bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of Pseudomonas aeruginosa DQ8, an Efficient Degrader of
n
-Alkanes and Polycyclic Aromatic Hydrocarbons
Authors: Gai Zhonghui , Zhang Zhengzhi , Wang Xiaoyu , Tao Fei , Tang Hongzhi , Xu Ping 
Published: October 2012

ABSTRACT

Pseudomonas aeruginosa
DQ8, which was isolated from the crude oil polluted soil in the Daqing oilfield of China, can efficiently degrade diesel, crude oil,
n
-alkanes, and polycyclic aromatic hydrocarbons (PAHs). Here, we present a 6.8-Mb assembly of its genome sequence. We have annotated 23 coding sequences (CDSs) responsible for catabolism of
n
-alkanes and PAHs.
Complete Genome Sequence of Burkholderia sp. Strain GG4, a Betaproteobacterium That Reduces 3-Oxo-
N
-Acylhomoserine Lactones and Produces Different
N
-Acylhomoserine Lactones
Authors: Hong Kar-Wai , Koh Chong-Lek , Sam Choon-Kook , Yin Wai-Fong , Chan Kok-Gan 
Published: October 2012

ABSTRACT

Burkholderia
sp. strain GG4, isolated from the ginger rhizosphere, possesses a unique
N
-acylhomoserine lactone (AHL)-modifying activity that reduces 3-oxo-AHLs to 3-hydroxy-AHLs. To the best of our knowledge, this is the first sequenced genome from a bacterium of the genus
Burkholderia
that shows both quorum-sensing and signaling confusion activities.
Genome Sequence of Pseudomonas mendocina DLHK, Isolated from a Biotrickling Reactor
Authors: Wong Chi Fat , Niu Hejingying , Jiang Jingwei , Li Jun , Chan Charis May Ngor , Leung Dennis Yiu Cheong , Leung Frederick Chi Ching 
Published: October 2012

ABSTRACT

Pseudomonas mendocina
DLHK is an aerobic bacterium isolated from a biotrickling reactor which can remove nitric oxide, a common air pollutant from combustion exhaust gas. Here, we present the draft genome of
Pseudomonas mendocina
DLHK.
Draft Genome Sequence of Rhodovulum sp. Strain PH10, a Phototrophic Alphaproteobacterium Isolated from a Soil Sample of Mangrove of Namkhana, India
Authors: Khatri Indu , Nupur  , Korpole Suresh , Subramanian Srikrishna , Pinnaka Anil Kumar 
Published: October 2012

ABSTRACT

We report the 4.8-Mb draft genome of
Rhodovulum
sp. strain PH10, a phototrophic bacterium belonging to class
Alphaproteobacteria
, isolated from a soil sample collected from the mangrove forest of Namkhana in India. This genome is the first from the genus
Rhodovulum
and will lead to a better understanding of the genes/pathways involved in activities like phototrophic growth and nitrogen fixation in this group of bacteria.
Enhanced Butanol Production Obtained by Reinforcing the Direct Butanol-Forming Route in Clostridium acetobutylicum
Authors: Jang Yu-Sin , Lee Jin Young , Lee Joungmin , Park Jin Hwan , Im Jung Ae , Eom Moon-Ho , Lee Julia , Lee Sang-Hyun , Song Hyohak , Cho Jung-Hee , Seung Do Young , Lee Sang Yup 
Published: October 2012

ABSTRACT

Butanol is an important industrial solvent and advanced biofuel that can be produced by biphasic fermentation by
Clostridium acetobutylicum
. It has been known that acetate and butyrate first formed during the acidogenic phase are reassimilated to form acetone-butanol-ethanol (cold channel). Butanol can also be formed directly from acetyl-coenzyme A (CoA) through butyryl-CoA (hot channel). However, little is known about the relative contributions of the two butanol-forming pathways. Here we report that the direct butanol-forming pathway is a better channel to optimize for butanol production through metabolic flux and mass balance analyses. Butanol production through the hot channel was maximized by simultaneous disruption of the
pta
and
buk
genes, encoding phosphotransacetylase and butyrate kinase, while the

adhE1
D485G

gene, encoding a mutated aldehyde/alcohol dehydrogenase, was overexpressed. The ratio of butanol produced through the hot channel to that produced through the cold channel increased from 2.0 in the wild type to 18.8 in the engineered BEKW(pPthlAAD
**
) strain. By reinforcing the direct butanol-forming flux in
C. acetobutylicum
, 18.9 g/liter of butanol was produced, with a yield of 0.71 mol butanol/mol glucose by batch fermentation, levels which are 160% and 245% higher than those obtained with the wild type. By fed-batch culture of this engineered strain with
in situ
recovery, 585.3 g of butanol was produced from 1,861.9 g of glucose, with the yield of 0.76 mol butanol/mol glucose and productivity of 1.32 g/liter/h. Studies of two butanol-forming routes and their effects on butanol production in
C. acetobutylicum
described here will serve as a basis for further metabolic engineering of clostridia aimed toward developing a superior butanol producer.

