bluuebunny/crossref_metadata_2025 huggingface dataset:
Louping Ill Virus Genome Sequence Derived from the Spinal Cord of an Infected Lamb
Authors: Marston Denise A. , Mansfield Karen L. , Mearns Rebecca , Ellis Richard J. , Fooks Anthony R. , Johnson Nicholas
Published: July 2013

Louping ill virus (LIV) is a zoonotic virus causing fatal encephalitis in young sheep and grouse. We have recovered the complete genome sequence from a spinal cord sample prepared from a lamb that was naturally infected with LIV. This is only the second LIV genome sequence reported and the first prepared from a clinical sample.
Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius
Authors: Zubair Saima , de Villiers Etienne P. , Younan Mario , Andersson Göran , Tettelin Herve , Riley David R. , Jores Joerg , Bongcam-Rudloff Erik , Bishop Richard P.
Published: July 2013

Streptococcus agalactiae
causes a range of clinical syndromes in camels (
Camelus dromedarius
). We report the genome sequences of two
S. agalactiae
isolates that induce abscesses in Kenyan camels. These genomes provide novel data on the composition of the
S. agalactiae
“pan genome” and reveal the presence of multiple genomic islands.
Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates
Authors: Hazen Tracy H. , Sahl Jason W. , Fraser Claire M. , Donnenberg Michael S. , Scheutz Flemming , Rasko David A.
Published: July 2013

We report the draft genome sequences of three enteropathogenic
Escherichia coli
(EPEC) isolates that display the O157 serogroup but do not have the Shiga toxin genes (
stx
), which are characteristic of O157 enterohemorrhagic
E. coli
(EHEC).
E. coli
strain RN587/1 has the O157:H8 serotype and possesses the EAF plasmid characteristic of typical EPEC (J. B. Kaper, J. P. Nataro, and H. L. Mobley, Nat. Rev. Microbiol. 2:123–140, 2004). The other two isolates, strains C844-97 and C639-08, are both O157:H45 and possess the locus of enterocyte effacement (LEE) pathogenicity island; however, they do not contain the EAF plasmid or the
stx
-carrying phage.
Complete Genome Sequence of a Human Enterovirus 71 Strain Isolated in Brunei in 2006
Authors: Zaini Zainun , McMinn Peter
Published: July 2013

The complete genome sequence of a human enterovirus 71 strain isolated in Brunei in 2006 was determined. Phylogenetic analysis based on the complete genome sequence classified this strain into subgenogroup B5.
Quality indicators of clinical cancer care (QC3) in colorectal cancer
Authors: Bianchi Valentina , Spitale Alessandra , Ortelli Laura , Mazzucchelli Luca , Bordoni Andrea ,   the QC3 CRC Working Group
Published: July 2013

Objectives

Assessing the quality of cancer care (QoCC) has become increasingly important to providers, regulators and purchasers of care worldwide. The aim of this study was to develop evidence-based quality indicators (QIs) for colorectal cancer (CRC) to be applied in a population-based setting.

Design

A comprehensive evidence-based literature search was performed to identify the initial list of QIs, which were then selected and developed using a two-step-modified Delphi process involving two multidisciplinary expert panels with expertise in CRC care, quality of care and epidemiology.

Setting

The QIs of the clinical cancer care (QC3) population-based project, which involves all the public and private hospitals and clinics present on the territory of Canton Ticino (South Switzerland).

Participants

Ticino Cancer Registry, The Colorectal Cancer Working Group (CRC-WG) and the external academic Advisory Board (AB).

Main outcome measures

Set of QIs which encompass the whole diagnostic-treatment process of CRC.

Results

Of the 149 QIs that emerged from 181 sources of literature, 104 were selected during the in-person meeting of CRC-WG. During the Delphi process, CRC-WG shortened the list to 89 QI. AB finally validated 27 QIs according to the phase of care: diagnosis (N=6), pathology (N=3), treatment (N=16) and outcome (N=2).

Conclusions

Using the validated Delphi methodology, including a literature review of the evidence and integration of expert opinions from local clinicians and international experts, we were able to develop a list of QIs to assess QoCC for CRC. This will hopefully guarantee feasibility of data retrieval, as well as acceptance and translation of QIs into the daily clinical practice to improve QoCC. Moreover, evidence-based selected QIs allow one to assess immediate changes and improvements in the diagnostic-therapeutic process that could be translated into a short-term benefit for patients with a possible gain both in overall and disease-free survival.
The epidemiology of malpractice claims in primary care: a systematic review
Authors: Wallace E , Lowry J , Smith S M , Fahey T
Published: July 2013

Objectives

The aim of this systematic review was to examine the epidemiology of malpractice claims in primary care.

Design

A computerised systematic literature search was conducted. Studies were included if they reported original data (≥10 cases) pertinent to malpractice claims, were based in primary care and were published in the English language. Data were synthesised using a narrative approach.

Setting

Primary care.

Participants

Malpractice claimants.

Primary outcome

Malpractice claim (defined as a written demand for compensation for medical injury). We recorded: medical misadventure cited in claims, missed/delayed diagnoses cited in claims, outcome of claims, prevalence of claims and compensation awarded to claimants.

