bluuebunny/crossref_metadata_2025 huggingface dataset:
How Innocent Is Corpus Callosum Dysgenesis?
Authors: Erol Fatih Serhat , Ozturk Sait , Akgun Bekir , Cakin Hakan , Kaplan Metin
Published: October 2013

Background/Aims: We aimed to investigate the relationship between corpus callosum dysgenesis (CCD) and associated asymptomatic closed spinal dysraphisms (CSDs). Methods: 2,840 pediatric patients who were referred to our outpatient clinic between the years 2005 and 2013 with the diagnosis of microcephaly, macrocephaly, congenital hydrocephaly, epilepsy, mental-motor retardation and suspicion of intracranial mass were evaluated. Eighty-five patients were identified with a CCD by cranial magnetic resonance imaging (MRI). The 85 patients with CCD were evaluated by whole spinal vertebral MRI for possible CSD and the results were evaluated. Results: 31/85 (36.4%) patients (20 males, 11 females) were detected to have radiological findings of CSD. The most common radiological finding was a low-lying conus medullaris, either alone, or as part of a multiple pathology in 26 of the 31 patients, followed by diastematomyelia in 16 of 31 cases and spinal lipoma in 4 of the 31 cases. Conclusion: When the neuroaxis emerges as a whole, the structures of embryological ectodermal origin and cranial and spinal structures are not independent regions from each other and thus, asymptomatic CSDs have been demonstrated to accompany CCD. In diseases of neural origin in which early diagnosis is of the utmost importance, each case with dysgenesis, diagnosed incidentally or during differential diagnosis, should be evaluated for possible CSD and should be treated with a multidisciplinary approach before any neurological deficit appears.
Clinicopathological Analysis of Breast Ductal Carcinoma in situ with ALDH1-Positive Cancer Stem Cells
Authors: Tsukabe Masami , Shimazu Kenzo , Morimoto Koji , Naoi Yasuto , Kagara Naofumi , Shimoda Masafumi , Shimomura Atsushi , Maruyama Naomi , Kim Seung Jin , Noguchi Shinzaburo
Published: October 2013

Objective: The aim of this study was to elucidate the clinicopathological characteristics of breast ductal carcinomas in situ (DCIS) with aldehyde dehydrogenase 1 (ALDH1)-positive cancer stem cells (CSCs). Methods: DCIS (n = 194) were subjected to immunohistochemical staining and results were examined for associations with various clinicopathological parameters. The ALDEFLUOR assay for breast cancer cell lines was also performed to determine the proportion of CSCs according to intrinsic subtype. Results: DCIS with ALDH1-positive CSCs were significantly (p < 0.05) more likely to be estrogen receptor-α (ER)-negative, progesterone receptor (PgR)-negative, Ki67-positive and HER2-positive tumors. Luminal A subtype (8.6%) showed a significantly (p < 0.001) lower ALDH1 positivity than the other subtypes [luminal B (50.0%), luminal HER2 (36.8%), HER2 (35.3%) and triple-negative subtype (26.7%)]. Double immunostaining revealed that ALDH1-positive CSCs did not overlap with ER-, PgR- or Ki67-positive tumor cells but did overlap with HER2-positive tumor cells. The percentage of ALDEFLUOR-positive CSCs was lower in the luminal A cell lines (0.02% for T-47D and 0.4% for MCF7) than in the luminal HER2 (9.1% for BT-474 and 9.5% for MDA-MB-361), HER2 (13.9% for AU565 and 33.2% for SK-BR-3) and triple-negative cell lines (28.4% for MDA-MB-231 and 30.7% for MDA-MB-468). Conclusions: Our results suggest that most CSCs in DCIS are in the G0 phase (Ki67 negative) and do not express ER or PgR, but they do express HER2 in HER2-positive tumors.
Genome-Wide Association Study Identifies 8 Novel Loci Associated With Blood Pressure Responses to Interventions in Han Chinese
Authors: He Jiang , Kelly Tanika N. , Zhao Qi , Li Hongfan , Huang Jianfeng , Wang Laiyuan , Jaquish Cashell E. , Sung Yun Ju , Shimmin Lawrence C. , Lu Fanghong , Mu Jianjun , Hu Dongsheng , Ji Xu , Shen Chong , Guo Dongshuang , Ma Jixiang , Wang Renping , Shen Jinjin , Li Shengxu , Chen Jing , Mei Hao , Chen Chung-Shiuan , Chen Shufeng , Chen Jichun , Li Jianxin , Cao Jie , Lu Xiangfeng , Wu Xigui , Rice Treva K. , Gu C. Charles , Schwander Karen , Hamm L. Lee , Liu Depei , Rao Dabeeru C. , Hixson James E. , Gu Dongfeng
Published: October 2013

