bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthesis of Cell Envelope-Associated Phenolic Glycolipids in Mycobacterium marinum
Authors: Vergnolle Olivia , Chavadi Sivagami Sundaram , Edupuganti Uthamaphani R. , Mohandas Poornima , Chan Catherine , Zeng Julie , Kopylov Mykhailo , Angelo Nicholas G. , Warren J. David , Soll Clifford E. , Quadri Luis E. N. 
Published: January 2015

ABSTRACT

Phenolic glycolipids (PGLs) are polyketide synthase-derived glycolipids unique to pathogenic mycobacteria. PGLs are found in several clinically relevant species, including various
Mycobacterium tuberculosis
strains,
Mycobacterium leprae
, and several nontuberculous mycobacterial pathogens, such as
M. marinum
. Multiple lines of investigation implicate PGLs in virulence, thus underscoring the relevance of a deep understanding of PGL biosynthesis. We report mutational and biochemical studies that interrogate the mechanism by which PGL biosynthetic intermediates (
p
-hydroxyphenylalkanoates) synthesized by the iterative polyketide synthase Pks15/1 are transferred to the noniterative polyketide synthase PpsA for acyl chain extension in
M. marinum
. Our findings support a model in which the transfer of the intermediates is dependent on a
p
-hydroxyphenylalkanoyl-AMP ligase (FadD29) acting as an intermediary between the iterative and the noniterative synthase systems. Our results also establish the
p
-hydroxyphenylalkanoate extension ability of PpsA, the first-acting enzyme of a multisubunit noniterative polyketide synthase system. Notably, this noniterative system is also loaded with fatty acids by a specific fatty acyl-AMP ligase (FadD26) for biosynthesis of phthiocerol dimycocerosates (PDIMs), which are nonglycosylated lipids structurally related to PGLs. To our knowledge, the partially overlapping PGL and PDIM biosynthetic pathways provide the first example of two distinct, pathway-dedicated acyl-AMP ligases loading the same type I polyketide synthase system with two alternate starter units to produce two structurally different families of metabolites. The studies reported here advance our understanding of the biosynthesis of an important group of mycobacterial glycolipids.
Absence of a Functional erm Gene in Isolates of Mycobacterium immunogenum and the Mycobacterium mucogenicum Group, Based on
In Vitro
Clarithromycin Susceptibility
Authors: Brown-Elliott Barbara A. , Hanson Kimberly , Vasireddy Sruthi , Iakhiaeva Elena , Nash Kevin A. , Vasireddy Ravikiran , Parodi Nicholas , Smith Terry , Gee Martha , Strong Anita , Barker Adam , Cohen Samuel , Muir Haleina , Slechta E. Susan , Wallace Richard J. 
Published: January 2015

ABSTRACT

Macrolide resistance has been linked to the presence of a functional erythromycin ribosomal methylase (
erm
) gene in most species of pathogenic rapidly growing mycobacteria (RGM). For these
Mycobacterium
isolates, extended incubation in clarithromycin is necessary to determine macrolide susceptibility. In contrast, the absence of a detectable
erm
gene in isolates of
M. chelonae
,
M. senegalense
, and
M. peregrinum
and a nonfunctional
erm
gene in
M. abscessus
subsp.
massiliense
and 15% to 20% of
M. abscessus
subsp.
abscessus
isolates renders these species intrinsically macrolide susceptible. Not all RGM species have been screened for the presence of an
erm
gene, including the
Mycobacterium mucogenicum
group (
M. mucogenicum
,
M. phocaicum
, and
M. aubagnense
) and
Mycobacterium immunogenum
. A total of 356 isolates of these two pathogenic RGM taxa from two reference laboratories (A.R.U.P. Reference Laboratories and the Mycobacteria/Nocardia Laboratory at the University of Texas Health Science Center at Tyler) underwent clarithromycin susceptibility testing with readings at 3 to 5 days and 14 days. Only 13 of the 356 isolates had resistant clarithromycin MICs at initial extended MIC readings, and repeat values on all available isolates were ≤2 μg/ml. These studies suggest that these two additional RGM groups do not harbor functional
erm
genes and, like
M. chelonae
, do not require extended clarithromycin susceptibility testing. We propose to the Clinical Laboratory and Standards Institute that isolates belonging to these above-mentioned six rapidly growing mycobacterial groups based on molecular identification with no known functional
erm
genes undergo only 3 to 5 days of susceptibility testing (to exclude mutational resistance).
Improving patient flow in pre-operative assessment
Authors: Stark Cameron , Gent Anne , Kirkland Linda 
Published: January 2015

