bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis
Authors: Nishimura Takeshi , Hayashi Ken‐ichiro , Suzuki Hiromi , Gyohda Atsuko , Takaoka Chihiro , Sakaguchi Yusuke , Matsumoto Sachiko , Kasahara Hiroyuki , Sakai Tatsuya , Kato Jun‐ichi , Kamiya Yuji , Koshiba Tomokazu 
Published: December 2013

SummaryIndole‐3–acetic acid (IAA), an auxin plant hormone, is biosynthesized from tryptophan. The indole‐3–pyruvic acid (IPyA) pathway, involving the tryptophan aminotransferase TAA1 and YUCCA (YUC) enzymes, was recently found to be a major IAA biosynthetic pathway in Arabidopsis. TAA1 catalyzes the conversion of tryptophan to IPyA, and YUC produces IAA from IPyA. Using a chemical biology approach with maize coleoptiles, we identified 5–(4–chlorophenyl)‐4H‐1,2,4–triazole‐3–thiol (yucasin) as a potent inhibitor of IAA biosynthesis in YUC‐expressing coleoptile tips. Enzymatic analysis of recombinant AtYUC1‐His suggested that yucasin strongly inhibited YUC1‐His activity against the substrate IPyA in a competitive manner. Phenotypic analysis of Arabidopsis YUC1 over‐expression lines (35S::YUC1) demonstrated that yucasin acts in IAA biosynthesis catalyzed by YUC. In addition, 35S::YUC1 seedlings showed resistance to yucasin in terms of root growth. A loss‐of‐function mutant of TAA1, sav3–2, was hypersensitive to yucasin in terms of root growth and hypocotyl elongation of etiolated seedlings. Yucasin combined with the TAA1 inhibitor l–kynurenine acted additively in Arabidopsis seedlings, producing a phenotype similar to yucasin‐treated sav3–2 seedlings, indicating the importance of IAA biosynthesis via the IPyA pathway in root growth and leaf vascular development. The present study showed that yucasin is a potent inhibitor of YUC enzymes that offers an effective tool for analyzing the contribution of IAA biosynthesis via the IPyA pathway to plant development and physiological processes.
A randomized controlled trial of larval therapy for the debridement of leg ulcers: Results of a multicenter, randomized, controlled, open, observer blind, parallel group study
Authors: Mudge Elizabeth , Price Patricia , Neal Walkley , Harding Keith G. 
Published: December 2013

AbstractIt has been known for centuries that the application of larvae is useful to heal certain wounds by facilitating debridement of necrotic tissue,1 yet the efficacy of larval therapy continues to be debatable. This study compared the clinical effectiveness of a larval therapy dressing (BioFOAM) with a standard debridement technique (Purilon gel; hydrogel) in terms of time to debridement of venous (VLU) or mixed arterial/venous (MLU) leg ulcers. Data analyses were conducted on 88 subjects. Sixty‐four subjects completed the full study. Of these, 31 of the 32 (96.9%) patients who completed treatment in the larvae arm debrided fully, compared with 11 of the 32 (34.4%) patients who completed the hydrogel arm. In addition, 42 (48%) ulcers fully debrided within the 21‐day intervention phase, 31 (67.4%) from the larvae arm (n = 46), and 11 (26.2%) from the hydrogel arm (n = 42), which was statistically significant (p = 0.001) in support of larvae. A statistically significant difference was also observed between treatment arms with regard to numbers of dressing changes during the intervention phase of the study (p < 0.001) in that subjects in the larvae arm required significantly fewer dressing changes(mean = 2.83) than those in the hydrogel arm (mean = 5.40). There were no statistically significant differences in the clinical condition of the wound bed and surrounding skin by intervention. Subjects in the larvae arm experienced more ulcer‐related pain or discomfort than subjects in the hydrogel arm (p < 0.001). This study provided good evidence to show that larval therapy, in the form of a BioFOAM dressing, debrided VLU and MLU considerably more quickly than a hydrogel, although the possibility of resloughing should be closely monitored.
The Chern–Ricci flow on complex surfaces
Authors: Tosatti Valentino , Weinkove Ben 
Published: December 2013