IMPORTANCE
Renewable biofuel is one of the answers to solving the energy crisis and climate change problems. Butanol produced naturally by clostridia has superior liquid fuel characteristics and thus has the potential to replace gasoline. Due to the lack of efficient genetic manipulation tools, however, strain improvement has been rather slow. Furthermore, complex metabolic characteristics of acidogenesis followed by solventogenesis in this strain have hampered development of engineered clostridia having highly efficient and selective butanol production capability. Here we report for the first time the results of systems metabolic engineering studies of two butanol-forming routes and their relative importances in butanol production. Based on these findings, a metabolically engineered
Clostridium acetobutylicum
strain capable of producing butanol to a high titer with high yield and selectivity could be developed by reinforcing the direct butanol-forming flux.
Significance of deep T-wave inversions in asymptomatic athletes with normal cardiovascular examinations: practical solutions for managing the diagnostic conundrum
Authors: Wilson M G , Sharma S , Carré F , Charron P , Richard P , O'Hanlon R , Prasad S K , Heidbuchel H , Brugada J , Salah O , Sheppard M , George K P , Whyte G , Hamilton B , Chalabi H 
Published: October 2012

Preparticipation screening programmes for underlying cardiac pathologies are now commonplace for many international sporting organisations. However, providing medical clearance for an asymptomatic athlete without a family history of sudden cardiac death (SCD) is especially challenging when the athlete demonstrates particularly abnormal repolarisation patterns, highly suggestive of an inherited cardiomyopathy or channelopathy. Deep T-wave inversions of ≥2 contiguous anterior or lateral leads (but not aVR, and III) are of major concern for sports cardiologists who advise referring team physicians, as these ECG alterations are a recognised manifestation of hypertrophic cardiomyopathy (HCM) and arrhythmogenic right ventricular cardiomyopathy (ARVC). Subsequently, inverted T-waves may represent the first and only sign of an inherited heart muscle disease, in the absence of any other features and before structural changes in the heart can be detected. However, to date, there remains little evidence that deep T-wave inversions are always pathognomonic of either a cardiomyopathy or an ion channel disorder in an asymptomatic athlete following long-term follow-up.This paper aims to provide a systematic review of the prevalence of T-wave inversion in athletes and examine T-wave inversion and its relationship to structural heart disease, notably HCM and ARVC with a view to identify young athletes at risk of SCD during sport. Finally, the review proposes clinical management pathways (including genetic testing) for asymptomatic athletes demonstrating significant T-wave inversion with structurally normal hearts.
Do big athletes have big hearts? Impact of extreme anthropometry upon cardiac hypertrophy in professional male athletes
Authors: Riding Nathan R , Salah Othman , Sharma Sanjay , Carré François , O'Hanlon Rory , George Keith P , Hamilton Bruce , Chalabi Hakim , Whyte Gregory P , Wilson Mathew G 
Published: October 2012

AimDifferentiating physiological cardiac hypertrophy from pathology is challenging when the athlete presents with extreme anthropometry. While upper normal limits exist for maximal left ventricular (LV) wall thickness (14 mm) and LV internal diameter in diastole (LVIDd, 65 mm), it is unknown if these limits are applicable to athletes with a body surface area (BSA) >2.3 m2.PurposeTo investigate cardiac structure in professional male athletes with a BSA>2.3 m2, and to assess the validity of established upper normal limits for physiological cardiac hypertrophy.Methods836 asymptomatic athletes without a family history of sudden death underwent ECG and echocardiographic screening. Athletes were grouped according to BSA (Group 1, BSA>2.3 m2, n=100; Group 2, 2–2.29 m2, n=244; Group 3, <1.99 m2, n=492).ResultsThere was strong linear relationship between BSA and LV dimensions; yet no athlete with a normal ECG presented a maximal wall thickness and LVIDd greater than 13 and 65 mm, respectively. In Group 3 athletes, Black African ethnicity was associated with larger cardiac dimensions than either Caucasian or West Asian ethnicity. Three athletes were diagnosed with a cardiomyopathy (0.4% prevalence); with two athletes presenting a maximal wall thickness >13 mm, but in combination with an abnormal ECG suspicious of an inherited cardiac disease.ConclusionRegardless of extreme anthropometry, established upper limits for physiological cardiac hypertrophy of 14 mm for maximal wall thickness and 65 mm for LVIDd are clinically appropriate for all athletes. However, the abnormal ECG is key to diagnosis and guides follow-up, particularly when cardiac dimensions are within accepted limits.
The provision of diagnosis at emergency department discharge: a pilot study
Authors: Wen Leana S , Kosowsky Joshua M , Gurrola Edith R , Camargo Carlos A 
Published: October 2012

