bluuebunny/crossref_metadata_2025_split huggingface dataset:
A prospective evaluation of the impact of second‐opinion histopathology on diagnostic testing, cost and treatment in dogs and cats with cancer
Authors: Regan R. C. , Rassnick K. M. , Malone E. K. , McDonough S. P. 
Published: February 2013

AbstractSecond‐opinion histopathology is a common practice in human medicine to avoid unnecessary procedures, costs and to optimize therapy. Histopathology review has been recommended in veterinary oncology as well. In this prospective evaluation of 52 tumours over a 1‐year period, there was diagnostic agreement between first and second opinions in 52% of cases. Twenty‐nine percent of cases had partial diagnostic disagreement, most often a change in grade, tumour subtype or margin status. Nineteen percent had complete diagnostic disagreement, including a change in cell of origin or a change from benign to malignant. Minor disagreements, which would not affect treatment or prognosis, were present in 21% of cases. Major disagreements, which would affect either treatment or prognosis, were present in 37% of cases. Costs of ideal staging and treatment recommendations were considerably different between first and second opinions.
Genetic removal of basal nitric oxide enhances contractile activity in isolated murine collecting lymphatic vessels
Authors: Scallan Joshua P. , Davis Michael J. 
Published: February 2013

Key points
Stimulation of nitric oxide (NO) production by lymphatic endothelium was originally thought to inhibit lymphatic contractile function.
However, recent studies have suggested that basal NO paradoxically increases the strength of contractions as a consequence of decreasing contraction frequency.
Here, we tested that hypothesis directly for the first time by establishing a new preparation where lymphatic vessels were isolated from transgenic mice and retained robust contractile activity.
Genetic removal of basal NO using endothelial NO synthase−/− mice led to an increase in contraction strength without increasing contraction frequency, opposing this hypothesis. In contrast, higher levels of NO production stimulated by ACh inhibited lymphatic contractile function in wild‐type and inducible NO synthase−/− mice, consistent with previous studies.
Our results show that NO functions in the peripheral lymphatic vasculature to depress contractile function, which will ultimately depress lymph flow that determines fluid homeostasis, humoral immunity and cancer metastasis.
Abstract  The role of nitric oxide (NO) in regulating lymphatic contractile function and, consequently, lymph flow has been the subject of intense study. Despite this, the precise effects of NO on lymphatic contractile activity remain unclear. Recent hypotheses posit that basal levels of endogenous NO increase lymphatic contraction strength as a consequence of lowering frequency (i.e. positive lusitropy), whereas higher agonist‐evoked concentrations of NO exert purely inhibitory effects on contractile function. We tested both hypotheses directly by isolating and cannulating collecting lymphatic vessels from genetically modified mice for ex vivo study. The effects of basal NO and agonist‐evoked NO were evaluated, respectively, by exposing wild‐type (WT), endothelial NO synthase (eNOS)−/− and inducible NO synthase (iNOS)−/− lymphatic vessels to controlled pressure steps followed by ACh doses. To compare with pharmacological inhibition of eNOS, we repeated both tests in the presence of l‐NAME. Surprisingly, genetic removal of basal NO enhanced contraction amplitude significantly without increasing contraction frequency. Higher levels of NO production stimulated by ACh evoked dilation, decreased tone, slowed contraction frequency and reduced fractional pump flow. We conclude that basal NO specifically depresses contraction amplitude, and that greater NO production then inhibits all other aspects of contractile function. Further, this work demonstrates definitively that mouse collecting lymphatic vessels exhibit autonomous, large‐amplitude contractions that respond to pressure similarly to collecting lymphatics of other mammalian species. At least in the peripheral lymphatic vasculature, NO production depresses contractile function, which influences lymph flow needed for fluid regulation, humoral immunity and cancer metastasis.
Complete Genome Sequence of the Pseudomonas fluorescens Bacteriophage UFV-P2
Authors: Eller Monique R. , Salgado Rafael L. , Vidigal Pedro M. P. , Alves Maura P. , Dias Roberto S. , de Oliveira Leandro L. , da Silva Cynthia C. , de Carvalho Antônio F. , De Paula Sérgio O. 
Published: February 2013