AbstractThe Chern–Ricci flow is an evolution equation of Hermitian metrics by their Chern–Ricci form, first introduced by Gill. Building on our previous work, we investigate this flow on complex surfaces. We establish new estimates in the case of finite time non-collapsing, analogous to some known results for the Kähler–Ricci flow. This provides evidence that the Chern–Ricci flow carries out blow-downs of exceptional curves on non-minimal surfaces. We also describe explicit solutions to the Chern–Ricci flow for various non-Kähler surfaces. On Hopf surfaces and Inoue surfaces these solutions, appropriately normalized, collapse to a circle in the sense of Gromov–Hausdorff. For non-Kähler properly elliptic surfaces, our explicit solutions collapse to a Riemann surface. Finally, we define a Mabuchi energy functional for complex surfaces with vanishing first Bott–Chern class and show that it decreases along the Chern–Ricci flow.
Salmonella Pathogenicity and Host Adaptation in Chicken-Associated Serovars
Authors: Foley Steven L. , Johnson Timothy J. , Ricke Steven C. , Nayak Rajesh , Danzeisen Jessica 
Published: December 2013

SUMMARY

Enteric pathogens such as
Salmonella enterica
cause significant morbidity and mortality.
S. enterica
serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts.
S. enterica
serovars such as
S
. Typhi,
S
. Dublin, and
S
. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while
S
. Enteritidis and
S
. Typhimurium have broad host ranges. This review examines how
S. enterica
has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect.
S
. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars.
S. enterica
serovars such as
S
. Kentucky and
S
. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of
Salmonella
to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.
Host-Directed Therapeutics for Tuberculosis: Can We Harness the Host?
Authors: Hawn Thomas R. , Matheson Alastair I. , Maley Stephen N. , Vandal Omar 
Published: December 2013

SUMMARY

Treatment of tuberculosis (TB) remains challenging, with lengthy treatment durations and complex drug regimens that are toxic and difficult to administer. Similar to the vast majority of antibiotics, drugs for
Mycobacterium tuberculosis
are directed against microbial targets. Although more effective drugs that target the bacterium may lead to faster cure of patients, it is possible that a biological limit will be reached that can be overcome only by adopting a fundamentally new treatment approach. TB regimens might be improved by including agents that target host pathways. Recent work on host-pathogen interactions, host immunity, and host-directed interventions suggests that supplementing anti-TB therapy with host modulators may lead to shorter treatment times, a reduction in lung damage caused by the disease, and a lower risk of relapse or reinfection. We undertook this review to identify molecular pathways of the host that may be amenable to modulation by small molecules for the treatment of TB. Although several approaches to augmenting standard TB treatment have been proposed, only a few have been explored in detail or advanced to preclinical and clinical studies. Our review focuses on molecular targets and inhibitory small molecules that function within the macrophage or other myeloid cells, on host inflammatory pathways, or at the level of TB-induced lung pathology.
The cladid crinoid
Cupressocrinites
Goldfuss in the Devonian of SW England
Authors: Donovan Stephen K. 
Published: December 2013

Summary

The cladid crinoid
Cupressocrinites
Goldfuss is a distinctive member of the Middle Devonian biota of SW England. These distinctive crinoids are easily identified to genus from incomplete specimens. They have characteristic columnals with tetragonal symmetry and peripheral canals; arm facets that extend the width of the radial plates; and uniserial, unbranched, triangular arms that are closely abutting. Although specimens from Devon are invariably incomplete, at least two species are recognizable from cups and arms. The specimens described by John Edward Lee (1808–1887) are redescribed with other material from the Natural History Museum, London. The four-fold symmetry of the column is unlikely to have persisted from a Late Ordovician ancestor.
Endolithic biota of belemnites from the Early Cretaceous Speeton Clay Formation of North Yorkshire, UK
Authors: Taylor Paul D. , Barnbrook Jane A. , Sendino Consuelo 
Published: December 2013