AbstractAnnual patient attendances at a pre-operative assessment department increased by 24.8% from 5659 in 2009, to 7062 in 2012. The unit was staffed by administrative staff, nurses, and health care assistants (HCA). Medical review was accessed via on call medical staff, or notes were sent to anaesthetists for further review.With rising demand, patient waits increased. The average lead time for a patient (time from entering the department to leaving) was 79 minutes. 9.3% of patients attended within two weeks of their scheduled surgery date. 10% of patients were asked to return on a later day, as there was not sufficient capacity to undertake their assessment. There were nine routes of referral in to the department.Patients moved between different clinic rooms and the waiting area several times. Work patterns were uneven, as many attendances were from out-patient clinics which meant peak attendance times were linked to clinic times. There were substantial differences in the approaches of different nurses, making the HCA role difficult. Patients reported dissatisfaction with waits.Using a Lean quality improvement process with rapid PDSA cycles, the service changed to one in which patients were placed in a room, and remained there for the duration of their assessment. Standard work was developed for HCWs and nurses. Rooms were standardised using 5S processes, and set up improved to reduce time spent looking for supplies. A co-ordinator role was introduced using existing staff to monitor flow and to organise the required medical assessments and ECGs. Timing of booked appointments were altered to take account of clinic times. Routes in to the department were reduced from nine to one.Ten months after the work began, the average lead time had reduced to 59 minutes. The proportion of people attending within two weeks of their surgery decreased from 9.3% to 5.3%. Referrals for an anaesthetic opinion decreased from 30% to 20%, and in the month reviewed no one had to return to be seen as a result of limited capacity.
Traffic lights: putting a stop to unsafe patient transfers
Authors: Parbhoo Anita , Batte Jemma 
Published: January 2015

AbstractPoor handover between doctors is a recognised cause of error in hospitals.[1] Watford General Hospital is a busy acute trust in southern England, where high admission rates necessitate timely patient transfers from the acute admissions unit (AAU) to the medical wards. We found that doctors were infrequently informed of patient transfers, and they rarely handed over patient care when a patient was moved. Our aim was to minimise preventable harm to patients by prompting handover of clinically unstable patients, and patients with outstanding investigations or referrals, at the time of transfer. We introduced a traffic light tool to categorise patients on the medical take as red, amber, or green according to their clinical status at time of admission to AAU. The traffic light colour, which was assigned both on paper and electronically, was designed to prompt a verbal handover between doctors at the time of patient transfer from AAU.
β-Catenin Promotes Regulatory T-cell Responses in Tumors by Inducing Vitamin A Metabolism in Dendritic Cells
Authors: Hong Yuan , Manoharan Indumathi , Suryawanshi Amol , Majumdar Tanmay , Angus-Hill Melinda L. , Koni Pandelakis A. , Manicassamy Balaji , Mellor Andrew L. , Munn David H. , Manicassamy Santhakumar 
Published: January 2015

Abstract
Tumors actively suppress antitumor immunity, creating formidable barriers to successful cancer immunotherapy. The molecular mechanisms underlying tumor-induced immune tolerance are largely unknown. In the present study, we show that dendritic cells (DC) in the tumor microenvironment acquire the ability to metabolize vitamin A to produce retinoic acid (RA), which drives regulatory T-cell responses and immune tolerance. Tolerogenic responses were dependent on induction of vitamin A–metabolizing enzymes via the β-catenin/T-cell factor (TCF) pathway in DCs. Consistent with this observation, DC-specific deletion of β-catenin in mice markedly reduced regulatory T-cell responses and delayed melanoma growth. Pharmacologic inhibition of either vitamin A–metabolizing enzymes or the β-catenin/TCF4 pathway in vivo had similar effects on tumor growth and regulatory T-cell responses. Hence, β-catenin/TCF4 signaling induces local regulatory DC and regulatory T-cell phenotypes via the RA pathway, identifying this pathway as an important target for anticancer immunotherapy. Cancer Res; 75(4); 656–65. ©2015 AACR.
Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis (TRIPOD)
Authors: Collins Gary S. , Reitsma Johannes B. , Altman Douglas G. , Moons Karel G.M. 
Published: January 2015

Background—
Prediction models are developed to aid health care providers in estimating the probability or risk that a specific disease or condition is present (diagnostic models) or that a specific event will occur in the future (prognostic models), to inform their decision making. However, the overwhelming evidence shows that the quality of reporting of prediction model studies is poor. Only with full and clear reporting of information on all aspects of a prediction model can risk of bias and potential usefulness of prediction models be adequately assessed.