Background—

Blood pressure (BP) responses to dietary sodium and potassium intervention and cold pressor test vary considerably among individuals. We aimed to identify novel genetic variants influencing individuals’ BP responses to dietary intervention and cold pressor test.

Methods and Results—

We conducted a genome-wide association study of BP responses in 1881 Han Chinese and de novo genotyped top findings in 698 Han Chinese. Diet-feeding study included a 7-day low-sodium (51.3 mmol/d), a 7-day high-sodium (307.8 mmol/d), and a 7-day high-sodium plus potassium supplementation (60 mmol/d). Nine BP measurements were obtained during baseline observation and each intervention period. The meta-analyses identified 8 novel loci for BP phenotypes, which physically mapped in or near
PRMT6
(
P
=7.29×10
–9
),
CDCA7
(
P
=3.57×10
–8
),
PIBF1
(
P
=1.78×10
–9
),
ARL4C
(
P
=1.86×10
–8
),
IRAK1BP1
(
P
=1.44×10
−10
),
SALL1
(
P
=7.01×10
–13
),
TRPM8
(
P
=2.68×10
–8
), and
FBXL13
(
P
=3.74×10
–9
). There was a strong dose–response relationship between the number of risk alleles of these independent single-nucleotide polymorphisms and the risk of developing hypertension during the 7.5-year follow-up in the study participants. Compared with those in the lowest quartile of risk alleles, odds ratios (95% confidence intervals) for those in the second, third, and fourth quartiles were 1.39 (0.97, 1.99), 1.72 (1.19, 2.47), and 1.84 (1.29, 2.62), respectively (
P
=0.0003 for trend).

Conclusions—

Our study identified 8 novel loci for BP responses to dietary sodium and potassium intervention and cold pressor test. The effect size of these novel loci on BP phenotypes is much larger than those reported by the previously published studies. Furthermore, these variants predict the risk of developing hypertension among individuals with normal BP at baseline.
New Gestational Phase–Specific Cutoff Values for the Use of the Soluble fms-Like Tyrosine Kinase-1/Placental Growth Factor Ratio as a Diagnostic Test for Preeclampsia
Authors: Verlohren Stefan , Herraiz Ignacio , Lapaire Olav , Schlembach Dietmar , Zeisler Harald , Calda Pavel , Sabria Joan , Markfeld-Erol Filiz , Galindo Alberto , Schoofs Katharina , Denk Barbara , Stepan Holger
Published: October 2013

To establish gestational phase adapted cutoffs for the use of the soluble fms-like tyrosine kinase-1 (sFlt-1)/placental growth factor (PlGF) ratio as a diagnostic tool for preeclampsia in the clinical setting, a multicenter case–control study including a total of 1149 patients was performed. We report normal values of sFlt-1, PlGF, and the sFlt-1/PlGF ratio based on the analysis of a total of 877 patients with uneventful pregnancy outcome. A total of 234 patients with preeclampsia and a matched cohort consisting of 468 patients with normal pregnancy outcome were compared, and sFlt-1 and PlGF were measured on an automated platform. Separate cutoffs for the sFlt-1/PlGF ratio were determined for the early (20+0–33+6 weeks) and the late gestational phase (34+0 weeks–delivery). For each of the 2 gestational phases, 2 independent cutoffs framing an equivocal zone were determined: the first cutoff with focus on high sensitivity, and the second focusing on high specificity. Between 20+0 and 33+6 weeks, the cutoffs at ≤33 and ≥85 resulted in a sensitivity/specificity of 95%/94% and 88%/99.5%, respectively. An sFlt-1/PlGF ratio of ≤33 had the lowest likelihood of a negative test (0.05; 95% confidence interval, 0.02–0.13), whereas values ≥85 had the highest likelihood of a positive test (176; 95% confidence interval, 24.88–1245). After 34+0 weeks, the cutoffs at ≤33 and ≥110 yielded a sensitivity/specificity of 89.6%/73.1% and 58.2%/95.5%, respectively. The approach to use multiple cutoffs for the early and late gestational phase enhances the diagnostic accuracy of the sFlt-1/PlGF ratio as a diagnostic tool for preeclampsia.
Growth in Percutaneous Coronary Intervention Capacity Relative to Population and Disease Prevalence
Authors: Langabeer James R. , Henry Timothy D. , Kereiakes Dean J. , DelliFraine Jami , Emert Jamie , Wang Zheng , Stuart Leilani , King Richard , Segrest Wendy , Moyer Peter , Jollis James G.
Published: October 2013