Summary

The Berriasian–Albian Speeton Clay Formation is renowned for its rich and diverse belemnite fauna. Borings occur in a considerable proportion of the belemnite guards that can be found in the type locality south of Filey, but have never been described. This preliminary survey of the endolithic biota colonizing Speeton belemnites reveals the presence of at least 15 ichnotaxa, including traces made by grazing echinoids (
Gnathichnus pentax
), brachiopod pedicles (
Podichnus centrifugalis
), and a variety of macro- and microendoliths. The commonest macroendolith borings belong to two ichnospecies of
Trypanites
and were probably excavated by polychaete worms. Examples of borings made by other suspension feeding animals, including bivalves (
Gastrochaenolites lapidicus
), acrothoracican barnacles (
Rogerella mathieui
) and sponges (
Entobia
), are less abundant. Among the microendoliths,
Orthogonum
ispp. and
Saccomorpha clava
, both of which are very common, were probably made by fungi, whereas
Semidendrina pulchra
is thought to be the trace of a boring foraminifer. The tentative identification of the microboring
Rhopalia catenata
, which is made by autotrophic chlorophyte algae, suggests that at least some of the Speeton Clay Formation was deposited within the photic zone. Endoliths in the Speeton belemnite guards have future potential for developing a better understanding of the changing environments on the seabed during the long period of deposition of the Speeton Clay.
SHON Is a Novel Estrogen-Regulated Oncogene in Mammary Carcinoma That Predicts Patient Response to Endocrine Therapy
Authors: Jung Yewon , Abdel-Fatah Tarek M.A. , Chan Stephen Y.T. , Nolan Christopher C. , Green Andrew R. , Ellis Ian O. , Li Lili , Huang Baiqu , Lu Jun , Xu Bing , Chen Longxin , Ma Runlin Z. , Zhang Min , Wang Jingru , Wu ZhengSheng , Zhu Tao , Perry Jo K. , Lobie Peter E. , Liu Dong-Xu 
Published: December 2013

Abstract
Endocrine therapies are the primary systemic intervention for patients with estrogen receptor–positive (ER+) breast cancer. However, a significant proportion of initially responsive ER+ tumors develop resistance, with relapses occurring in up to 50% of patients. Lack of reliable predictive biomarkers remains an unfilled need for enhanced clinical management of this disease. In this study, we address this need in identifying a novel estrogen-regulated gene called SHON (secreted hominoid-specific oncogene). Enforced expression of SHON in breast cancer cells increased their proliferation, survival, migration, and invasion in vitro. Furthermore, SHON enhanced the oncogenicity of these cells in xenograft models of human breast cancer and was also sufficient to oncogenically transform MCF10A human mammary epithelial cells. Conversely, SHON attenuation mediated by RNA interference- or antibody-based methods reduced the oncogenicity of breast cancer cells. Mechanistic investigations indicated that the oncogenic transforming properties of SHON were mediated by BCL-2 and NF-κB. In primary clinical specimens, SHON was immunohistochemically detected in 62% of breast cancers, in which its expression was positively correlated with ER expression. In this setting, SHON expression predicted a favorable response to endocrine therapy in high-risk patients with ER+ breast cancer. Taken together, our findings identify SHON as a novel human oncogene with predictive utility in ER+ breast cancer, perhaps offering a simple biomarker to predict the therapeutic efficacy of antiestrogen therapy in patients with breast cancer. Cancer Res; 73(23); 6951–62. ©2013 AACR.
Metastasis Dormancy in Estrogen Receptor–Positive Breast Cancer
Authors: Zhang Xiang H.-F. , Giuliano Mario , Trivedi Meghana V. , Schiff Rachel , Osborne C. Kent 
Published: December 2013