ABSTRACT

Milk proteolysis caused by
Pseudomonas fluorescens
is a serious problem in the dairy industries as a result of its ability to grow under refrigeration. The use of phages to control contaminants in food has been considered an alternative to traditional methods; therefore, a thorough understanding of such organisms is vital for their use. In this study, we show the complete genome sequence and analysis of a
P. fluorescens
phage isolated from wastewater of a dairy industry in Brazil.
Complete Genome Sequence of Simiduia agarivorans SA1

T

, a Marine Bacterium Able To Degrade a Variety of Polysaccharides
Authors: Lin Silk Yu , Shieh Wung Yang , Chen Jwo-Sheng , Tang Sen-Lin 
Published: February 2013

ABSTRACT

Simiduia agarivorans
strain SA1

T

is able to degrade a variety of polysaccharides found in marine algae, plants, and animals. The genome of
S. agarivorans
SA1

T

consists of a single chromosome (4,309,711 bp), and its information may provide insights into the polysaccharide-degrading capability, cell division, flagellar motility, and chemotaxis of this bacterium.
Whole-Genome Shotgun Sequencing of Mycobacterium abscessus M156, an Emerging Clinical Pathogen in Malaysia
Authors: Choo Siew Woh , Wong Yan Ling , Beh Ching Yew , Lokanathan Naline , Leong Mee Lian , Ong Chia Sui , Ng Kee Peng , Ngeow Yun Fong 
Published: February 2013

ABSTRACT

Mycobacterium abscessus
is an emerging clinical pathogen commonly associated with non-tuberculous mycobacterial infections. We report herein the draft genome of
M. abscessus
strain M156.
Draft Genome Sequence of Uropathogenic Escherichia coli Strain J96
Authors: Klein Eric A. , Gitai Zemer 
Published: February 2013

ABSTRACT

Escherichia coli
J96 (O4:K6) was isolated from a human pyelonephritis patient. Here, we report the draft genome sequence of
E. coli
J96, which contains virulence genes, including adhesion factors, alpha-hemolysins, and cytotoxic necrotizing factor. J96 infects the kidney and bladder, making it an important tool for studying
E. coli
pathogenesis.
NOAA's Second-Generation Global Medium-Range Ensemble Reforecast Dataset
Authors: Hamill Thomas M. , Bates Gary T. , Whitaker Jeffrey S. , Murray Donald R. , Fiorino Michael , Galarneau Thomas J. , Zhu Yuejian , Lapenta William 
Published: February 2013

A multidecadal ensemble reforecast database is now available that is approximately consistent with the operational 0000 UTC cycle of the 2012 NOAA Global Ensemble Forecast System (GEFS). The reforecast dataset consists of an 11-member ensemble run once each day from 0000 UTC initial conditions. Reforecasts are run to +16 days. As with the operational 2012 GEFS, the reforecast is run at T254L42 resolution (approximately 1/2° grid spacing, 42 levels) for week +1 forecasts and T190L42 (approximately 3/4° grid spacing) for the week +2 forecasts. Reforecasts were initialized with Climate Forecast System Reanalysis initial conditions, and perturbations were generated using the ensemble transform with rescaling technique. Reforecast data are available from 1985 to present.
Reforecast datasets were previously demonstrated to be very valuable for detecting and correcting systematic errors in forecasts, especially forecasts of relatively rare events and longer-lead forecasts. What is novel about this reforecast dataset relative to the first-generation NOAA reforecast is that (i) a modern, currently operational version of the forecast model is used (the previous reforecast used a model version from 1998); (ii) a much larger set of output data has been saved, including variables relevant for precipitation, hydrologic, wind energy, solar energy, severe weather, and tropical cyclone forecasting; and (iii) the archived data are at much higher resolution.
The article describes more about the reforecast configuration and provides a few examples of how this second-generation reforecast data may be used for research and a variety of weather forecast applications.
Development of sol-gel-derived multi-wall carbon nanotube/hydroxyapatite nanocomposite powders for bone substitution
Authors: Hooshmand Tabassom , Abrishamchian Alireza , Najafi Farhood , Mohammadi Mohammadreza , Najafi Hossein , Tahriri Mohammadreza 
Published: February 2013

