record is now submerged, means we have an incomplete understanding of the role that geography, climate and environment played in shaping human pre-history in this region. From a review of the literature, we conclude that there must have been a substantial environmental barrier resulting in a genetic separation between east and west Sundaland that persisted even though a terrestrial connection was present for most of the Pleistocene. This barrier is likely to be a north–south corridor of open non-forest vegetation, and its existence may have encouraged the rapid dispersal of early humans through the interior of Sundaland and on to Sahul. We conclude that more reliable terrestrial palaeoenvironmental records are required to better understand the links between past environments and dispersal events. We highlight avenues of particular research value, such as focusing on eastern Sumatra, western/southern Borneo and the islands in the Java Sea, where the purported savanna corridor most probably existed, and including edaphic factors in palaeovegetation modelling.
DIG
Authors: Nguyen Thanhvu , Kapur Deepak , Weimer Westley , Forrest Stephanie
Published: September 2014

This article describes and evaluates DIG, a dynamic invariant generator that infers invariants from observed program traces, focusing on numerical and array variables. For numerical invariants, DIG supports both nonlinear equalities and inequalities of arbitrary degree defined over numerical program variables. For array invariants, DIG generates nested relations among multidimensional array variables. These properties are nontrivial and challenging for current static and dynamic invariant analysis methods. The key difference between DIG and existing dynamic methods is its generative technique, which infers invariants directly from traces, instead of using traces to filter out predefined templates. To generate accurate invariants, DIG employs ideas and tools from the mathematical and formal methods domains, including equation solving, polyhedra construction, and theorem proving; for example, DIG represents and reasons about polynomial invariants using geometric shapes. Experimental results on 27 mathematical algorithms and an implementation of AES encryption provide evidence that DIG is effective at generating invariants for these programs.
On the Comprehension of Program Comprehension
Authors: Maalej Walid , Tiarks Rebecca , Roehm Tobias , Koschke Rainer
Published: September 2014

Research in program comprehension has evolved considerably over the past decades. However, only little is known about how developers practice program comprehension in their daily work. This article reports on qualitative and quantitative research to comprehend the strategies, tools, and knowledge used for program comprehension. We observed 28 professional developers, focusing on their comprehension behavior, strategies followed, and tools used. In an online survey with 1,477 respondents, we analyzed the importance of certain types of knowledge for comprehension and where developers typically access and share this knowledge.

We found that developers follow pragmatic comprehension strategies depending on context. They try to avoid comprehension whenever possible and often put themselves in the role of users by inspecting graphical interfaces. Participants confirmed that standards, experience, and personal communication facilitate comprehension. The team size, its distribution, and open-source experience influence their knowledge sharing and access behavior. While face-to-face communication is preferred for accessing knowledge, knowledge is frequently shared in informal comments.

Our results reveal a gap between research and practice, as we did not observe any use of comprehension tools and developers seem to be unaware of them. Overall, our findings call for reconsidering the research agendas towards context-aware tool support.
Some Code Smells Have a Significant but Small Effect on Faults
Authors: Hall Tracy , Zhang Min , Bowes David , Sun Yi
Published: September 2014

We investigate the relationship between faults and five of Fowler et al.'s least-studied smells in code: Data Clumps, Switch Statements, Speculative Generality, Message Chains, and Middle Man. We developed a tool to detect these five smells in three open-source systems: Eclipse, ArgoUML, and Apache Commons. We collected fault data from the change and fault repositories of each system. We built Negative Binomial regression models to analyse the relationships between smells and faults and report the McFadden effect size of those relationships. Our results suggest that Switch Statements had no effect on faults in any of the three systems; Message Chains increased faults in two systems; Message Chains which occurred in larger files reduced faults; Data Clumps reduced faults in Apache and Eclipse but increased faults in ArgoUML; Middle Man reduced faults only in ArgoUML, and Speculative Generality reduced faults only in Eclipse. File size alone affects faults in some systems but not in all systems. Where smells did significantly affect faults, the size of that effect was small (always under 10 percent). Our findings suggest that some smells do indicate fault-prone code in some circumstances but that the effect that these smells have on faults is small. Our findings also show that smells have different effects on different systems. We conclude that arbitrary refactoring is unlikely to significantly reduce fault-proneness and in some cases may increase fault-proneness.
Privacy amplification with asymptotically optimal entropy loss
Authors: Chandran Nishanth , Kanukurthi Bhavana , Ostrovsky Rafail , Reyzin Leonid
Published: September 2014

We study the problem of “privacy amplification”: key agreement between two parties who both know a weak secret
w
, such as a password. (Such a setting is ubiquitous on the internet, where passwords are the most commonly used security device.) We assume that the key agreement protocol is taking place in the presence of an active computationally unbounded adversary Eve. The adversary may have partial knowledge about
w
, so we assume only that
w
has some entropy from Eve’s point of view. Thus, the goal of the protocol is to convert this nonuniform secret
w
into a uniformly distributed string
R
that is fully secret from Eve.
R
may then be used as a key for running symmetric cryptographic protocols (such as encryption, authentication, etc.).

