bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data
Authors: LOHSE MARC , NAGEL AXEL , HERTER THOMAS , MAY PATRICK , SCHRODA MICHAEL , ZRENNER RITA , TOHGE TAKAYUKI , FERNIE ALISDAIR R. , STITT MARK , USADEL BJÖRN 
Published: November 2013

AbstractNext‐generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan‐to‐GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator.
Glucose inhibits root meristem growth via ABA INSENSITIVE 5, which represses PIN1 accumulation and auxin activity in Arabidopsis
Authors: YUAN TING‐TING , XU HENG‐HAO , ZHANG KUN‐XIAO , GUO TING‐TING , LU YING‐TANG 
Published: November 2013

AbstractGlucose functions as a hormone‐like signalling molecule that modulates plant growth and development in Arabidopsis thaliana. However, the role of glucose in root elongation remains elusive. Our study demonstrates that high concentrations of glucose reduce the size of the root meristem zone by repressing PIN1 accumulation and thereby reducing auxin levels. In addition, we verified the involvement of ABA INSENSITIVE 5 (ABI5) in this process by showing that abi5‐1 is less sensitive to glucose than the wild type, whereas glucose induces ABI5 expression and the inducible overexpression of ABI5 reduces the size of the root meristem zone. Furthermore, the inducible overexpression of ABI5 in PIN1::PIN1‐GFP plants reduces the level of PIN1‐GFP, but glucose reduces the level of PIN1‐GFP to a lesser extent in abi5‐1 PIN1::PIN1‐GFP plants than in the PIN1::PIN1‐GFP control, suggesting that ABI5 is involved in glucose‐regulated PIN1 accumulation. Taken together, our data suggest that ABI5 functions in the glucose‐mediated inhibition of the root meristem zone by repressing PIN1 accumulation, thus leading to reduced auxin levels in roots.
Sporolithon tenue sp. nov. (Sporolithales, Corallinophycidae, Rhodophyta): A new rhodolith‐forming species from the tropical southwestern Atlantic
Authors: Bahia Ricardo G. , Amado‐Filho Gilberto M. , Maneveldt Gavin W. , Adey Walter H. , Johnson Gabriel , Marins Bianca V. , Longo Leila L. 
Published: November 2013

SummaryA new species conforming to the generic description of Sporolithon was found forming small (1–3 cm in diameter) rhodoliths at 18–75 m depth on the eastern coast of Brazil. Sporolithon tenue Bahia, Amado‐Filho, Maneveldt et W.H. Adey, sp. nov. differs from other species of Sporolithon in having a thin, primary vegetative thallus of only 45–250 μm in thickness composed of up to 20 cell layers. Sporolithon tenue can build thicker crusts by overgrowths of thalli with new hypothallia. The absence of a layer of elongate cells at the base of the tetrasporangial chambers and the shedding of senescent tetrasporangial sori are also characters that separate the new species from all other currently recognized species within the genus. Observations from recently collected material and from herbarium specimens show that specimens previously designated as Sporolithon africanum (Foslie) J. Afonso‐Carillo in Brazil correspond to Sporolithon tenue. Molecular phylogenetic analyses of psbA sequence alignments show that the new species is phylogenetically distinct within the genus Sporolithon.
The spatial and temporal distribution of grain‐size breaks in turbidites
Authors: Stevenson Christopher J. , Talling Peter J. , Masson Douglas G. , Sumner Esther J. , Frenz Michael , Wynn Russell B. 
Published: November 2013

ABSTRACTGrain‐size breaks are surfaces where abrupt changes in grain size occur vertically within deposits. Grain‐size breaks are common features in turbidites around the world, including ancient and modern systems. Despite their widespread occurrence, grain‐size breaks have been regarded as exceptional, and not included within idealized models of turbidity current deposition. This study uses ca 100 shallow sediment cores, from the Moroccan Turbidite System, to map out five turbidite beds for distances in excess of 2000 km. The vertical and spatial distributions of grain‐size breaks within these beds are examined. Five different types of grain‐size break are found: Type I – in proximal areas between coarse sand and finer grained structureless sand; Type II – in proximal areas between inversely graded sand overlain by finer sand; Type III – in proximal areas between sand overlain by ripple cross‐laminated finer sand; Type IV – throughout the system between clean sand and mud; and Type V – in distal areas between mud‐rich (debrite) sand and mud. This article interprets Types I and V as being generated by sharp vertical concentration boundaries, controlled by sediment and clay concentrations within the flows, whilst Types II and III are interpreted as products of spatial/temporal fluctuations in flow capacity. Type IV are interpreted as the product of fluid mud layers, which hinder the settling of non‐cohesive grains and bypasses them down slope. Decelerating suspensions with sufficient clay will always form cohesive layers near to bed, promoting the generation of Type IV grain‐size breaks. This may explain why Type IV grain‐size breaks are widespread in all five turbidites examined and are commonplace within turbidite sequences studied elsewhere. Therefore, Type IV grain‐size breaks should be understood as the norm, not the exception, and regarded as a typical feature within turbidite beds.
Numbers defy the law of large numbers
Authors: Falk Ruma , Lann Avital Lavie 
Published: November 2013