Methods—
The Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) Initiative developed a set of recommendations for the reporting of studies developing, validating, or updating a prediction model, whether for diagnostic or prognostic purposes. This article describes how the TRIPOD Statement was developed. An extensive list of items based on a review of the literature was created, which was reduced after a Web-based survey and revised during a 3-day meeting in June 2011 with methodologists, health care professionals, and journal editors. The list was refined during several meetings of the steering group and in e-mail discussions with the wider group of TRIPOD contributors.

Results—
The resulting TRIPOD Statement is a checklist of 22 items, deemed essential for transparent reporting of a prediction model study. The TRIPOD Statement aims to improve the transparency of the reporting of a prediction model study regardless of the study methods used. The TRIPOD Statement is best used in conjunction with the TRIPOD explanation and elaboration document.

Conclusions—

To aid the editorial process and readers of prediction model studies, it is recommended that authors include a completed checklist in their submission (also available at
www.tripod-statement.org
).
Effects of Daily Almond Consumption on Cardiometabolic Risk and Abdominal Adiposity in Healthy Adults With Elevated LDL‐Cholesterol: A Randomized Controlled Trial
Authors: Berryman Claire E. , West Sheila G. , Fleming Jennifer A. , Bordi Peter L. , Kris‐Etherton Penny M. 
Published: January 2015

Background
Evidence consistently shows that almond consumption beneficially affects lipids and lipoproteins. Almonds, however, have not been evaluated in a controlled‐feeding setting using a diet design with only a single, calorie‐matched food substitution to assess their specific effects on cardiometabolic risk factors.

Methods and Results

In a randomized, 2‐period (6 week/period), crossover, controlled‐feeding study of 48 individuals with elevated
LDL
‐C (149±3 mg/dL), a cholesterol‐lowering diet with almonds (1.5 oz. of almonds/day) was compared to an identical diet with an isocaloric muffin substitution (no almonds/day). Differences in the nutrient profiles of the control (58%
CHO
, 15%
PRO
, 26% total fat) and almond (51%
CHO
, 16%
PRO
, 32% total fat) diets were due to nutrients inherent to each snack; diets did not differ in saturated fat or cholesterol. The almond diet, compared with the control diet, decreased non‐
HDL
‐C (−6.9±2.4 mg/dL;
P
=0.01) and
LDL
‐C (−5.3±1.9 mg/dL;
P
=0.01); furthermore, the control diet decreased
HDL
‐C (−1.7±0.6 mg/dL;
P
<0.01). Almond consumption also reduced abdominal fat (−0.07±0.03 kg;
P
=0.02) and leg fat (−0.12±0.05 kg;
P
=0.02), despite no differences in total body weight.

Conclusions

Almonds reduced non‐
HDL
‐C,
LDL
‐C, and central adiposity, important risk factors for cardiometabolic dysfunction, while maintaining
HDL
‐C concentrations. Therefore, daily consumption of almonds (1.5 oz.), substituted for a high‐carbohydrate snack, may be a simple dietary strategy to prevent the onset of cardiometabolic diseases in healthy individuals.

Clinical Trial Registration

URL
:
www.clinicaltrials.gov
; Unique Identifier:
NCT
01101230.
Implementation of the Third Universal Definition of Myocardial Infarction After Coronary Artery Bypass Grafting: A Survey Study in Western Europe
Authors: van Beek Dianne E. C. , van Zaane Bas , Buijsrogge Marc P. , van Klei Wilton A. 
Published: January 2015

Background
Diagnosing a postoperative myocardial infarction in patients undergoing coronary artery bypass grafting is challenging, as the normally used criteria are more difficult to interpret. The rate of implementation of the consensus‐based new diagnostic criteria for postoperative myocardial infarction proposed by the third universal definition of myocardial infarction is unknown. Therefore, the primary objective of this study was to address the implementation of the third universal definition of postoperative myocardial infarction following coronary artery bypass grafting.