ObjectivesUnderstanding the cause of patients’ symptoms usually involves identification of a pathological diagnosis. Anecdotal reports suggest that emergency department (ED) providers do not prioritise giving pathological diagnoses, and often reiterate the patient's symptom as the discharge ‘diagnosis’. Our pilot study sought to identify the proportion of patients at a large teaching hospital who receive a symptomatic versus pathological diagnosis at ED discharge.MethodsWe performed a chart review of all adult patients who were discharged from an urban ED in the USA, with an 88 000 annual visit volume. All charts of patients presenting with the three most common ED chief complaints (chest pain, abdominal pain and headache) were reviewed by two reviewers. Charts were coded as either symptomatic or pathological diagnosis based on the discharge diagnosis provided by the attending physician. Those with discrepant coding by the two reviewers were subject to review by a third adjudicator.Results797 charts met the inclusion criteria. Five charts (0.6%) were coded differently by the two reviewers; a discussion with the third reviewer resulted in consensus in all cases. For patients presenting with chest pain, abdominal pain and headache, the proportion that received a pathological ED discharge diagnosis were 17%, 43% and 41%, respectively.ConclusionsAccording to our pilot study, most patients are discharged from the ED without a pathological diagnosis that explains the likely cause of their symptoms. Future studies will investigate whether this finding is consistent across institutions, and whether provision of a pathological diagnosis affects clinical outcomes and patient satisfaction.
Endovascular treatment of ruptured dissecting aneurysms of the posterior inferior cerebellar artery
Authors: Ishihara Hideaki , Tateshima Satoshi , Jahan Reza , Gonzalez Nestor , Duckwiler Gary , Vinuela Fernando 
Published: October 2012

BackgroundDissecting aneurysms of the posterior inferior cerebellar artery (PICA) are rare, with optimal treatment strategies not well established according to the location of the aneurysm on the PICA. We present our single-center experience of endovascular treatment of ruptured dissecting aneurysms of the PICA.MethodsNine patients with ruptured dissecting aneurysms of the PICA were treated with endovascular embolization at our facility from August 1997 to December 2011. A retrospective chart review study was conducted to examine the efficacy of endovascular treatment and clinical outcome.ResultsThe shape of the aneurysms was saccular in five cases, fusiform in three cases and an abrupt cut-off of the PICA in one case. Aneurysmal sac embolization was feasible in five cases and parent artery (PICA) occlusion was performed in four cases. Eight cases (89%) achieved good recovery (modified Rankin Score ≤2). There were no clinical/technical complications in this small series.ConclusionsEndovascular treatment of ruptured dissecting aneurysms of the PICA is safe and efficient.
Long‐term outcome of Cavalier King Charles spaniel dogs with clinical signs associated with Chiari‐like malformation and syringomyelia
Authors: Plessas I. N. , Rusbridge C. , Driver C. J. , Chandler K. E. , Craig A. , McGonnell I. M. , Brodbelt D. C. , Volk H. A. 
Published: October 2012