Results

Of the 7152 articles retrieved by electronic search, a total of 34 studies met the inclusion criteria and were included in the narrative analysis. Twenty-eight studies presented data from medical indemnity malpractice claims databases and six studies presented survey data. Fifteen studies were based in the USA, nine in the UK, seven in Australia, one in Canada and two in France. The commonest medical misadventure resulting in claims was failure to or delay in diagnosis, which represented 26–63% of all claims across included studies. Common missed or delayed diagnoses included cancer and myocardial infarction in adults and meningitis in children. Medication error represented the second commonest domain representing 5.6–20% of all claims across included studies. The prevalence of malpractice claims in primary care varied across countries. In the USA and Australia when compared with other clinical disciplines, general practice ranked in the top five specialties accounting for the most claims, representing 7.6–20% of all claims. However, the majority of claims were successfully defended.

Conclusions

This review of malpractice claims in primary care highlights diagnosis and medication error as areas to be prioritised in developing educational strategies and risk management systems.
Physiological variables associated with the development of acute mountain sickness at the South Pole
Authors: Harrison Michael F , Anderson Paul J , Miller Andrew D , O'Malley Kathy A , Richert Maile L , Johnson Jacob B , Johnson Bruce D
Published: July 2013

Exposure to altitudes >2500 m can result in acute mountain sickness (AMS), a mild and usually self-limiting condition. Research has attempted to identify factors associated with developing AMS without controlling important factors related to the ascent or collecting a comprehensive set of variables.

Objectives

The Antarctic Study of Altitude Physiology (ASAP) investigated variables associated with the development of AMS in adults experiencing rapid passive transport to altitude by airplane.

Design

Our prospective observational trial collected data, including personal history, anthropometrics, vital signs, blood samples and pulmonary function, at sea level and at altitude. Statistical analysis utilised independent sample t tests to investigate between-group differences (p<0.05) and a forward, step-wise binary logisitic regression analysis was performed.

Participants

Of 248 eligible ASAP participants, those who did not use acetazolamide (N=98) were included in the present analysis.

Primary outcome measures

The diagnosis of AMS using the Lake Louise Symptom Score.

Results

Analysis of participants not using acetazolamide (n=90) found 30 participants developed AMS and 60 participants did not. Estimated plasma volume decreased significantly at altitude (p=0.025) in the AMS group as compared with the No AMS group while body weight did not change (p=0.125). Serum sodium (p=0.045) and low-density lipoprotein (LDL) (p=0.049) levels were higher in the No AMS group. A logistic regression analysis emphasised the contributions of LDL and eosinophil levels in the development of AMS.

Conclusions

These results suggest that the body water regulation and inflammation are key factors in AMS development when all other factors such as the level of physical exertion during ascent, the rate and magnitude of ascent and the use of acetazolamide are controlled.
Accuracy of evidence-based criteria for identifying an incident hip fracture in the absence of the date of injury: a retrospective database study
Authors: Vu Trang , Davie Gabrielle , Barson David , Day Lesley , Finch Caroline F
Published: July 2013

Objectives

Hospital discharge data (HDD) in many health systems do not capture the date of injury (DOI); the absence of this date hinders researchers’ ability to distinguish repeat from incident injury admissions. Various approaches using somewhat arbitrary criteria have been explored to increase the accuracy of incident injury identification. However, these approaches have not been validated against a data source which contains DOI. The aim of this study was to determine the accuracy of evidence-based criteria for identifying fall-related incident hip fractures in the absence of DOI using HDD containing DOI as the reference standard.

Design

Retrospective database study.

Setting

New Zealand.

Participants

8761 patients aged 65+ years admitted for fall-related hip fracture between 1 July 2005 and 30 June 2008, inclusive.

Outcome measures

We defined person-identifying HDD containing DOI as the reference standard and calculated measures of the accuracy of evidence-based criteria for identifying fall-related incident hip fractures from HDD not containing DOI. The criteria were principal diagnosis of hip fracture, mechanism of injury indicating a fall, admission type emergency, admission source other than a transfer and presence of hip operation code(s). For a subsequent fall-related hip fracture, additional criteria were time between successive hip fractures ≥120 days, and all external cause-of-injury codes being different to those for the previous hip fracture.

Results

The sensitivity and specificity of the criteria for identifying fall-related incident hip fractures from data not containing DOI were 96.7% and 99.3%, respectively, compared with the reference standard. The application of these criteria resulted in a slight underestimation of the percentage of patients with multiple hip fractures.

Conclusions

Although it is preferable to have DOI; this study demonstrates that evidence-based criteria can be used to reliably identify fall-related incident hip fractures from the person-identifying HDD when DOI is unavailable.
Quality evaluation through self-assessment: a novel method to gain insight into ERCP performance
Authors: Ekkelenkamp Vivian E , Koch Arjun D , Haringsma Jelle , Poley Jan-Werner , van Buuren Henk R , Kuipers Ernst J , de Man Robert A
Published: July 2013

Background

The American Society for Gastrointestinal Endoscopy Committee on Outcomes Research has recommended monitoring nine endoscopic retrograde cholangiopancreatography (ERCP)-specific quality indicators for quality assurance in ERCP. With the development of a self-assessment tool for ERCP (Rotterdam Assessment Form for ERCP—RAF-E), key indicators can easily be assessed.

Objective

The aim of this study was to test in daily practice an easy-to-use form for assessment of procedural quality in ERCP and to determine ERCP quality outcomes in a tertiary referral hospital.

Design

This was a prospective study carried out in a tertiary referral hospital. In January 2008, a quality self-assessment programme was started. Five qualified endoscopists participated in this study. All ERCPs were appraised using RAF-E. Primary parameters were common bile duct (CBD) cannulation rate and procedural success. The indication was classified and procedural difficulty was graded; success rates of therapeutic interventions were measured for all different difficulty degrees.