Methods and Results

We conducted a web‐based survey by sending 4 waves of invitations via e‐mail to cardiothoracic surgeons in 12 Western European countries. Of the 302 participating cardiothoracic specialists, from 182 different centers, 213 (71%) were aware that troponin is the preferred biomarker and 112 (37%) knew that using a cut‐off level of >10 times the 99th percentile is recommended. Overall, 90 (30%) participants (strongly) agreed with implementation of this cut‐off level in their clinical practice. Troponin was used in clinical practice by 149 (49%) of the participants. In total, 117 (89%) of the 131 participants with a local guideline confirmed
ECG
changes as a diagnostic criterion in that guideline.
ST
segmental changes (75, 64%) were used more often for diagnosing postoperative myocardial infarction than Q waves (64, 55%) or new left bundle branch blocks (34, 29%).

Conclusions

Cardiac biomarkers and
ECG
changes were not used in concordance with the third universal definition, and only a minority had a positive attitude toward implementation of the proposed cut‐off level for troponin in their clinical practice.
Association of Fluid Retention With Anemia and Clinical Outcomes Among Patients With Chronic Kidney Disease
Authors: Hung Szu‐Chun , Kuo Ko‐Lin , Peng Ching‐Hsiu , Wu Che‐Hsiung , Wang Yi‐Chun , Tarng Der‐Cherng 
Published: January 2015

Background

Observational studies have demonstrated an association between anemia and adverse outcomes in patients with chronic kidney disease (
CKD
). However, randomized trials failed to identify a benefit of higher hemoglobin concentrations, suggesting that the anemia‐outcome association may be confounded by unknown factors.

Methods and Results

We evaluated the influence of fluid status on hemoglobin concentrations and the cardiovascular and renal outcomes in a prospective cohort of 326 patients with stage 3 to 5
CKD
. Fluid status, as defined by overhydration (
OH
) level measured with bioimpedance, was negatively correlated with hemoglobin concentrations at baseline (
r
=−0.438,
P
<0.001). In multivariate regression analysis,
OH
remained an independent predictor of hemoglobin, second only to estimated glomerular filtration rate. Patients were stratified into 3 groups: no anemia (n=105), true anemia (n=82), and anemia with excess
OH
(n=139) (relative
OH
level ≥7%, the 90th percentile for the healthy population). During a median follow‐up of 2.2 years, there was no difference in cardiovascular and renal risks between patients with true anemia and those with no anemia in the adjusted Cox proportional hazards models. However, patients with anemia with excess
OH
had a significantly increased risk of cardiovascular morbidity and mortality and
CKD
progression relative to those with true anemia and those with no anemia, respectively.

Conclusions

Fluid retention is associated with the severity of anemia and adverse cardiovascular and renal outcomes in patients with
CKD
. Further research is warranted to clarify whether the correction of fluid retention, instead of increasing erythropoiesis, would improve outcomes of
CKD
‐associated anemia.
Taxonomic revision of the flathead fish genus Platycephalus Bloch, 1785 (Teleostei: Platycephalidae) from Australia, with description of a new species
Authors: IMAMURA HISASHI 
Published: January 2015

The taxonomy of the fish genus Platycephalus Bloch, 1785 from Australia is revised following examination of all extant primary types of Australian species, including those previously synonymized. The following 16 Australian species, including a single new species, are recognized in this study: Platycephalus angustus Steindachner, 1866, Platycephalus aurimaculatus Knapp, 1987, Platycephalus bassensis Cuvier, 1829, Platycephalus caeruleopunctatus McCulloch, 1922, Platycephalus chauliodous Knapp, 1991, Platycephalus conatus Waite & McCulloch, 1915, Platycephalus endrachtensis Quoy & Gaimard, 1825, Platycephalus fuscus Cuvier, 1829, Platycephalus grandispinis Cuvier, 1829, Platycephalus laevigatus Cuvier, 1829, Platycephalus marmoratus Stead, 1908, Platycephalus orbitalis Imamura & Knapp, 2009, Platycephalus richardsoni Castelnau, 1872, Platycephalus speculator Klunzinger, 1872, Platycephalus westraliae (Whitley, 1938) and Platycephalus australis sp. nov. [formerly confused with Platycephalus indicus (Linnaeus, 1758)]. Previously suggested synonymies of several species are reevaluated and a key provided for all Australian species of Platycephalus.
Impacts of Climate Modes on Air–Sea Heat Exchange in the Red Sea
Authors: Abualnaja Yasser , Papadopoulos Vassilis P. , Josey Simon A. , Hoteit Ibrahim , Kontoyiannis Harilaos , Raitsos Dionysios E. 
Published: January 2015