Background

The access to and growth of percutaneous coronary intervention (
PCI
) has not been fully explored with regard to geographic equity and need. Economic factors and timely access to primary
PCI
provide the impetus for growth in
PCI
centers, and this is balanced by volume standards and the benefits of regionalized care.

Methods and Results

Geospatial and statistical analyses were used to model capacity, growth, and access of
PCI
hospitals relative to population density and myocardial infarction (
MI
) prevalence at the state level. Longitudinal data were obtained for 2003–2011 from the
A
merican
H
ospital
A
ssociation, the
U
.
S
. Census, and the
C
enters for
D
isease
C
ontrol and
P
revention (CDC) with geographical modeling to map
PCI
locations. The number of
PCI
centers has grown 21.2% over the last 8 years, with 39% of all hospitals having interventional cardiology capabilities. During the same time, the
US
population has grown 8.3%, from 217 million to 235 million, and
MI
prevalence rates have decreased from 4.0% to 3.7%. The most densely concentrated states have a ratio of 8.1 to 12.1
PCI
facilities per million of population with significant variability in both
MI
prevalence and average distance between
PCI
facilities.

Conclusions

Over the last decade, the growth rate for
PCI
centers is 1.5× that of the population growth, while
MI
prevalence is decreasing. This has created geographic imbalances and access barriers with excess
PCI
centers relative to need in some regions and inadequate access in others.
Cerebrospinal Fluid τ Protein in Differential Diagnosis of Alzheimer’s Disease and Vascular Dementia in Chinese population
Authors: Liu Bo , Tang Yulan , Shen Yuefei , Cen Luan , Han Min
Published: October 2013

Background:

To assess whether biomarker τ protein could differentiate between Alzheimer’s disease (AD) and vascular dementia (VaD).

Methods:

We conducted a comprehensive search to identify studies on τ protein, patients with AD, and patients with VaD. Cerebrospinal fluid (CSF) τ protein levels were compared to discriminate among patients with AD, healthy controls, and patients with VaD by a meta-analysis.

Results:

Patients with AD exhibit significantly higher CSF τ protein levels than healthy controls or patients with VaD in the Chinese population.

Conclusion:

Our findings suggested that CSF τ protein levels were found to be significantly associated with AD in the Chinese population. Measurement of τ protein could help in attenuating the strict distinction between AD and VaD.
Molecular epidemiology of Orientia tsutsugamushi in chiggers and ticks from domestic rodents in Shandong, northern China
Authors: Zhang Meng , Zhao Zhong-Tang , Yang Hui-Li , Zhang Ai-Hua , Xu Xing-Qu , Meng Xiang-Peng , Zhang Hai-Yu , Wang Xian-Jun , Li Zhong , Ding Shu-Jun , Yang Li , Zhang Lu-Yan
Published: October 2013

Background

Scrub typhus is endemic to a 13,000,000-km2 area of the Asia-Pacific region, and causes an annual incidence of 1 million people. The mortality rate of scrub typhus ranges from 6.1% to 25% in Southeast Asia. Natural infection of Orientia tsutsugamushi has been identified in domestic rodents in Shandong Province. However, infestation of chiggers and ticks on the domestic rodents and prevalence and genotypes of O. tsutsugamushi in these Acarina remain unclear.

Methods

During September 2010 to March 2012, 3134 chiggers and 89 ticks were collected from domestic rodents captured in three counties of Shandong Province. We amplified and sequenced the 56-kDa type-specific antigen gene of O. tsutsugamushi from DNA samples of these Acarina and designated to genotype according to sequence analysis.