Abstract
About 20% to 40% of patients with breast cancer eventually develop recurrences in distant organs, which are often not detected until years to decades after the primary tumor diagnosis. This phenomenon is especially pronounced in estrogen receptor–positive (ER+) breast cancer, suggesting that ER+ cancer cells may stay dormant for a protracted period of time, despite adjuvant therapies. Multiple mechanisms have been proposed to explain how cancer cells survive and remain in dormancy, and how they become reactivated and exit dormancy. These mechanisms include angiogenic switch, immunosurveillance, and interaction with extracellular matrix and stromal cells. How to eradicate or suppress these dormant cancer cells remains a major clinical issue because of the lack of knowledge about the biologic and clinical nature of these cells. Herein, we review the clinical manifestation of metastasis dormancy in ER+ tumors, the current biologic insights regarding tumor dormancy obtained from various experimental models, and the clinical challenges to predict, detect, and treat dormant metastases. We also discuss future research directions toward a better understanding of the biologic mechanisms and clinical management of ER+ dormant metastasis. Clin Cancer Res; 19(23); 6389–97. ©2013 AACR.
Estimating the Effects of Anthropogenic Modification on Water Balance in the Aral Sea Watershed Using GRACE: 2003–12
Authors: Zmijewski Kirk , Becker Richard 
Published: December 2013

AbstractThe decrease in size the Aral Sea in central Asia, seen as both lower water levels and reduction in areal extent, has been one of the greatest examples of anthropogenic modification of a natural system in recent history. Many studies have monitored the extent and rate of this water loss and provided estimates on the expected life span of the remaining water. However, with little data for groundwater monitoring in the post-Soviet era, it is unclear what the water balance currently is in the remainder of the watershed. Redistribution of water upstream in the watershed including damming to create reservoirs and groundwater recharge from irrigation has not only deprived the sea of water but also increased evapotranspiration and altered local climate patterns. Using Tropical Rainfall Measurement Mission (TRMM) and Global Precipitation Climatology Centre (GPCC) data, rainfall trends for the Aral Sea watershed were analyzed over 10- and 30-yr periods and only minimal changes in rainfall were detected. Using Gravity Recovery and Climate Experiment (GRACE) gravity data from 2003 to 2012, trends in equivalent water mass were determined for the entire watershed. Estimates show up to 14 km3 of equivalent water mass has been lost from the watershed annually from 2002 to 2013. The mass loss throughout the basin is most likely attributable to increased evapotranspiration due to the inefficient irrigation systems and other human modification increasing the need for international cooperation and conservation programs to minimize negative impacts throughout the region.
Objective Identification of Tornado Seasons and Ideal Spatial Smoothing Radii
Authors: Dixon P. Grady , Mercer Andrew E. , Grala Katarzyna , Cooke William H. 
Published: December 2013

Abstract
The fundamental purpose of this research is to highlight the spatial seasonality of tornado risk. This requires the use of objective methods to determine the appropriate spatial extent of the bandwidth used to calculate tornado density values (i.e., smoothing the raw tornado data). With the understanding that a smoothing radius depends partially upon the period of study, the next step is to identify objectively ideal periods of tornado analysis. To avoid decisions about spatial or temporal boundaries, this project makes use of storm speed and tornado pathlength data, along with statistical cluster analysis, to establish tornado seasons that display significantly different temporal and spatial patterns. This method yields four seasons with unique characteristics of storm speed and tornado pathlength.
The results show that the ideal bandwidth depends partially upon the temporal analysis period and the lengths of the tornadoes studied. Hence, there is not a “one size fits all,” but the bandwidth can be quantitatively chosen for a given dataset. Results from this research, based upon tornado data for 1950–2011, yield ideal bandwidths ranging from 55 to 180 km. The ideal smoothing radii are then applied via a kernel density analysis of each new tornado season.
Evaluation of ERA-Interim and MERRA Cloudiness in the Southern Ocean
Authors: Naud Catherine M. , Booth James F. , Del Genio Anthony D. 
Published: December 2013