Abstract
The impacts of various climate modes on the Red Sea surface heat exchange are investigated using the MERRA reanalysis and the OAFlux satellite reanalysis datasets. Seasonality in the atmospheric forcing is also explored. Mode impacts peak during boreal winter [December–February (DJF)] with average anomalies of 12–18 W m−2 to be found in the northern Red Sea. The North Atlantic Oscillation (NAO), the east Atlantic–west Russia (EAWR) pattern, and the Indian monsoon index (IMI) exhibit the strongest influence on the air–sea heat exchange during the winter. In this season, the largest negative anomalies of about −30 W m−2 are associated with the EAWR pattern over the central part of the Red Sea. In other seasons, mode-related anomalies are considerably lower, especially during spring when the mode impacts are negligible. The mode impacts are strongest over the northern half of the Red Sea during winter and autumn. In summer, the southern half of the basin is strongly influenced by the multivariate ENSO index (MEI). The winter mode–related anomalies are determined mostly by the latent heat flux component, while in summer the shortwave flux is also important. The influence of the modes on the Red Sea is found to be generally weaker than on the neighboring Mediterranean basin.
A Rossby Wave Bridge from the Tropical Atlantic to West Antarctica
Authors: Li Xichen , Gerber Edwin P. , Holland David M. , Yoo Changhyun 
Published: January 2015

Abstract
Tropical Atlantic sea surface temperature changes have recently been linked to circulation anomalies around Antarctica during austral winter. Warming in the tropical Atlantic associated with the Atlantic multidecadal oscillation forces a positive response in the southern annular mode, strengthening the Amundsen–Bellingshausen Sea low in particular. In this study, observational and reanalysis datasets and a hierarchy of atmospheric models are used to assess the seasonality and dynamical mechanism of this teleconnection. Both the reanalyses and models reveal a robust link between tropical Atlantic SSTs and the Amundsen–Bellingshausen Sea low in all seasons except austral summer. A Rossby wave mechanism is then shown to both explain the teleconnection and its seasonality. The mechanism involves both changes in the excitation of Rossby wave activity with season and the formation of a Rossby waveguide across the Pacific, which depends critically on the strength and extension of the subtropical jet over the west Pacific. Strong anticyclonic curvature on the poleward flank of the jet creates a reflecting surface, channeling quasi-stationary Rossby waves from the subtropical Atlantic to the Amundsen–Bellingshausen Sea region. In summer, however, the jet is weaker than in other seasons and no longer able to keep Rossby wave activity trapped in the Southern Hemisphere. The mechanism is supported by integrations with a comprehensive atmospheric model, initial-value calculations with a primitive equation model on the sphere, and Rossby wave ray tracing analysis.
Climatology, Storm Morphologies, and Environments of Tornadoes in the British Isles: 1980–2012
Authors: Mulder Kelsey J. , Schultz David M. 
Published: January 2015

Abstract
A climatology is developed for tornadoes during 1980–2012 in the British Isles, defined in this article as England, Scotland, Wales, Northern Ireland, Republic of Ireland, Channel Islands, and the Isle of Man. The climatology includes parent storm type, interannual variability, annual and diurnal cycles, intensities, occurrence of outbreaks (defined as three or more tornadoes in the same day), geographic distribution, and environmental conditions derived from proximity soundings of tornadoes. Tornado reports are from the Tornado and Storm Research Organization (TORRO). Over the 33 years, there were a mean of 34.3 tornadoes and 19.5 tornado days (number of days in which at least one tornado occurred) annually. Tornadoes and tornado outbreaks were most commonly produced from linear storms, defined as radar signatures at least 75 km long and approximately 3 times as long as wide. Most (78%) tornadoes occurred in England. The probability of a tornado within 10 km of a point was highest in the south, southeast, and west of England. On average, there were 2.5 tornado outbreaks every year. Where intensity was known, 95% of tornadoes were classified as F0 or F1 with the remainder classified as F2. There were no tornadoes rated F3 or greater during this time period. Tornadoes occurred throughout the year with a maximum from May through October. Finally, tornadoes tended to occur in low-CAPE, high-shear environments. Tornadoes in the British Isles were difficult to predict using only sounding-derived parameters because there were no clear thresholds between null, tornadic, outbreak, and significant tornado cases.