Results

Overall, the infestation rate of chiggers on domestic rodents was 17.0%, and the chigger index was 5.38. The infestation rate of ticks on rodents was 3.1%. Natural infection of O. tsutsugamushi was found in Leptotrombidium taishanicum, L. linhuaikongense, L. intermedium, L. scutellare, L. palpale, and Ixodes spp., the minimum positive rates of which were 5.9%, 3.2%, 1.2%, 0.8%, 0.8%, and 2.2%, respectively. Kawasaki-like genotypes were predominant in chiggers and ticks on domestic rodents, which were detected from L. taishanicum, L. intermedium, L. scutellare, L. palpale, and Ixodes spp. Shimokoshi-like genotype was detected from L. palpale.

Conclusions

In the present study we investigated the infestation of chiggers and ticks on domestic rodents in Shandong Province, and identified the prevalence and genotypes of O. tsutsugamushi in the Acarina. Infestation of vector chiggers in domestic rodents, prevalence of O. tsutsugamushi in infested chiggers, and high nucleotide homologies among the O. tsutsugamushi sequences from the Acarina, their animal hosts and scrub typhus patients, implied that domestic rodents may play an important role in the transmission of scrub typhus in Shandong, China. Further studies are needed to verify the vector significance of chiggers and ticks that tested positive for O. tsutsugamushi, and to assess the risk of human exposure to chiggers and ticks on domestic rodents.
The metabolic phenotype of rodent sepsis: cause for concern?
Authors: Zolfaghari Parjam S , Pinto Bernardo Bollen , Dyson Alex , Singer Mervyn
Published: October 2013

Purpose

Rodent models of sepsis are frequently used to investigate pathophysiological mechanisms and to evaluate putative therapeutic strategies. However, preclinical efficacy in these models has failed to translate to the clinical setting. We thus questioned the representativeness of such models and herein report a detailed comparison of the metabolic and cardiovascular phenotypes of long-term faecal peritonitis in fluid-resuscitated rats and mice with similar mortality profiles.

Methods

We conducted prospective laboratory-controlled studies in adult male Wistar rats and C57 black mice. Animals were made septic by intraperitoneal injection of faecal slurry. Rats received continuous intravenous fluid resuscitation, whereas mice received intermittent fluid boluses subcutaneously. Sham-treated animals served as controls. Survival was assessed over 72 h. In separate studies, whole body metabolism (O2 consumption, CO2 production) was measured over 24 h with echocardiography performed at early (6 h) and established (24 h) phases of sepsis. Blood gas analysis was performed at 6 h (rats) and 24 h (rats, mice).

Results

Similar survival curves were seen in both rodent models with approximately 75% mortality at 72 h. In mice, sepsis caused severity-dependent falls in core temperature and global metabolism. Oxygen consumption in severely septic mice fell by 38% within 2 h, and 80% at 22 h compared with baseline values. This was only partially restored by external warming. By contrast, septic rats maintained core temperature; only severely affected animals showed a pre-mortem decline in oxygen consumption. Significant myocardial dysfunction was seen in mice during early and established sepsis, whereas peak velocity and other hemodynamic variables in rats were similar at 6 h and significantly worse by 24 h in severely septic animals only.

Conclusions

Markedly differing metabolic and cardiovascular profiles were seen in long-term fluid-resuscitated rat and mouse models of bacterial sepsis despite similar mortality. The mouse model, in particular, does not represent the human condition. We urge caution in applying findings in murine models to septic patients, both with regard to our understanding of pathophysiology and the failure to translate preclinical efficacy into successful clinical trials.
Isolation of AMP-activated protein kinase (AMPK) alleles required for neuronal maintenance in Drosophila melanogaster
Authors: Swick Lance L. , Kazgan Nevzat , Onyenwoke Rob U. , Brenman Jay E.
Published: October 2013

The maintenance of energetic homeostasis in the face of limited available nutrients is a complex problem faced by all organisms. One important mechanism to maintain energetic homeostasis involves the activation of the energy sensor AMP-activated protein kinase (AMPK). AMPK is a cell-autonomous energy sensor that is highly sensitive to and regulated by the ATP to ADP and ATP to AMP ratios. However, the genetic analysis of AMPK signaling in vertebrates has been complicated by the existence of multiple redundant AMPK subunits. Here, we describe the identification of mutations in the single Drosophila melanogaster AMPK catalytic subunit (AMPKα) and their implications for neural maintenance and integrity. This article provides a citation replacement for previously published ampkα alleles, transgenes and neuronal phenotypes, which remain accurate; however, they were used in a previously published study that has subsequently been retracted (Mirouse et al., 2013).
The First-Order Approach to Merger Analysis
Authors: Jaffe Sonia , Weyl E. Glen
Published: October 2013