SummaryAs the number of independent tosses of a fair coin grows, the rates of heads and tails tend to equality. This is misinterpreted by many students as being true also for the absolute numbers of the two outcomes, which, conversely, depart unboundedly from each other in the process. Eradicating that misconception, as by coin‐tossing experiments, should be incorporated early on into learning the law of large numbers.
Prevalence and clustering of soil‐transmitted helminth infections in a tribal area in southern India
Authors: Kaliappan Saravanakumar Puthupalayam , George Santosh , Francis Mark Rohit , Kattula Deepthi , Sarkar Rajiv , Minz Shantidani , Mohan Venkata Raghava , George Kuryan , Roy Sheela , Ajjampur Sitara Swarna Rao , Muliyil Jayaprakash , Kang Gagandeep 
Published: November 2013

AbstractObjectivesTo estimate the prevalence, spatial patterns and clustering in the distribution of soil‐transmitted helminth (STH) infections, and factors associated with hookworm infections in a tribal population in Tamil Nadu, India.MethodsCross‐sectional study with one‐stage cluster sampling of 22 clusters. Demographic and risk factor data and stool samples for microscopic ova/cysts examination were collected from 1237 participants. Geographical information systems mapping assessed spatial patterns of infection.ResultsThe overall prevalence of STH was 39% (95% CI 36%–42%), with hookworm 38% (95% CI 35–41%) and Ascaris lumbricoides 1.5% (95% CI 0.8–2.2%). No Trichuris trichiura infection was detected. People involved in farming had higher odds of hookworm infection (1.68, 95% CI 1.31–2.17, P < 0.001). In the multiple logistic regression, adults (2.31, 95% CI 1.80–2.96, P < 0.001), people with pet cats (1.55, 95% CI 1.10–2.18, P = 0.011) and people who did not wash their hands with soap after defecation (1.84, 95% CI 1.27–2.67, P = 0.001) had higher odds of hookworm infection, but gender and poor usage of foot wear did not significantly increase risk. Cluster analysis, based on design effect calculation, did not show any clustering of cases among the study population; however, spatial scan statistic detected a significant cluster for hookworm infections in one village.ConclusionMultiple approaches including health education, improving the existing sanitary practices and regular preventive chemotherapy are needed to control the burden of STH in similar endemic areas.
The Pseudomonas syringae effector HopF2 suppresses Arabidopsis immunity by targeting BAK1
Authors: Zhou Jinggeng , Wu Shujing , Chen Xin , Liu Chenglong , Sheen Jen , Shan Libo , He Ping 
Published: November 2013

SummaryPseudomonas syringae delivers a plethora of effector proteins into host cells to sabotage immune responses and modulate physiology to favor infection. The P. syringae pv. tomato DC3000 effector HopF2 suppresses Arabidopsis innate immunity triggered by multiple microbe‐associated molecular patterns (MAMP) at the plasma membrane. We show here that HopF2 possesses distinct mechanisms for suppression of two branches of MAMP‐activated MAP kinase (MAPK) cascades. In addition to blocking MKK5 (MAPK kinase 5) activation in the MEKK1 (MAPK kinase kinase 1)/MEKKs–MKK4/5–MPK3/6 cascade, HopF2 targets additional component(s) upstream of MEKK1 in the MEKK1–MKK1/2–MPK4 cascade and the plasma membrane‐localized receptor‐like cytoplasmic kinase BIK1 and its homologs. We further show that HopF2 directly targets BAK1, a plasma membrane‐localized receptor‐like kinase that is involved in multiple MAMP signaling. The interaction between BAK1 and HopF2 and between two other P. syringae effectors, AvrPto and AvrPtoB, was confirmed in vivo and in vitro. Consistent with BAK1 as a physiological target of AvrPto, AvrPtoB and HopF2, the strong growth defects or lethality associated with ectopic expression of these effectors in wild‐type Arabidopsis transgenic plants were largely alleviated in bak1 mutant plants. Thus, our results provide genetic evidence to show that BAK1 is a physiological target of AvrPto, AvrPtoB and HopF2. Identification of BAK1 as an additional target of HopF2 virulence not only explains HopF2 suppression of multiple MAMP signaling at the plasma membrane, but also supports the notion that pathogen virulence effectors act through multiple targets in host cells.
A method to synchronize signals from multiple patient monitoring devices through a single input channel for inclusion in list‐mode acquisitions
Authors: O’Connor J. Michael , Pretorius P. Hendrik , Johnson Karen , King Michael A. 
Published: November 2013