The disease complex Chiari‐like malformation (CM) and syringomyelia (SM) has been associated with the development of neuropathic pain (NeP), and commonly affects Cavalier King Charles spaniels (CKCS). This prospective cohort study followed 48 CKCSs with CM and/or SM and clinical signs suggestive of NeP for a period of 39 (± 14.3) months from diagnosis. At the end of the study, 36 dogs were still alive; five dogs died of an unrelated or unknown cause, and seven were euthanased due to severe clinical signs suggestive of NeP. During the follow‐up period, the clinical signs of scratching, facial rubbing behaviour, vocalisation and exercise ability were evaluated. Nine out of 48 dogs stopped scratching (P< 0.001), but there was no statistically significant change in the number of dogs exhibiting exercise intolerance, vocalisation or facial rubbing behaviour. The overall severity of clinical signs based on a visual analogue scale (VAS) (0 mm: no clinical signs 100 mm: severe clinical signs) increased (from median 75 mm (interquartile ranges (IQR) 68–84) to 84 mm (IQR 71.5–91), P< 0.001). A quarter of the dogs were static or improved. In general, the majority of the owners felt that the quality of life of their dogs was acceptable. Medical treatments received were gabapentin or pregabalin and/or intermittently, carprofen. The owner's perception of their animal's progress, and progress based on VAS, had strong positive correlation (Spearman's rank correlation (sr) 0.74, P< 0.001). Overall, this study suggests that clinical signs suggestive of NeP progress in three‐quarters of CKCSs with CM and/or SM.
Androgen Receptor Signaling in Circulating Tumor Cells as a Marker of Hormonally Responsive Prostate Cancer
Authors: Miyamoto David T. , Lee Richard J. , Stott Shannon L. , Ting David T. , Wittner Ben S. , Ulman Matthew , Smas Malgorzata E. , Lord Jenna B. , Brannigan Brian W. , Trautwein Julie , Bander Neil H. , Wu Chin-Lee , Sequist Lecia V. , Smith Matthew R. , Ramaswamy Sridhar , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A. 
Published: October 2012

Abstract
Androgen deprivation therapy (ADT) is initially effective in treating metastatic prostate cancer, and secondary hormonal therapies are being tested to suppress androgen receptor (AR) reactivation in castration-resistant prostate cancer (CRPC). Despite variable responses to AR pathway inhibitors in CRPC, there are no reliable biomarkers to guide their application. Here, we used microfluidic capture of circulating tumor cells (CTC) to measure AR signaling readouts before and after therapeutic interventions. Single-cell immunofluorescence analysis revealed predominantly “AR-on” CTC signatures in untreated patients, compared with heterogeneous (“AR-on, AR-off, and AR-mixed”) CTC populations in patients with CRPC. Initiation of first-line ADT induced a profound switch from “AR-on” to “AR-off” CTCs, whereas secondary hormonal therapy in CRPC resulted in variable responses. Presence of “AR-mixed” CTCs and increasing “AR-on” cells despite treatment with abiraterone acetate were associated with an adverse treatment outcome. Measuring treatment-induced signaling responses within CTCs may help guide therapy in prostate cancer.
Significance: Acquired resistance to first-line hormonal therapy in prostate cancer is heterogeneous in the extent of AR pathway reactivation. Measurement of pre- and posttreatment AR signaling within CTCs may help target such treatments to patients most likely to respond to second-line therapies. Cancer Discov; 2(11); 995–1003. ©2012 AACR.
Read the Commentary on this article by Pantel and Alix-Panabières, p. 974.
This article is highlighted in the In This Issue feature, p. 961
The Potential of Circulating Tumor Cells as a Liquid Biopsy to Guide Therapy in Prostate Cancer
Authors: Pantel Klaus , Alix-Panabières Catherine 
Published: October 2012

Abstract
Summary: Miyamoto and colleagues present data that prostate-specific antigen/prostate-specific membrane antigen (PSA/PSMA)–based measurements of androgen receptor (AR) signaling in circulating tumor cells (CTC) enable real-time quantitative monitoring of intratumoral AR signaling. This finding indicates that measuring AR signaling within CTCs may help to guide therapy in metastatic prostate cancer and highlights the use of CTCs as liquid biopsy. Cancer Discov; 2(11); 974–5. ©2012 AACR.
Commentary on Miyamoto et al., p. 995.
The Safety of Cardiopulmonary Exercise Testing in a Population With High-Risk Cardiovascular Diseases
Authors: Skalski Joseph , Allison Thomas G. , Miller Todd D. 
Published: October 2012

Background—

Cardiopulmonary exercise testing (CPX) with measurement of peak oxygen uptake (V
o
2
) is a powerful test for assessment and quantification of functional impairment resulting from cardiovascular disease. The safety of CPX has been established in patients with coronary artery disease and congestive heart failure, but clinical use of CPX in other cardiac diseases has been limited, in part because of a paucity of safety data. This study investigates the safety of CPX in a heterogeneous cohort of patients with a wide variety of underlying high-risk cardiac diagnoses.