Results

A total number of 1691 ERCPs were performed. 1515 (89.6%) of these were appraised using RAF-E. Median CBD cannulation success rate was 94.1%. Successful sphincterotomy was accomplished in almost all patients (median 100%; range 98.2–100%). Stent placement was successful in 97.8% and complete stone extraction, if indicated, was achieved in 86.8%.

Conclusions

Quality indicators for ERCP can be measured using the Rotterdam self-assessment programme for ERCP. Outcome data in ERCPs obtained with this RAF-E provide insight into the quality of individual as well as group performance and can be used to assess and set standards for quality control in ERCP.
False positivity in HER2 testing of breast cancer: novel paths for approaching an old dilemma
Authors: Nunes Cristiana Buzelin , Rocha Rafael Malagoli , Buzelin Marcelo Araújo , Balabram Débora , de Souza Foureaux Fernanda , Porto Simone Souza , Gobbi Helenice
Published: July 2013

Aims

Variability in determining HER2 status has been reported, especially, differences in sensitivity and specificity among commercially available antibodies, with false positive and false negative results. We compared the sensitivity and specificity of five anti-HER2 antibodies by immunohistochemistry (IHC), using the new dual colour brightfield in situ hybridisation (DDISH) as the gold standard, on invasive breast carcinomas (IBC) arrays.

Material and methods

Serial sections from tissue microarrays (TMA) containing 200 preselected primary IBC were submitted to DDISH (VENTANA INFORM HER2 Dual ISH assay), and immunohistochemistry, using Dako A0485 and HercepTest (polyclonal), Novocastra CB11 (mouse monoclonal), NeoMarkers SP3 and Ventana 4B5 (rabbit monoclonal).

Results

From the initial 200 cases, 184 were assessed by DDISH and IHC. The concordance among the antibodies was considered very good (kappa statistics varied from 0.82 to 0.9). The overall concordance between IHC and DDISH ranged from 94.1% for CB11 to 96.6% for A0485. The antibodies A0485, HercepTest, SP3 and 4B5 were over 95% sensitive and specific. CB11 was the most specific antibody (97.1%). 60% (CB11) to 83.3% (SP3) of the 2+ cases showed no gene amplification by DDISH. False negative cases varied from 0.5% (A0485) to 3.8% (CB11) of the cases, and false positive from 1.6% (CB11) to 2.7% (HercepTest, SP3 and 4B5) of the 184 cases.

Conclusions

There was very good agreement among the five anti-HER2 antibodies. CB11 was the most specific antibody, but showed more false negative cases. A0485, SP3, 4B5 and HercepTest were highly sensitive and specific, but showed more false positive cases.
Investing in health: is social housing value for money? A cost-utility analysis
Authors: Lawson K D , Kearns A , Petticrew M , Fenwick E A L
Published: July 2013

Background

There is a healthy public policy agenda investigating the health impacts of improving living conditions. However, there are few economic evaluations, to date, assessing value for money. We conducted the first cost-effectiveness analysis of a nationwide intervention transferring social and private tenants to new-build social housing, in Scotland.

Methods

A quasi-experimental prospective study was undertaken involving 205 intervention households and 246 comparison households, over 2 years. A cost-utility analysis assessed the average cost per change in health utility (a single score summarising overall health-related quality of life), generated via the SF-6D algorithm. Construction costs for new builds were included. Analysis was conducted for all households, and by family, adult and elderly households; with estimates adjusted for baseline confounders. Outcomes were annuitised and discounted at 3.5%.

Results

The average discounted cost was £18 708 per household, at a national programme cost of £28.4 million. The average change in health utility scores in the intervention group attributable to the intervention were +0.001 for all households, +0.001 for family households, −0.04 for adult households and −0.03 for elderly households. All estimates were statistically insignificant.

Conclusions

At face value, the interventions were not value for money in health terms. However, because the policy rationale was the amenity provision of housing for disadvantaged groups, impacts extend beyond health and may be fully realised over the long term. Before making general value-for-money inferences, economic evaluation should attempt to estimate the full social value of interventions, model long-term impacts and explicitly incorporate equity considerations.
Alcohol-related mortality in deprived UK cities: worrying trends in young women challenge recent national downward trends
Authors: Shipton Deborah , Whyte Bruce , Walsh David
Published: July 2013

Background

Glasgow, the largest city in Scotland, has high levels of deprivation and a poor-health profile compared with other parts of Europe, which cannot be fully explained by the high levels of deprivation. The ‘excess’ premature mortality in Glasgow is now largely attributable to deaths from alcohol, drugs, suicide and violence.

Methods

Alcohol-related mortality in Glasgow from 1980 to 2011 was examined relative to the equally deprived UK cities of Manchester and Liverpool with the aim of identifying differences across the cities, with respect to gender, age and birth cohort, that could help explain the ‘excess’ mortality in Glasgow.

Results

In the 1980s, alcohol-related mortality in Glasgow was three times higher than in Manchester and Liverpool. Alcohol-related mortality increased in all three cities over the subsequent three decades, but a sharp rise in deaths in the early 1990s was unique to Glasgow. The increase in numbers of deaths in Glasgow was greater than in Manchester and Liverpool, but there was little difference in the pattern of alcohol-related deaths, by sex or birth cohort that could explain the excess mortality in Glasgow. The recent modest decrease in alcohol-related mortality was largely experienced by all birth cohorts, with the notable exception of the younger cohort (born between 1970 and 1979): women in this cohort across all three cities experienced disproportionate increases in alcohol-related mortality.