Purpose:This technical note documents a method that the authors developed for combining a signal to synchronize a patient‐monitoring device with a second physiological signal for inclusion into list‐mode acquisition. Our specific application requires synchronizing an external patient motion‐tracking system with a medical imaging system by multiplexing the tracking input with the ECG input. The authors believe that their methodology can be adapted for use in a variety of medical imaging modalities including single photon emission computed tomography (SPECT) and positron emission tomography (PET).Methods:The authors insert a unique pulse sequence into a single physiological input channel. This sequence is then recorded in the list‐mode acquisition along with the R‐wave pulse used for ECG gating. The specific form of our pulse sequence allows for recognition of the time point being synchronized even when portions of the pulse sequence are lost due to collisions with R‐wave pulses. This was achieved by altering our software used in binning the list‐mode data to recognize even a portion of our pulse sequence. Limitations on heart rates at which our pulse sequence could be reliably detected were investigated by simulating the mixing of the two signals as a function of heart rate and time point during the cardiac cycle at which our pulse sequence is mixed with the cardiac signal.Results:The authors have successfully achieved accurate temporal synchronization of our motion‐tracking system with acquisition of SPECT projections used in 17 recent clinical research cases. In our simulation analysis the authors determined that synchronization to enable compensation for body and respiratory motion could be achieved for heart rates up to 125 beats‐per‐minute (bpm).Conclusions:Synchronization of list‐mode acquisition with external patient monitoring devices such as those employed in motion‐tracking can reliably be achieved using a simple method that can be implemented using minimal external hardware and software modification through a single input channel, while still recording cardiac gating signals.
Automated evaluation of setup errors in carbon ion therapy using PET: Feasibility study
Authors: Kuess Peter , Helmbrecht Stephan , Fiedler Fine , Birkfellner Wolfgang , Enghardt Wolfgang , Hopfgartner Johannes , Georg Dietmar 
Published: November 2013

Purpose:To investigate the possibility of detecting patient mispositioning in carbon‐ion therapy with particle therapy positron emission tomography (PET) in an automated image registration based manner.Methods:Tumors in the head and neck (H&N), pelvic, lung, and brain region were investigated. Biologically optimized carbon ion treatment plans were created with TRiP98. From these treatment plans, the reference β+‐activity distributions were calculated using a Monte Carlo simulation. Setup errors were simulated by shifting or rotating the computed tomography (CT). The expected β+ activity was calculated for each plan with shifts. Finally, the reference particle therapy PET images were compared to the “shifted” β+‐activity distribution simulations using the Pearsonˈs correlation coefficient (PCC). To account for different PET monitoring options the inbeam PET was compared to three different inroom scenarios. Additionally, the dosimetric effects of the CT misalignments were investigated.Results:The automated PCC detection of patient mispositioning was possible in the investigated indications for cranio‐caudal shifts of 4 mm and more, except for prostate tumors. In the rather homogeneous pelvic region, the generated β+‐activity distribution of the reference and compared PET image were too much alike. Thus, setup errors in this region could not be detected. Regarding lung lesions the detection strongly depended on the exact tumor location: in the center of the lung tumor misalignments could be detected down to 2 mm shifts while resolving shifts of tumors close to the thoracic wall was more challenging. Rotational shifts in the H&N and lung region of +6° and more could be detected using inroom PET and partly using inbeam PET. Comparing inroom PET to inbeam PET no obvious trend was found. However, among the inroom scenarios a longer measurement time was found to be advantageous.Conclusions:This study scopes the use of various particle therapy PET verification techniques in four indications. The automated detection of patientsˈ setup errors was investigated in a broad accumulation of data sets. The evaluation of introduced setup errors is performed automatically, which is of utmost importance to introduce highly required particle therapy monitoring devices into the clinical routine.
Distinct Roles of Candida albicans Drug Resistance Transcription Factors
TAC1
,
MRR1
, and
UPC2
in Virulence
Authors: Lohberger Andrea , Coste Alix T. , Sanglard Dominique 
Published: November 2013