Abstract
The Southern Ocean cloud cover modeled by the Interim ECMWF Re-Analysis (ERA-Interim) and Modern-Era Retrospective Analysis for Research and Applications (MERRA) reanalyses are compared against Moderate Resolution Imaging Spectroradiometer (MODIS) and Multiangle Imaging Spectroradiometer (MISR) observations. ERA-Interim monthly mean cloud amounts match the observations within 5%, while MERRA significantly underestimates the cloud amount. For a compositing analysis of clouds in warm season extratropical cyclones, both reanalyses show a low bias in cloud cover. They display a larger bias to the west of the cyclones in the region of subsidence behind the cold fronts. This low bias is larger for MERRA than for ERA-Interim. Both MODIS and MISR retrievals indicate that the clouds in this sector are at a low altitude, often composed of liquid, and of a broken nature. The combined CloudSat–Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) cloud profiles confirm these passive observations, but they also reveal that low-level clouds in other parts of the cyclones are also not properly represented in the reanalyses. The two reanalyses are in fairly good agreement for the dynamic and thermodynamic characteristics of the cyclones, suggesting that the cloud, convection, or boundary layer schemes are the problem instead. An examination of the lower-tropospheric stability distribution in the cyclones from both reanalyses suggests that the parameterization of shallow cumulus clouds may contribute in a large part to the problem. However, the differences in the cloud schemes and in particular in the precipitation processes, which may also contribute, cannot be excluded.
Impacts of Postdam Land Use/Land Cover Changes on Modification of Extreme Precipitation in Contrasting Hydroclimate and Terrain Features
Authors: Woldemichael Abel T. , Hossain Faisal , Pielke Roger 
Published: December 2013

Abstract
Understanding the impact of postdam climate feedbacks, resulting from land use/land cover (LULC) variability, on modification of extreme precipitation (EP) remains a challenge for a twenty-first-century approach to dam design and operation. In this study, the Regional Atmospheric Modeling System (RAMS, version 6.0) was used, involving a number of predefined LULC scenarios to address the important question regarding dams and their impoundments: How sensitive are the hydroclimatology and terrain features of a region in modulating the postdam response of climate feedbacks to EP? The study region covered the Owyhee Dam/Reservoir on the Owyhee River watershed (ORW), located in eastern Oregon. A systematic perturbation of the relative humidity in the initial and boundary condition of the model was carried out to simulate EP. Among the different LULC scenarios used in the simulation over the ORW, irrigation expansion in the postdam era resulted in an increase in EP up to 6% in the 72-h precipitation total. The contribution of the reservoir on EP added 8% to the 72-h total when compared to the predam LULC conditions. To address the science question, a previously completed investigation on the Folsom Dam [American River watershed (ARW)] in California was compared with the ORW findings on the basis of contrasting differences in hydroclimatology and terrain features. The results indicate that the postdam LULC change scenarios impact EP of ORW (Owyhee Dam) much greater than the EP of the ARW (Folsom Dam) because of its semiarid climate and flat terrain. EP was less sensitive to LULC changes on the windward side of the mountainous terrain of ARW as compared to the leeward side of the flat terrain of ORW.
Annular Typhoons in the Western North Pacific
Authors: Chu Kekuan , Tan Zhe-Min 
Published: December 2013

Abstract
Annular hurricanes, characterized by annular structure, are a subset of mature-stage intense tropical cyclones, and they tend to be stronger and persist longer than average tropical cyclones. The characteristics of annular hurricanes in the North Atlantic and eastern-central North Pacific Oceans are well documented by Knaff et al. However, little is known about the annular typhoons in the western North Pacific (WNP). This study investigates the general features of annular typhoons in the WNP based on a 20-yr analysis (1990–2009) of global storm-centered infrared brightness temperature and passive microwave satellite datasets. Similar to annular hurricanes, annular typhoons also only form under a specific combination of environmental conditions, resulting in a quite low occurrence rate (~4%), and only 12 annular typhoons occur during this period. The concentric eyewall replacement is one effective pathway to annular typhoon formation. Three annular typhoons experienced the concentric eyewall replacement within 24 h prior to their annular phases during this period. There are two seedbeds, located east of Taiwan and in the central WNP, for annular typhoon formation within a narrow zonal belt (20°–30°N). The former is conducive to the landfall of annular typhoons, in particular six of the nine annular typhoons that formed in this region eventually made landfall. Because the average time interval between landfall of the annular typhoons and the end of their annular phase is relatively short, about 30 h, they can maintain near-peak intensities and hit the landfalling areas with record intensities. They present a unique threat to eastern Asia but have received little attention from the scientific community so far.