Conclusions

It is imperative that this early warning sign in young women in the UK is acted on if deaths from alcohol are to reduce in the long term.
Dental treatment on a German warship during a three-month deployment
Authors: von Wilmowsky Cornelius , Kiesewetter M R , Moest T
Published: July 2013

Introduction

Despite routine dental screenings and treatments before military deployments, dental emergencies may arise due to acute infections, trauma or failed restorations. The purpose of this study is to evaluate the dental service during a three-month deployment on a German warship.

Methods

A retrospective analysis of dental attendances and treatments in a German naval task group of three ships with an average total of 650 soldiers. Diagnosis, treatments performed, percentage of emergencies, routine procedures and numbers of appointments were recorded.

Results

Out of 650 soldiers, there were 71 patients (10.92%) with a mean age of 25.1±5.3 years. Out of 136 treatments, 17.65% were for emergency treatment, which is equivalent to 3.69% of all servicemen of the task group. Combining the reasons for dental emergencies, 95.84% were caused by caries.

Conclusions

The pre-screening of sailors before an overseas deployment is necessary to avoid severe dental treatments. Caries remains the main cause for dental emergencies, and medical doctors should be trained to treat caries lesions if a dentist is not on board.
A modern combat trauma
Authors: Popivanov Georgi , Mutafchiyski V M , Belokonski E I , Parashkevov A B , Koutin G L
Published: July 2013

Introduction

The world remains plagued by wars and terrorist attacks, and improvised explosive devices (IED) are the main weapons of our current enemies, causing almost two-thirds of all combat injuries. We wished to analyse the pattern of blast trauma on the modern battlefield and to compare it with combat gunshot injuries.

Materials and methods

Analysis of a consecutive series of combat trauma patients presenting to two Bulgarian combat surgical teams in Afghanistan over 11 months. Demographics, injury patterns and Injury Severity Scores (ISS) were compared between blast and gunshot-injured casualties using Fisher's Exact Test.

Results

The blast victims had significantly higher median ISS (20.54 vs 9.23) and higher proportion of ISS>16 (60% vs 33.92%, p=0.008) than gunshot cases. They also had more frequent involvement of three or more body regions (47.22% vs 3.58%, p<0.0001). A significantly higher frequency of head (27.27% vs 3.57%), facial (20% vs 0%) and extremities injuries (85.45% vs 42.86%) and burns (12.72% vs 0%) was noted among the victims of explosion (p<0.0001). Based on clinical examination and diagnostic imaging, primary blast injury was identified in 24/55 (43.6%), secondary blast injury in 37 blast cases (67.3%), tertiary in 15 (27.3%) and quaternary blast injury (all burns) in seven (12.72%).

Conclusions

Our results corroborate the ‘multidimensional’ injury pattern of blast trauma. The complexity of the blast trauma demands a good knowledge and a special training of the military surgeons and hospital personnel before deployment.
Safety and efficacy of percutaneous femoral artery access followed by Mynx closure in cerebral neurovascular procedures: a single center analysis
Authors: Grandhi Ramesh , Kanaan Hilal , Shah Aalap , Harrison Gillian , Bonfield Christopher , Jovin Tudor , Jankowitz Brian , Horowitz Michael
Published: July 2013

Background and purpose

Percutaneous transfemoral arterial procedures rely on a variety of vascular closure methods. We studied closure success and complications after using the Mynx vascular closure device in cerebral neurovascular procedures.

Methods

We prospectively analyzed patients undergoing diagnostic cerebral angiogram or neurointervention with arteriotomy closure using the Mynx device. Patient demographics and procedural factors were recorded. Statistical analyses compared groups and identified predictors of device failure and complication.

Results

A total of 766 patients, 59% women, mean age 55.5 years (SD 14.2), mean body mass index (BMI) 29.1 kg/m2(SD 7.4), underwent 937 neurovascular procedures in a 10 month period. Device success was achieved in 92% of patients; lower BMI, higher number of antithrombotic medications, larger sheath size, and performance of a neurointerventional procedure predicted Mynx failure. Complications occurred in 2.45% of procedures, with older age, lower BMI, higher number of antithrombotic medicines used, higher international normalized ratio, lower platelet count, and Mynx device failure conferring an increased risk of complication.

Conclusions

The Mynx device is safe and effective for cerebral neurovascular procedures. However, specific patient populations may warrant particular attention and thorough consideration of risks and benefits prior to employing the Mynx device for femoral arteriotomy closure.
NOTE ON CONSISTENT TRUNCATION OVER HIGHER-DIMENSIONAL SPHERE IN SUPERGRAVITY
Authors: SATO MATSUO , TSUCHIYA ASATO
Published: July 2013

We comment on consistent truncation over higher-dimensional sphere in supergravity.
A LOW OFFSET COMPARATOR FOR HIGH SPEED LOW POWER ADC
Authors: ZHU ZHANGMING , WANG WEITIE , GUAN YUHENG , LIU SHUBIN , XIAO YU , LIU LIANXI , YANG YINTANG
Published: July 2013