ABSTRACT

Azoles are widely used in antifungal therapy in medicine. Resistance to azoles can occur in
Candida albicans
principally by overexpression of multidrug transporter gene
CDR1
,
CDR2
, or
MDR1
or by overexpression of
ERG11
, which encodes the azole target. The expression of these genes is controlled by the transcription factors (TFs)
TAC1
(involved in the control of
CDR1
and
CDR2
),
MRR1
(involved in the control of
MDR1
), and
UPC2
(involved in the control of
ERG11
). Several gain-of-function (GOF) mutations are present in hyperactive alleles of these TFs, resulting in the overexpression of target genes. While these mutations are beneficial to
C. albicans
survival in the presence of the antifungal drugs, their effects could potentially alter the fitness and virulence of
C. albicans
in the absence of the selective drug pressure. In this work, the effect of GOF mutations on
C. albicans
virulence was addressed in a systemic model of intravenous infection by mouse survival and kidney fungal burden assays. We engineered a set of strains with identical genetic backgrounds in which hyperactive alleles were reintroduced in one or two copies at their genomic loci. The results obtained showed that neither
TAC1
nor
MRR1
GOF mutations had a significant effect on
C. albicans
virulence. In contrast, the presence of two hyperactive
UPC2
alleles in
C. albicans
resulted in a significant decrease in virulence, correlating with diminished kidney colonization compared to that by the wild type. In agreement with the effect on virulence, the decreased fitness of an isolate with
UPC2
hyperactive alleles was observed in competition experiments with the wild type
in vivo
but not
in vitro
. Interestingly,
UPC2
hyperactivity delayed filamentation of
C. albicans
after phagocytosis by murine macrophages, which may at least partially explain the virulence defects. Combining the
UPC2
GOF mutation with another hyperactive TF did not compensate for the negative effect of
UPC2
on virulence. In conclusion, among the major TFs involved in azole resistance, only
UPC2
had a negative impact on virulence and fitness, which may therefore have consequences for the epidemiology of antifungal resistance.
Renal failure: unusual clinical presentation of an isolated intrarenal hydatid cyst
Authors: Nadeem Mehwash , Biyabani Syed Raziuddin , Pervez Shahid 
Published: November 2013

SummaryCystic echinococcosis or hydatid disease is a zoonotic parasitic infection caused by larval stage of cestodeEchinococcusspp. Humans are an accidental intermediate host and present with the involvement of different organs, the liver being the most common while kidney is the rarest site. Here, authors are reporting a case of a 55-year-old woman who presented with renal failure and was found to have a right-sided intrarenal hydatid cyst, diagnosed and treated with nephroscopy without sacrificing the kidney. She had an uneventful postoperative course and her renal function improved dramatically. She is now on oral albendazole therapy and doing well on follow-up. To the best of our knowledge, renal failure has never been reported in the literature as clinical manifestation of intrarenal hydatid cyst in adult population.
The association of cycling with all-cause, cardiovascular and cancer mortality: findings from the population-based EPIC-Norfolk cohort
Authors: Sahlqvist Shannon , Goodman Anna , Simmons Rebecca K , Khaw Kay-Tee , Cavill Nick , Foster Charlie , Luben Robert , Wareham Nicholas J , Ogilvie David 
Published: November 2013

ObjectivesTo investigate associations between modest levels of total and domain-specific (commuting, other utility, recreational) cycling and mortality from all causes, cardiovascular disease and cancer.DesignPopulation-based cohort study (European Prospective Investigation into Cancer and Nutrition study-Norfolk).SettingParticipants were recruited from general practices in the east of England and attended health examinations between 1993 and 1997 and again between 1998 and 2000. At the first health assessment, participants reported their average weekly duration of cycling for all purposes using a simple measure of physical activity. At the second health assessment, participants reported a more detailed breakdown of their weekly cycling behaviour using the EPAQ2 physical activity questionnaire.ParticipantsAdults aged 40–79 years at the first health assessment.Primary outcome measureAll participants were followed for mortality (all-cause, cardiovascular and cancer) until March 2011.ResultsThere were 22 450 participants with complete data at the first health assessment, of whom 4398 died during follow-up; and 13 346 participants with complete data at the second health assessment, of whom 1670 died during follow-up. Preliminary analyses using exposure data from the first health assessment showed that cycling for at least 60 min/week in total was associated with a 9% reduced risk of all-cause mortality (adjusted HR 0.91, 95% CI 0.84 to 0.99). Using the more precise measures of cycling available from the second health assessment, all types of cycling were associated with greater total moderate-to-vigorous physical activity; however, there was little evidence of an association between overall or domain-specific cycling and mortality.ConclusionsCycling, in particular for utility purposes, was associated with greater moderate-to-vigorous and total physical activity. While this study provides tentative evidence that modest levels of cycling may reduce the risk of mortality, further research is required to confirm how much cycling is sufficient to induce health benefits.