Carbon nanotubes with unique physical and mechanical properties have shown great potential for biological applications, including tissue engineering and mimicking the structure and properties of human bones. In the present work, sol-gel synthesized nanocomposite powder of multi-wall carbon nanotube/hydroxyapatite characterized using field-emission scanning electron microscopy, transmission electron microscope, X-ray diffraction, Fourier transform infra-red spectroscopy and thermal analyses. The results show homogenous dispersion of nanotube in well-crystallized hydroxyapatite ceramic matrix. Scanning electron microscopy and transmission electron microscope observations show the sodium dodecyl sulfate–adsorbed multi-wall nanotube almost wrapped completely by crystals of hydroxyapatite that will help better integration of bone substitute materials with the surrounding bone tissue. Eventually, in vitro study confirms the biocompatibility of composite powder comparable to monolithic hydroxyapatite.
The Flat Cat
Authors: Murphy Kate , Hibbert Angie 
Published: February 2013

Aim: Detailed information regarding the causes and treatment of acute collapse in the cat can be difficult to locate in a single published source. This two-part review aims to provide a logical approach to the clinical assessment and stabilisation of the critically ill collapsed cat. Practical relevance: Cats are particularly challenging when presented as emergency patients, often in the later stages of an illness or with a vague history and non-specific signs. The nuances of the critically ill cat are considered, especially for shock and its management. Clinical challenges: Shocked cats do not present in the classic stages typically seen in dogs, and the signs are more subtle. Therefore, the clinician must consider whether physical parameters are appropriate for the state and environment of the patient; for example, a normal heart rate in a shocked cat would be considered inappropriate. Audience: This review is directed at any veterinarian working with feline patients, and particularly those dealing with emergencies on a regular basis. Evidence base: There is an extensive body of published literature, both original studies and textbook chapters, pertaining to the causes and treatment of collapse in the cat. In this article the authors draw on information from original publications, reviews and their clinical experience to provide practical guidance to assist in the emergency setting.
Feline Mandibular Fractures
Authors: Woodbridge Nicolas , Owen Martin 
Published: February 2013

Practical relevance: Mandibular fractures occur commonly in cats and appropriate treatment is vital to ensure restoration of dental occlusion and masticatory function. Clinical challenges: Historically, a relatively high complication rate has been reported in association with mandibular fracture repair, and these complications can represent a significant challenge for the veterinary surgeon. Audience: General practitioners as well as specialists in small animal surgery are presented with fractures of the mandible on a regular basis. Patient group: Cats of all ages can suffer mandibular fracture; however, young cats (mean age 30 months) are over-represented. No sex predilection is reported. Equipment: The nature of the equipment required for mandibular fracture repair varies greatly, depending on the fracture type and location. An uncomplicated mandibular symphyseal fracture requires only basic orthopaedic equipment whereas the surgeon must ensure they have access to a wide range of orthopaedic equipment prior to undertaking repair of a complex mandibular fracture. Evidence base: Management of mandibular fractures is a complex subject. Over the past three decades many fixation techniques have been described in the veterinary literature, with authors analysing and discussing the surgical management of these potentially challenging injuries.
A computational method for detecting copy number variations using scale-space filtering
Authors: Lee Jongkeun , Lee Unjoo , Kim Baeksop , Yoon Jeehee 
Published: February 2013

Abstract

Background
As next-generation sequencing technology made rapid and cost-effective sequencing available, the importance of computational approaches in finding and analyzing copy number variations (CNVs) has been amplified. Furthermore, most genome projects need to accurately analyze sequences with fairly low-coverage read data. It is urgently needed to develop a method to detect the exact types and locations of CNVs from low coverage read data.

Results
Here, we propose a new CNV detection method, CNV_SS, which uses scale-space filtering. The scale-space filtering is evaluated by applying to the read coverage data the Gaussian convolution for various scales according to a given scaling parameter. Next, by differentiating twice and finding zero-crossing points, inflection points of scale-space filtered read coverage data are calculated per scale. Then, the types and the exact locations of CNVs are obtained by analyzing the finger print map, the contours of zero-crossing points for various scales.