A novel low offset, high speed, low power comparator architecture is proposed in this paper. In order to achieve low offset, both offset cancellation and dynamic amplifier techniques are adopted. Active resistors are chosen to implement the static amplifier circuit to obtain reduction in equivalent input referred offset voltage as well as to increase the circuit speed. The comparator is designed in TSMC 0.18 μm CMOS process. Monte Carlo simulation shows that the comparator has the offset voltage as low as 0.3 mV at 1 sigma at 250 MHz while dissipates 342 μW from a 1.8 V supply.
INFLUENCE OF EXERCISE ON THREE TYPES OF FONTAN MODIFICATIONS: COMPARISON BY NUMERICAL SIMULATIONS
Authors: SUN QI , LIU JINLONG , ZHANG HAIBO , ZHENG JINGHAO , HONG HAIFA , SUN YANJUN , CHEN HUIWEN , LIU JINFEN , WANG QIAN , LIU YINGZHENG
Published: July 2013

Low energy efficiency of Fontan-type connections in exercise conditions may lead to limited post-operative exercise capacity of patients. The objective of this study was to compare the energy efficiency of different types of Fontan modifications in exercise conditions. In this study, the flow rate of the inferior vena cava (IVC) was increased artificially to simulate exercise conditions. The control volume power loss and energy efficiency were investigated in three types of Fontan modifications using the method of computational fluid dynamics (CFD). In the intracardiac tunnel Fontan, the power loss was 7.9 times of that calculated in resting state when the flow rate of IVC increased to three times of that measured at the right pulmonary artery flow ratio of 50%. The energy efficiency of it decreased prominently from 91.9% to 79.9%. On the contrary, in the extracardiac Fontan with direct cavopulmonary anastomosis (direct Fontan), the magnitude of power loss was only 2.9 times of that in resting state and the energy efficiency changed only from 91.8% to 89.1%. The results of extracardiac conduit Fontan fell in between. It showed that direct Fontan had higher energy efficiency than intracardiac tunnel or extracardiac conduit Fontan in exercise conditions.
Altered mineral uptake into fresh arc magmas: insights from U–Th isotopes of samples from Andean volcanoes under differential crustal stress regimes
Authors: Zellmer Georg F. , Freymuth Heye , Cembrano José M. , Clavero Jorge E. , Veloso Eugenio A. E. , Sielfeld Gerd G.
Published: July 2013

Uranium–thorium (U–Th) isotope compositions of whole rocks, groundmasses and minerals from mafic to intermediate Andean arc magmas were determined to assess the influence of crustal stress on rates of pre-eruptive crystallization and the significance of crystal uptake. Volcanoes investigated include Lascar in the central Andes, situated in a compressional regime, and Callaqui and Lonquimay in the southern Andes, situated in a transtensional regime. In the southern Andes, Calbuco volcano, which experienced variations in the local stress field due to volcano unloading triggered by large debris avalanches, was also targeted. In U–Th equiline space, whole rock and groundmass coincide in each studied sample, and are close to secular equilibrium or in slight U-excess. No isochronal relationships are displayed by the mineral separates, although many are out of secular equilibrium. Further, (
234
U/
238
U) activity ratios of some mineral separates from the southern Andes are in disequilibrium and vary significantly between different phases of individual rock samples. The combined data indicate that many crystals are foreign to the melts they are carried in, and that some mineral phases have experienced incipient weathering before their incorporation into the melt. Using Calbuco as an example, we speculate that volcano loading may affect secondary alteration processes at depth.
Using detrital garnet compositions to determine provenance: a new compositional database and procedure
Authors: Suggate Simon M. , Hall Robert
Published: July 2013

Detrital garnet compositions can be used to help determine the provenance of sedimentary rocks. In this study a garnet compositional database consisting of more than 2500 wet chemical and electron microprobe analyses was compiled from the literature. For the garnets in the database the six principal garnet end-member compositions (pyrope, almandine, spessartine, uvarovite, grossular and andradite) were calculated. A multi-stage methodology was devised to match garnet compositions to source rocks, and a series of garnet provenance fields on ternary plots were identified. The method was tested using compositional data from detrital garnet studies in several areas where provenance has already been identified, with good results. The methodology was then used to assess the provenance of detrital garnets from Neogene sandstones of northern Sabah, Borneo for which provenance is unknown and in a region where there are few garnet analyses for comparison. Comparison of garnet compositions from possible sources on Palawan, Philippines and in Borneo combined with the ternary plots excludes some known garnet-bearing rocks as potential sources and suggests derivation of metamorphic and igneous garnets from Palawan during the Early Miocene.

Supplementary material:

The compositional database and garnet data plotting spreadsheets are available at
www.geolsoc.org.uk/SUP18649
.
An Environmental Sociology for the Twenty-First Century
Authors: Pellow David N. , Nyseth Brehm Hollie
Published: July 2013

Environmental sociology has become a mature field within the discipline of sociology. We consider several of the key theories that define the core and boundaries of the field, calling attention to debates and unresolved questions. We contend that two of the defining features of this field are (a) attention to the inseparability of human and nonhuman natures and (b) attention to the role that power and social inequality play in shaping human/nonhuman interactions. These two characteristics of environmental sociology also reveal strong links between this field and the broader discipline, in light of recent reexaminations of classical sociological writings. We conclude with a consideration of new directions environmental sociologists might take toward building an even more robust, interdisciplinary, and critical area of study.
The Causal Effects of Father Absence
Authors: McLanahan Sara , Tach Laura , Schneider Daniel
Published: July 2013