Using information local to the premerger equilibrium, we derive approximations of the expected changes in prices and welfare generated by a merger. We extend the pricing pressure approach of recent work to allow for non-Bertrand conduct, adjusting the diversion ratio and incorporating the change in anticipated accommodation. To convert pricing pressures into quantitative estimates of price changes, we multiply them by the merger pass-through matrix, which (under conditions we specify) is approximated by the premerger rate at which cost increases are passed through to prices. Weighting the price changes by quantities gives the change in consumer surplus. (JEL D43, G34, L11, L13)
Meirihluti og margræði. Ríkisstjórnarmyndanir 1939-1959
Authors: Óskarsdóttir Stefanía
Published: October 2013

Á Íslandi þróaðist það fyrirkomulag að ríkisstjórnir eru jafnan samsteypustjórnir með tryggan þingmeirihluta á bak við sig. Í nágrannaríkjum okkar, Danmörku, Svíþjóð og Noregi, urðu minnihlutastjórnir hins vegar algengasta ríkisstjórnarformið. Hér réð úrslitum skipulag kjördæma- og flokkakerfisins, staða þings gagnvart ríkisstjórn/framkvæmdarvaldi og skipulag samskipta aðila vinnumarkaðarins. Þar sem samráðskerfi á vinnumarkaði var ekki fyrir hendi fyrr en síðar, og opinber afskipti af efnahagslífinu voru mikil, hvíldi sú ábyrgð á íslenskum ríkisstjórnum að reyna að hafa einhliða hemil á verðbólgu og halda uppi atvinnu í efnahagsumhverfi sem oft einkenndist af þenslu á vinnumarkaði, tíðum verkfallsátökum og skammlífum kjarasamningum. Ríkisstjórnir urðu að styðjast við góðan þingmeirihluta því þær þurftu að hafa pólitískt bolmagn til að fylgja eftir aðgerðum sem voru oft og tíðum óvinsælar en voru eigi að síður taldar óhjákvæmilegar til að tryggja samkeppnisstöðu útflutningsgreinanna. Þetta sýnir saga ríkisstjórnamyndanna á árunum 1939-1959. Ríkisstjórnir á þessu tímabili urðu hins vegar skammlífar þar sem oft urðu átök á milli stjórnarflokka um nauðsyn og útfærslu efnahagsaðgerða. Íslenskt stjórnkerfi mótaðist því ekki síður af efnahagslegum veruleika en pólitískum aðstæðum.
Stjórnsækni og stefnufesta
Authors: Kristinsson Gunnar Helgi , Indriðason Indriði H.
Published: October 2013

Í þessari grein er tekist á við spurninguna um hlutfallslegt vægi stjórnsækni og stefnufestu hjá íslenskum stjórnmálaflokkum. Við myndun samsteypustjórna þurfa flokkar oft að meta kosti þess að komast í stjórnaraðstöðu á móti því að gefa eftir einhver stefnumál sín. Rannsóknir benda til þess að íslenskir stjórnmálaflokkar séu fremur stjórnsæknir og setji það tiltölulega lítið fyrir sig að gefa eftir stefnumál sín. Þrjár tilgátur eru settar fram um það í greininni hvaða afleiðingar þetta hefur fyrir íslensk stjórnmál: Í fyrsta lagi að íslenskir stjórnmálaflokkar hafi tilhneigingu til að mynda lágmarks sigursamsteypur og myndi síður minnihlutastjórnir eða stjórnir með aukaflokka innanborðs en flokkar í nálægum ríkjum, í öðru lagi að stjórnarsáttmálar séu styttri en í öðrum ríkjum og í þriðja lagi að skipting ráðuneyta sé tiltölulega hagstæð smærri stjórnarflokkum vegna harðrar samkeppni um að komast í stjórnaraðstöðu. Tilgáturnar fá í meginatriðum stuðning af gögnum sem skoðuð voru að undanskilinni annarri tilgátunni. Þótt stjórnarsáttmálar séu afar stuttir á Íslandi er ekki almennt samband á milli stjórnsækni og lengdar stjórnarsáttmála af því tagi sem tilgátan gerir ráð fyrir, í þeim löndum sem samanburðargögn eru til um. Á hinn bóginn kemur í ljós að þar sem stjórnarsáttmálar eru stuttir hafa forsætisráðherrar þess meiri völd. Á Íslandi fara hins vegar saman valdalitlir forsætisráðherrar og stuttir stjórnarsáttmálar, sem samrýmist vel hugmyndum um stjórnsækni íslenskra stjórnmálaflokka.
Prionic diseases
Authors: Araujo Abelardo Q-C
Published: October 2013