Conclusions
The performance of CNV_SS showed that FNR and FPR stay in the range of 1.27% to 2.43% and 1.14% to 2.44%, respectively, even at a relatively low coverage (0.5x ≤C ≤2x). CNV_SS gave also much more effective results than the conventional methods in the evaluation of FNR, at 3.82% at least and 76.97% at most even when the coverage level of read data is low. CNV_SS source code is freely available from http://dblab.hallym.ac.kr/CNV SS/.
Developing a tool for obtaining maternal skinfold thickness measurements and assessing inter-observer variability among pregnant women who are overweight and obese
Authors: Kannieappan Lavern M , Deussen Andrea R , Grivell Rosalie M , Yelland Lisa , Dodd Jodie M 
Published: February 2013

Abstract

Background
It is estimated that between 34% and 50% of Australian women entering pregnancy are overweight and obese, which is associated with an increased risk in complications for both the woman and her infant. Current tools used in clinical and research practice for measuring body composition include body mass index (BMI), waist circumference and bioimpedance analysis. Not all of these measures are applicable for use during pregnancy due to a lack of differentiation between maternal and fetal contributions. While skinfold thickness measurement (SFTM) is increasingly being used in pregnancy, there is limited data and a lack of a standard tool for its use in overweight and obese pregnant women.

Methods
We developed a standard tool for evaluating SFTM among women with a BMI ≥ 25 kg/m2. Forty-nine women were measured as part of a prospective cohort study nested within a multicentre randomised controlled trial (The LIMIT Randomised Controlled Trial). Two blinded observers each performed 2 skinfold measurements on the biceps, triceps and subscapular of each woman. Intraclass correlation coefficients (ICC) and standard error of measurement (SEM) were used to analyse SFTM, body fat percentage (BF%) and inter-observer variability.

Results
The ICC for inter-observer variability in measurements were considered moderate for biceps SFTM (ICC = 0.56) and triceps SFTM (ICC = 0.51); good for subscapular SFTM (ICC = 0.71) and BF% (ICC = 0.74); and excellent for arm circumference (ICC = 0.97). The standard error of measurements ranged from 0.53 cm for arm circumference to 3.58 mm for the subscapular SFTM.

Conclusion
Our findings indicate that arm circumference and biceps, triceps and subscapular SFTM can be reliably obtained from overweight and obese pregnant women to calculate BF%, using multiple observers, and can be used in a research setting.

Trial registration
Australian and New Zealand Clinical Trials Registry ACTRN12607000161426
Immune cell profile of sentinel lymph nodes in patients with malignant melanoma – FOXP3+ cell density in cases with positive sentinel node status is associated with unfavorable clinical outcome
Authors: Mohos Anita , Sebestyén Tímea , Liszkay Gabriella , Plótár Vanda , Horváth Szabolcs , Gaudi István , Ladányi Andrea 
Published: February 2013

Abstract

Background
Besides being a preferential site of early metastasis, the sentinel lymph node (SLN) is also a privileged site of T-cell priming, and may thus be an appropriate target for investigating cell types involved in antitumor immune reactions.

Methods
In this retrospective study we determined the prevalence of OX40+ activated T lymphocytes, FOXP3+ (forkhead box P3) regulatory T cells, DC-LAMP+ (dendritic cell-lysosomal associated membrane protein) mature dendritic cells (DCs) and CD123+ plasmacytoid DCs by immunohistochemistry in 100 SLNs from 60 melanoma patients. Density values of each cell type in SLNs were compared to those in non-sentinel nodes obtained from block dissections (n = 37), and analyzed with regard to associations with clinicopathological parameters and disease outcome.

Results
Sentinel nodes showed elevated amount of all cell types studied in comparison to non-sentinel nodes. Metastatic SLNs had higher density of OX40+ lymphocytes compared to tumor-negative nodes, while no significant difference was observed in the case of the other cell types studied. In patients with positive sentinel node status, high amount of FOXP3+ cells in SLNs was associated with shorter progression-free (P = 0.0011) and overall survival (P = 0.0014), while no significant correlation was found in the case of sentinel-negative patients. The density of OX40+, CD123+ or DC-LAMP+ cells did not show significant association with the outcome of the disease.

Conclusions
Taken together, our results are compatible with the hypothesis of functional competence of sentinel lymph nodes based on the prevalence of the studied immune cells. The density of FOXP3+ lymphocytes showed association with progression and survival in patients with positive SLN status, while the other immune markers studied did not prove of prognostic importance. These results, together with our previous findings on the prognostic value of activated T cells and mature DCs infiltrating primary melanomas, suggest that immune activation-associated markers in the primary tumor may have a higher impact than those in SLNs on the prognosis of the patients. On the other hand, FOXP3+ cell density in SLNs, but not in the primary tumor, was found predictive of disease outcome in melanoma patients.
Effects of Panax ginseng-containing herbal plasters on compressed intervertebral discs in an in vivo rat tail model
Authors: Chow Daniel H K , Lai Alon , Tang Fuk-Hay , Leung Mason C P 
Published: February 2013

Abstract

Background

Tienchi (Panax notoginseng) has been used in conservative treatments for back pain as a major ingredient of many herbal medicines. This study aims to investigate the effects of a herbal medicine containing tienchi on compressed intervertebral discs in rats.