The literature on father absence is frequently criticized for its use of cross-sectional data and methods that fail to take account of possible omitted variable bias and reverse causality. We review studies that have responded to this critique by employing a variety of innovative research designs to identify the causal effect of father absence, including studies using lagged dependent variable models, growth curve models, individual fixed effects models, sibling fixed effects models, natural experiments, and propensity score matching models. Our assessment is that studies using more rigorous designs continue to find negative effects of father absence on offspring well-being, although the magnitude of these effects is smaller than what is found using traditional cross-sectional designs. The evidence is strongest and most consistent for outcomes such as high school graduation, children's social-emotional adjustment, and adult mental health.
Characterization of CFTR High Expresser cells in the intestine
Authors: Jakab Robert L. , Collaco Anne M. , Ameen Nadia A.
Published: July 2013

The CFTR High Expresser (CHE) cells express eightfold higher levels of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl−channel compared with neighboring enterocytes and were first identified by our laboratory (Ameen et al., Gastroenterology 108: 1016, 1995). We used double-label immunofluorescence microscopy to further study these enigmatic epithelial cells in rat intestine in vivo or ex vivo. CHE cells were found in duodenum, most frequent in proximal jejunum, and absent in ileum and colon. CFTR abundance increased in CHE cells along the crypt-villus axis. The basolateral Na+K+Cl−cotransporter NKCC1, a key transporter involved in Cl−secretion, was detected at similar levels in CHE cells and neighboring enterocytes at steady state. Microvilli appeared shorter in CHE cells, with low levels of Myosin 1a, a villus enterocyte-specific motor that retains sucrase/isomaltase in the brush-border membrane (BBM). CHE cells lacked alkaline phosphatase and absorptive villus enterocyte BBM proteins, including Na+H+exchanger NHE3, Cl−/HCO3−exchanger SLC26A6 (putative anion exchanger 1), and sucrase/isomaltase. High levels of the vacuolar-ATPase proton pump were observed in the apical domain of CHE cells. Levels of the NHE regulatory factor NHERF1, Na-K-ATPase, and Syntaxin 3 were similar to that of neighboring enterocytes. cAMP or acetylcholine stimulation robustly increased apical CFTR and basolateral NKCC1 disproportionately in CHE cells relative to neighboring enterocytes. These data strongly argue for a specialized role of CHE cells in Cl−-mediated “high-volume” fluid secretion on the villi of the proximal small intestine.
Tumor protein D52 controls trafficking of an apical endolysosomal secretory pathway in pancreatic acinar cells
Authors: Messenger Scott W. , Thomas Diana D. H. , Falkowski Michelle A. , Byrne Jennifer A. , Gorelick Fred S. , Groblewski Guy E.
Published: July 2013

Zymogen granule (ZG) formation in acinar cells involves zymogen cargo sorting from trans-Golgi into immature secretory granules (ISGs). ISG maturation progresses by removal of lysosomal membrane and select content proteins, which enter endosomal intermediates prior to their apical exocytosis. Constitutive and stimulated secretion through this mechanism is termed the constitutive-like and minor-regulated pathways, respectively. However, the molecular components that control membrane trafficking within these endosomal compartments are largely unknown. We show that tumor protein D52 is highly expressed in endosomal compartments following pancreatic acinar cell stimulation and regulates apical exocytosis of an apically directed endolysosomal compartment. Secretion from the endolysosomal compartment was detected by cell-surface antigen labeling of lysosome-associated membrane protein LAMP1, which is absent from ZGs, and had incomplete overlap with surface labeling of synaptotagmin 1, a marker of ZG exocytosis. Although culturing (16–18 h) of isolated acinar cells is accompanied by a loss of secretory responsiveness, the levels of SNARE proteins necessary for ZG exocytosis were preserved. However, levels of endolysosomal proteins D52, EEA1, Rab5, and LAMP1 markedly decreased with culture. When D52 levels were restored by adenoviral delivery, the levels of these regulatory proteins and secretion of both LAMP1 (endolysosomal) and amylase was strongly enhanced. These secretory effects were absent in alanine and aspartate substitutions of serine 136, the major D52 phosphorylation site, and were inhibited by brefeldin A, which does not directly affect the ZG compartment. Our results indicate that D52 directly regulates apical endolysosomal secretion and are consistent with previous studies, suggesting that this pathway indirectly regulates ZG secretion of digestive enzymes.
Regional susceptibility to stress-induced intestinal injury in the mouse
Authors: Novosad Veronica L. , Richards Jennifer L. , Phillips Neil A. , King Michelle A. , Clanton Thomas L.
Published: July 2013