Methods and Results—

This single-center retrospective review examined 5060 CPX studies performed in 4250 unique patients, including 1748 (35%) female subjects and 686 (14%) subjects aged ≥75 years. The primary end point was major adverse event during stress testing. The study population included patients with a variety of high-risk cardiac diseases, including congestive heart failure (n=1289, 25.5%), hypertrophic cardiomyopathy (n=598, 11.8%), pulmonary hypertension (n=194, 3.8%), and aortic stenosis (n=212, 4.2%). This patient population generally had severe functional impairment, including 1192 (24%) patients with peak V
o
2
<14 mL/kg/min. Eight adverse events occurred during CPX, for an adverse event rate of 0.16%. The most common adverse event (n=6) was sustained ventricular tachycardia. There were no fatal events.

Conclusions—
CPX is generally a safe procedure, even in a population with underlying high-risk cardiovascular diagnoses.
Optimal Rainfall Estimation by Considering Elevation in the Han River Basin, South Korea
Authors: Yoon Seong-Sim , Bae Deg-Hyo 
Published: October 2012

AbstractMore than 70% of South Korea has mountainous terrain, which leads to significant spatiotemporal variability of rainfall. The country is exposed to the risk of flash floods owing to orographic rainfall. Rainfall observations are important in mountainous regions because flood control measures depend strongly on rainfall data. In particular, radar rainfall data are useful in these regions because of the limitations of rain gauges. However, radar rainfall data include errors despite the development of improved estimation techniques for their calculation. Further, the radar does not provide accurate data during heavy rainfall in mountainous areas. This study presents a radar rainfall adjustment method that considers the elevation in mountainous regions. Gauge rainfall and radar rainfall field data are modified by using standardized ordinary cokriging considering the elevation, and the conditional merging technique is used for combining the two types of data. For evaluating the proposed technique, the Han River basin was selected; a high correlation between rainfall and elevation can be seen in this basin. Further, the proposed technique was compared with the mean field bias and original conditional merging techniques. Comparison with kriged rainfall showed that the proposed method has a lesser tendency to oversmooth the rainfall distribution when compared with the other methods, and the optimal mean areal rainfall is very similar to the value obtained using gauges. It reveals that the proposed method can be applied to an area with significantly varying elevation, such as the Han River basin, to obtain radar rainfall data of high accuracy.
Evidence of Very Shallow Summertime Katabatic Flows in Dronning Maud Land, Antarctica
Authors: Kouznetsov Rostislav , Tisler Priit , Palo Timo , Vihma Timo 
Published: October 2012

AbstractThe three-axis “Latan-3” Doppler sodar was operated near the Finnish Antarctic station Aboa in Dronning Maud Land (73.04°S, 13.40°W) in the austral summer of 2010/11. The measuring site is located at a practically flat, slightly sloped (about 1%) surface of the glacier. The sodar was operated in multiple-frequency parallel mode with 20–800-m sounding range, 20-m vertical resolution, and 10-s temporal resolution. To reveal the wind and temperature profiles below the sounding range as well as turbulent fluxes at 2 and 10 m, the data from a 10-m meteorological mast were used. During the measurements, the atmospheric boundary layer was within the sounding range of the sodar most of the time. Despite a large variety of observed sodar echo patterns and wind speed profiles, several cases of clear steady katabatic flows were observed. Practically all of them were easterly, whereas the uphill direction is southern. The thickness of the katabatic flow varied from a few tens to several hundreds of meters; the wind speed maximum could be as low as 5 m. Thin katabatic flows had lower wind speed and much stronger temperature gradients (up to 1 K m−1) but had smaller surface heat flux than did the thicker ones.
Data Assimilation as a Problem in Optimal Tracking: Application of Pontryagin’s Minimum Principle to Atmospheric Science
Authors: Lakshmivarahan S. , Lewis J. M. , Phan D. 
Published: October 2012

Abstract
A data assimilation strategy based on feedback control has been developed for the geophysical sciences—a strategy that uses model output to control the behavior of the dynamical system. Whereas optimal tracking through feedback control had its early history in application to vehicle trajectories in space science, the methodology has been adapted to geophysical dynamics by forcing the trajectory of a deterministic model to follow observations in accord with observation accuracy. Fundamentally, this offline (where it is assumed that the observations in a given assimilation window are all given) approach is based on Pontryagin’s minimum principle (PMP) where a least squares fit of idealized path to dynamic law follows from Hamiltonian mechanics. This utilitarian process optimally determines a forcing function that depends on the state (the feedback component) and the observations. It follows that this optimal forcing accounts for the model error. From this model error, a correction to the one-step transition matrix is constructed. The above theory and technique is illustrated using the linear Burgers’ equation that transfers energy from the large scale to the small scale.