Methods
Using an in vivo rat tail model, intervertebral disc compression was simulated in the caudal 8–9 discs of 25 rats by continuous static compression (11 N) for 2 weeks. An herbal medicine plaster (in which the major ingredient was tienchi) was externally applied to the compressed disc (n=9) for three weeks, and held in place by an adhesive bandage, in animals in the Chinese Medicine (CM) group. The effect of the bandage was evaluated in a separate placebo group (n=9), while no intervention with unrestricted motion was provided to rats in an additional control group (n=7). Disc structural properties were quantified by in vivo disc height measurement and in vitro morphological analysis.

Results
Disc height decreased after the application of compression (P < 0.001). The disc height decreased continuously in the control (P = 0.006) and placebo (P = 0.003) groups, but was maintained in the CM group (P = 0.494). No obvious differences in disc morphology were observed among the three groups (P = 0.896).

Conclusion
The tienchi-containing herbal plaster had no significant effect on the morphology of compressed discs, but maintained disc height in rats.
Cost-effectiveness of enzyme replacement therapy for Fabry disease
Authors: Rombach Saskia M , Hollak Carla EM , Linthorst Gabor E , Dijkgraaf Marcel GW 
Published: February 2013

Abstract

Background
The cost-effectiveness of enzyme replacement therapy (ERT) compared to standard medical care was evaluated in the Dutch cohort of patients with Fabry disease.

Methods
Cost-effectiveness analysis was performed using a life-time state-transition model. Transition probabilities, effectiveness data and costs were derived from retrospective data and prospective follow-up of the Dutch study cohort consisting of males and females aged 5–78 years. Intervention with ERT (either agalsidase alfa or agalsidase beta) was compared to the standard medical care. The main outcome measures were years without end organ damage (renal, cardiac en cerebrovascular complications), quality adjusted life years (QALYs), and costs.

Results
Over a 70 year lifetime, an untreated Fabry patient will generate 55.0 years free of end-organ damage (53.5 years in males, 56.9 years in females) and 48.6 QALYs (47.8 in males, 49.7 in females). Starting ERT in a symptomatic patient increases the number of years free of end-organ damage by 1.5 year (1.6 in males, 1.3 in females), while the number of QALYs gained increases by a similar amount (1.7 in males, 1.4 in females). The costs of ERT starting in the symptomatic stage are between €9 - €10 million (£ 7.9 - £ 8.8 million, $13.0- $14.5 million) during a patient’s lifetime. Consequently, the extra costs per additional year free of end-organ damage and the extra costs per additional QALY range from €5.5 - €7.5 million (£ 4.8 – £ 6.6 million, $ 8.0 – $ 10.8 million), undiscounted.

Conclusions
In symptomatic patients with Fabry disease, ERT has limited effect on quality of life and progression to end organ damage. The pharmaco-economic evaluation shows that this modest effectiveness drives the costs per QALY and the costs per year free of end-organ damage to millions of euros. Differentiation of patients who may benefit from ERT should be improved to enhance cost-effectiveness.
Nuclear protein IK undergoes dynamic subcellular translocation and forms unique nuclear bodies during the cell cycle
Authors: Hu Liyan , Yang Feikun , Liu Xianan , Xu Dazhong , Dai Wei 
Published: February 2013

Abstract
IK is a nuclear protein containing a unique domain named RED due to the presence of a repetitive arginine (R), aspartic (E), and glutamic acid (D) sequence. To date, the function of this protein remains largely unknown despite of a couple of previous studies in the literature. Here we report that depletion of IK via RNA interference results in mitotic arrest. We also demonstrate that IK undergoes dynamic translocation during interphase and mitosis. In particular, IK is primarily present in some interphase cells as nuclear foci/bodies which do not co-localize with nucleoli, PMA bodies and Cajal bodies. Pull-down analysis coupled with mass spectrometry reveals that IK is associated with DHX15, a putative ATP-dependent RNA helicase. Our results strongly suggest that IK may participate in pre-mRNA splicing and that it may be a useful biomarker for a new nuclear structure in the cell.