Injury to the intestinal mucosa is a life-threatening problem in a variety of clinical disorders, including hemorrhagic shock, trauma, burn, pancreatitis, and heat stroke. The susceptibility to injury of different regions of intestine in these disorders is not well understood. We compared histological injury across the small intestine in two in vivo mouse models of injury, hemorrhagic shock (30% loss of blood volume) and heat stroke (peak core temperature 42.4°C). In both injury models, areas near the duodenum showed significantly greater mucosal injury and reductions in villus height. To determine if these effects were dependent on circulating factors, experiments were performed on isolated intestinal segments to test for permeability to 4-kDa FITC-dextran. The segments were exposed to hyperthermia (42°C for 90 min), moderate simulated ischemia (Po2 ∼30 Torr, Pco2 ∼60 Torr, pH 7.1), severe ischemia (Po2 ∼20 Torr, Pco2 ∼80 Torr, pH 6.9), or severe hypoxia (Po2 ∼0 Torr, Pco2 ∼35 Torr) for 90 min, and each group was compared with sham controls. All treatments resulted in marked elevations in permeability within segments near the duodenum. In severe hypoxia or hyperthermia, permeability was also moderately elevated in the jejunum and ileum; in moderate or severe ischemia, permeability was unaffected in these regions. The results demonstrate increased susceptibility of proximal regions of the small intestine to acute stress-induced damage, irrespective of circulating factors. The predominant injury in the duodenum may impact the pattern of acute inflammatory responses arising from breach of the intestinal barrier, and such knowledge may be useful for designing therapeutic strategies.
Glucocorticoid receptor-dependent immunomodulatory effect of ursodeoxycholic acid on liver lymphocytes in mice
Authors: Takigawa Toshimichi , Miyazaki Hiromi , Kinoshita Manabu , Kawarabayashi Nobuaki , Nishiyama Kiyoshi , Hatsuse Kazuo , Ono Satoshi , Saitoh Daizoh , Seki Shuhji , Yamamoto Junji
Published: July 2013

Although ursodeoxycholic acid (UDCA) has long been used for patients with chronic cholestatic liver diseases, particularly primary biliary cirrhosis, it may modulate the host immune response. This study investigated the effect of UDCA feeding on experimental hepatitis, endotoxin shock, and bacterial infection in mice. C57BL/6 mice were fed a diet supplemented with or without 0.3% (wt/vol) UDCA for 4 wk. UDCA improved hepatocyte injury and survival in concanavalin-A (Con-A)-induced hepatitis by suppressing IFN-γ production by liver mononuclear cells (MNC), especially NK and NKT cells. UDCA also increased survival after lipopolysaccharide (LPS)-challenge; however, it increased mortality of mice following Escherichia coli infection due to the worsening of infection. UDCA-fed mice showed suppressed serum IL-18 levels and production of IL-18 from liver Kupffer cells, which together with IL-12 potently induce IFN-γ production. However, unlike normal mice, exogenous IL-18 pretreatment did not increase the serum IFN-γ levels after E. coli, LPS, or Con-A challenge in the UDCA-fed mice. Interestingly, however, glucocorticoid receptor (GR) expression was significantly upregulated in the liver MNC of the UDCA-fed mice but not in their whole liver tissue homogenates. Silencing GR in the liver MNC abrogated the suppressive effect of UDCA on LPS- or Con-A-induced IFN-γ production. Furthermore, RU486, a GR antagonist, restored the serum IFN-γ level in UDCA-fed mice after E. coli, LPS, or Con-A challenge. Taken together, these results suggest that IFN-γ-reducing immunomodulatory property of UDCA is mediated by elevated GR in the liver lymphocytes in an IL-12/18-independent manner.
Multiple inert gas elimination technique by micropore membrane inlet mass spectrometry—a comparison with reference gas chromatography
Authors: Kretzschmar Moritz , Schilling Thomas , Vogt Andreas , Rothen Hans Ulrich , Borges João Batista , Hachenberg Thomas , Larsson Anders , Baumgardner James E. , Hedenstierna Göran
Published: July 2013

The mismatching of alveolar ventilation and perfusion (VA/Q) is the major determinant of impaired gas exchange. The gold standard for measuring VA/Q distributions is based on measurements of the elimination and retention of infused inert gases. Conventional multiple inert gas elimination technique (MIGET) uses gas chromatography (GC) to measure the inert gas partial pressures, which requires tonometry of blood samples with a gas that can then be injected into the chromatograph. The method is laborious and requires meticulous care. A new technique based on micropore membrane inlet mass spectrometry (MMIMS) facilitates the handling of blood and gas samples and provides nearly real-time analysis. In this study we compared MIGET by GC and MMIMS in 10 piglets: 1) 3 with healthy lungs; 2) 4 with oleic acid injury; and 3) 3 with isolated left lower lobe ventilation. The different protocols ensured a large range of normal and abnormal VA/Q distributions. Eight inert gases (SF6, krypton, ethane, cyclopropane, desflurane, enflurane, diethyl ether, and acetone) were infused; six of these gases were measured with MMIMS, and six were measured with GC. We found close agreement of retention and excretion of the gases and the constructed VA/Q distributions between GC and MMIMS, and predicted PaO2from both methods compared well with measured PaO2. VA/Q by GC produced more widely dispersed modes than MMIMS, explained in part by differences in the algorithms used to calculate VA/Q distributions. In conclusion, MMIMS enables faster measurement of VA/Q, is less demanding than GC, and produces comparable results.
Nose-only water-pipe smoking effects on airway resistance, inflammation, and oxidative stress in mice
Authors: Nemmar Abderrahim , Raza Haider , Yuvaraju Priya , Beegam Sumaya , John Annie , Yasin Javed , Hameed Rasheed S. , Adeghate Ernest , Ali Badreldin H.
Published: July 2013