Prion diseases are neurodegenerative illnesses due to the accumulation of small infectious pathogens containing protein but apparently lacking nucleic acid, which have long incubation periods and progress inexorably once clinical symptoms appear. Prions are uniquely resistant to a number of normal decontaminating procedures. The prionopathies [Kuru, Creutzfeldt-Jakob disease (CJD) and its variants, Gerstmann-Sträussler-Scheinker (GSS) syndrome and fatal familial insomnia (FFI)] result from accumulation of abnormal isoforms of the prion protein in the brains of normal animals on both neuronal and non-neuronal cells. The accumulation of this protein or fragments of it in neurons leads to apoptosis and cell death. There is a strong link between mutations in the gene encoding the normal prion protein in humans (PRNP) - located on the short arm of chromosome 20 – and forms of prion disease with a familial predisposition (familial CJD, GSS, FFI). Clinically a prionopathy should be suspected in any case of a fast progressing dementia with ataxia, myoclonus, or in individuals with pathological insomnia associated with dysautonomia. Magnetic resonance imaging, identification of the 14-3-3 protein in the cerebrospinal fluid, tonsil biopsy and genetic studies have been used for in vivo diagnosis circumventing the need of brain biopsy. Histopathology, however, remains the only conclusive method to reach a confident diagnosis. Unfortunately, despite numerous treatment efforts, prionopathies remain short-lasting and fatal diseases.
Continuous Glucose Monitoring Systems: A Review
Authors: Vashist Sandeep
Published: October 2013

There have been continuous advances in the field of glucose monitoring during the last four decades, which have led to the development of highly evolved blood glucose meters, non-invasive glucose monitoring (NGM) devices and continuous glucose monitoring systems (CGMS). Glucose monitoring is an integral part of diabetes management, and the maintenance of physiological blood glucose concentration is the only way for a diabetic to avoid life-threatening diabetic complications. CGMS have led to tremendous improvements in diabetic management, as shown by the significant lowering of glycated hemoglobin (HbA1c) in adults with type I diabetes. Most of the CGMS have been minimally-invasive, although the more recent ones are based on NGM techniques. This manuscript reviews the advances in CGMS for diabetes management along with the future prospects and the challenges involved.
Why vouchers matter in botanical research
Authors: Culley Theresa M.
Published: October 2013

What is a voucher and why is it important in research? As a preserved specimen of an identified taxon deposited in a permanent and accessible storage facility, the voucher serves as the supporting material for published studies of the taxon and ensures that the science is repeatable. Vouchers are crucial in authenticating the taxonomy of an organism, as a tool for identifying localities of the taxon, and for additional taxonomic, genetic, ecological, and/or environmental research.
Adequacy of fine-needle aspiration specimens for human papillomavirus infection molecular testing in head and neck squamous cell carcinoma
Authors: Lastra Ricardo R. , Pramick Michelle R. , Nakashima Megan O. , Weinstein Gregory S. , Montone Kathleen T. , LiVolsi Virginia A. , Baloch Zubair W.
Published: October 2013

Background:

Head and neck squamous cell carcinoma is often associated with human papillomavirus (HPV) infection. Positive HPV status has been associated with increased response to treatment and improved prognosis in terms of recurrence-free and overall survival. In certain instances, diagnosis is performed through fine-needle aspiration of lymph nodes with metastatic carcinoma, often demonstrating extensive tumor necrosis. We evaluated the effect of tumor necrosis on deoxyribonucleic acid (DNA) adequacy for HPV molecular testing.