Because we make no computational assumptions, the entropy in
R
can come only from
w
. Thus, such a protocol must minimize the entropy loss during its execution, so that
R
is as long as possible. The best previous results have entropy loss of Θ(
κ
2
), where
κ
is the security parameter, thus requiring the password to be very long even for small values of
κ
. In this work, we present the first protocol for information-theoretic key agreement that has entropy loss linear in the security parameter. The result is optimal up to constant factors. We achieve our improvement through a somewhat surprising application of error-correcting codes for the edit distance.

The protocol can be extended to provide also “information reconciliation,” that is, to work even when the two parties have slightly different versions of
w
(e.g., when biometrics are involved).
Spatial and temporal isolation of virtual CAN controllers
Authors: Herber Christian , Richter Andre , Rauchfuss Holm , Herkersdorf Andreas
Published: September 2014

Virtualization is a key technology to enable the use of multi-core processors in automotive embedded systems. For side-by-side execution of mixed-criticality applications that access shared communication infrastructures, a secure and safe virtualization of I/O devices is required, which features a complete spatial and temporal isolation of individual virtual interfaces. We extended existing approaches of hardware-based CAN virtualization to achieve a full isolation while maintaining the bounded latencies achieved in previous implementations. It is shown, that even a denial-of-service attack towards one virtual controller does not influence the behavior of other virtual controllers. In addition, the scheduling mechanism implemented to guarantee temporal isolation can be configured to provide differentiated service levels for real-time and best effort application domains.
Tropical Forests in the Anthropocene
Authors: Malhi Yadvinder , Gardner Toby A. , Goldsmith Gregory R. , Silman Miles R. , Zelazowski Przemyslaw
Published: September 2014

The Anthropocene is characterized as an epoch when human influence has begun to fundamentally alter many aspects of the Earth system and many of the planet's biomes. Here, we review and synthesize our understanding of Anthropocene changes in tropical forests. Key facets include deforestation driven by agricultural expansion, timber and wood extraction, the loss of fauna that maintain critical ecological connections, the spread of fire, landscape fragmentation, the spread of second-growth forests, new species invasion and pathogen spread, increasing CO2, and climate change. The patterns of change are spatially heterogeneous, are often characterized by strong interactions among different drivers, can have both large-scale and remote effects, and can play out through ecological cascades over long timescales. As a consequence, most tropical forests are on a trajectory to becoming altered ecosystems, with the degree of alteration dependent on the intensity and duration of the current bottleneck of human-induced pressures. We highlight the importance of this understanding to develop the strategies necessary for shaping the transition of tropical forests through the early Anthropocene, as well as highlight the opportunities and challenges for the tropical forest science community in the coming decades.
Advances in Measuring the Environmental and Social Impacts of Environmental Programs
Authors: Ferraro Paul J. , Hanauer Merlin M.
Published: September 2014

Inspired by the success of evidence-based medicine, environmental scholars and practitioners have grown enthusiastic about applying a similar evidence-based approach to solve some of the world's most pressing environmental problems. An important component of the evidence-based movement is the empirical evaluation of program and policy impacts. Impact evaluations draw heavily from recent advances in the empirical study of causal relationships—the effect of one thing on another. This review highlights the key components of these advances and characterizes the way in which they contribute to better evaluations of the environmental and social impacts of environmental programs. The review emphasizes that a solid understanding of these advances is required before environmental scholars and practitioners can begin to collect the relevant data, analyze them within credible research designs, and generate reliable evidence about the effectiveness of the myriad proposed solutions to the world's environmental and social problems.
Networks and the Challenge of Sustainable Development
Authors: Henry Adam Douglas , Vollan Björn
Published: September 2014

Network concepts are central to at least three challenges of interest in the sustainability science literature: how to link knowledge with action, how to enhance collective action, and how to promote social learning. Although each challenge has developed into a coherent literature, social network concepts—which examine the particular ways in which social agents relate to one another—emerge as a common theme across all three challenges. To build a synthetic understanding of networks and sustainability, we must consider how structural properties of networks relate to sustainability outcomes, how networks evolve over time, and how institutional context influences this evolutionary process. A better understanding of these questions can inform strategies to promote patterns of social interaction that support sustainability.
Lagrangian Coherent Structures
Authors: Haller George
Published: September 2014

Typical fluid particle trajectories are sensitive to changes in their initial conditions. This makes the assessment of flow models and observations from individual tracer samples unreliable. Behind complex and sensitive tracer patterns, however, there exists a robust skeleton of material surfaces, Lagrangian coherent structures (LCSs), shaping those patterns. Free from the uncertainties of single trajectories, LCSs frame, quantify, and even forecast key aspects of material transport. Several diagnostic quantities have been proposed to visualize LCSs. More recent mathematical approaches identify LCSs precisely through their impact on fluid deformation. This review focuses on the latter developments, illustrating their applications to geophysical fluid dynamics.