Water-pipe smoking (WPS) is a common practice in the Middle East and is now gaining popularity in Europe and the United States. However, there is a limited number of studies on the respiratory effects of WPS. More specifically, the underlying pulmonary pathophysiological mechanisms related to WPS exposure are not understood. Presently, we assessed the respiratory effects of nose-only exposure to mainstream WPS generated by commercially available honey flavored “moasel ” tobacco. The duration of the session was 30 min/day and 5 days/wk for 1 mo. Control mice were exposed to air only. Here, we measured in BALB/c mice the airway resistance using forced-oscillation technique. Lung inflammation was assessed histopathologically and by biochemical analysis of bronchoalveolar lavage (BAL) fluid, and oxidative stress was evaluated biochemically by measuring lipid peroxidation, reduced glutathione and several antioxidant enzymes. Pulmonary inflammation assessment showed an increase in neutrophil and lymphocyte numbers. Likewise, airway resistance was significantly increased in the WPS group compared with controls. Tumor necrosis factor α and interleukin 6 concentrations were significantly increased in BAL fluid. Lipid peroxidation in lung tissue was significantly increased whereas the level and activity of antioxidants including reduced glutathione, glutathione S transferase, and superoxide dismutase were all significantly decreased following WPS exposure, indicating the occurrence of oxidative stress. Moreover, carboxyhemoglobin levels were significantly increased in the WPS group. We conclude that 1-mo nose-only exposure to WPS significantly increased airway resistance, inflammation, and oxidative stress. Our results provide a mechanistic explanation for the limited clinical studies that reported the detrimental respiratory effects of WPS.
Pulmonary circulation and gas exchange at exercise in Sherpas at high altitude
Authors: Faoro Vitalie , Huez Sandrine , Vanderpool Rebecca , Groepenhoff Herman , de Bisschop Claire , Martinot Jean-Benoît , Lamotte Michel , Pavelescu Adriana , Guénard Hervé , Naeije Robert
Published: July 2013

Tibetans have been reported to present with a unique phenotypic adaptation to high altitude characterized by higher resting ventilation and arterial oxygen saturation, no excessive polycythemia, and lower pulmonary arterial pressures (Ppa) compared with other high-altitude populations. How this affects exercise capacity is not exactly known. We measured aerobic exercise capacity during an incremental cardiopulmonary exercise test, lung diffusing capacity for carbon monoxide (DlCO) and nitric oxide (DlNO) at rest, and mean Ppa (mPpa) and cardiac output by echocardiography at rest and at exercise in 13 Sherpas and in 13 acclimatized lowlander controls at the altitude of 5,050 m in Nepal. In Sherpas vs. lowlanders, arterial oxygen saturation was 86 ± 1 vs. 83 ± 2% (mean ± SE; P = nonsignificant), mPpa at rest 19 ± 1 vs. 23 ± 1 mmHg ( P < 0.05), DlCOcorrected for hemoglobin 61 ± 4 vs. 37 ± 2 ml·min−1·mmHg−1( P < 0.001), DlNO226 ± 18 vs. 153 ± 9 ml·min−1·mmHg−1( P < 0.001), maximum oxygen uptake 32 ± 3 vs. 28 ± 1 ml·kg−1·min−1( P = nonsignificant), and ventilatory equivalent for carbon dioxide at anaerobic threshold 40 ± 2 vs. 48 ± 2 ( P < 0.001). Maximum oxygen uptake was correlated directly to DlCOand inversely to the slope of mPpa-cardiac index relationships in both Sherpas and acclimatized lowlanders. We conclude that Sherpas compared with acclimatized lowlanders have an unremarkable aerobic exercise capacity, but with less pronounced pulmonary hypertension, lower ventilatory responses, and higher lung diffusing capacity.
Changes in neurochemicals within the ventrolateral medullary respiratory column in awake goats after carotid body denervation
Authors: Miller Justin Robert , Neumueller Suzanne , Muere Clarissa , Olesiak Samantha , Pan Lawrence , Hodges Matthew R. , Forster Hubert V.
Published: July 2013

A current and major unanswered question is why the highly sensitive central CO2/H+ chemoreceptors do not prevent hypoventilation-induced hypercapnia following carotid body denervation (CBD). Because perturbations involving the carotid bodies affect central neuromodulator and/or neurotransmitter levels within the respiratory network, we tested the hypothesis that after CBD there is an increase in inhibitory and/or a decrease in excitatory neurochemicals within the ventrolateral medullary column (VMC) in awake goats. Microtubules for chronic use were implanted bilaterally in the VMC within or near the pre-Bötzinger Complex (preBötC) through which mock cerebrospinal fluid (mCSF) was dialyzed. Effluent mCSF was collected and analyzed for neurochemical content. The goats hypoventilated (peak +22.3 ± 3.4 mmHg PaCO2) and exhibited a reduced CO2 chemoreflex (nadir, 34.8 ± 7.4% of control ΔV̇E/ΔPaCO2) after CBD with significant but limited recovery over 30 days post-CBD. After CBD, GABA and glycine were above pre-CBD levels (266 ± 29% and 189 ± 25% of pre-CBD; P < 0.05), and glutamine and dopamine were significantly below pre-CBD levels ( P < 0.05). Serotonin, substance P, and epinephrine were variable but not significantly ( P > 0.05) different from control after CBD. Analyses of brainstem tissues collected 30 days after CBD exhibited 1) a midline raphe-specific reduction ( P < 0.05) in the percentage of tryptophan hydroxylase–expressing neurons, and 2) a reduction ( P < 0.05) in serotonin transporter density in five medullary respiratory nuclei. We conclude that after CBD, an increase in inhibitory neurotransmitters and a decrease in excitatory neuromodulation within the VMC/preBötC likely contribute to the hypoventilation and attenuated ventilatory CO2 chemoreflex.