Materials and Methods:

Retrospective review of the pathology files at our institution identified cases of squamous cell carcinoma (SCC) diagnosed by fine-needle aspiration (FNA) on which HPV DNA molecular testing was performed. The cases were classified according to percent tumor necrosis into three categories (<10% necrosis, 10-70% necrosis and >70% necrosis) and the percentage of cases with adequate HPV DNA for molecular testing in each of the categories was compared. When available, p16 immunohistochemistry performed on the cases was compared with HPV status by molecular testing.

Results:

A total of 70 cases from 67 patients were included in the study. Adequate DNA for molecular HPV testing was obtained from samples of 47 cases (67%) while samples from 23 cases (33%) were inadequate for molecular testing. Of the adequate samples, 36 (77%) were positive and 11 (23%) were negative for high-risk HPV. Adequate DNA for testing was obtained in 22 out of 33 cases showing no necrosis (67%), 10 out of 16 cases showing partial necrosis (63%) and in 13 out of 17 cases showing extensive necrosis (76%).

Conclusion:

Our study found that HPV molecular testing is not influenced by percent tumor necrosis or method by which FNA was performed. We believe that a portion of the FNA specimen obtained from head and neck lesions diagnosed as SCC during the rapid on-site evaluation should be sent for HPV DNA testing, independent of the amount of tumor necrosis, thus guaranteeing availability of specimen for HPV testing.
Sulfur dioxide (SO2) as observed by MIPAS/Envisat: temporal development and spatial distribution at 15–45 km altitude
Authors: Höpfner M. , Glatthor N. , Grabowski U. , Kellmann S. , Kiefer M. , Linden A. , Orphal J. , Stiller G. , von Clarmann T. , Funke B. , Boone C. D.
Published: October 2013

Abstract. We present a climatology of monthly and 10° zonal mean profiles of sulfur dioxide (SO2) volume mixing ratios (vmr) derived from MIPAS/Envisat measurements in the altitude range 15–45 km from July 2002 until April 2012. The vertical resolution varies from 3.5–4 km in the lower stratosphere up to 6–10 km at the upper end of the profiles, with estimated total errors of 5–20 pptv for single profiles of SO2. Comparisons with the few available observations of SO2 up to high altitudes from ATMOS for a volcanically perturbed situation from ACE-FTS and, at the lowest altitudes, with stratospheric in situ observations reveal general consistency of the datasets. The observations are the first empirical confirmation of features of the stratospheric SO2 distribution, which have only been shown by models up to now: (1) the local maximum of SO2 at around 25–30 km altitude, which is explained by the conversion of carbonyl sulfide (COS) as the precursor of the Junge layer; and (2) the downwelling of SO2-rich air to altitudes of 25–30 km at high latitudes during winter and its subsequent depletion on availability of sunlight. This has been proposed as the reason for the sudden appearance of enhanced concentrations of condensation nuclei during Arctic and Antarctic spring. Further, the strong increase of SO2 to values of 80–100 pptv in the upper stratosphere through photolysis of H2SO4 has been confirmed. Lower stratospheric variability of SO2 could mainly be explained by volcanic activity, and no hints of a strong anthropogenic influence have been found. Regression analysis revealed a QBO (quasi-biennial oscillation) signal of the SO2 time series in the tropics at about 30–35 km, an SAO (semi-annual oscillation) signal at tropical and subtropical latitudes above 32 km and annual periodics predominantly at high latitudes. Further, the analysis indicates a correlation with the solar cycle in the tropics and southern subtropics above 30 km. Significant negative linear trends are found in the tropical lower stratosphere, probably due to reduced tropical volcanic activity and at southern mid-latitudes above 35 km. A positive trend is visible in the lower and middle stratosphere at polar to subtropical southern latitudes.
Aerosol optical depth assimilation for a size-resolved sectional model: impacts of observationally constrained, multi-wavelength and fine mode retrievals on regional scale analyses and forecasts
Authors: Saide P. E. , Carmichael G. R. , Liu Z. , Schwartz C. S. , Lin H. C. , da Silva A. M. , Hyer E.
Published: October 2013

Abstract. An aerosol optical depth (AOD) three-dimensional variational data assimilation technique is developed for the Gridpoint Statistical Interpolation (GSI) system for which WRF-Chem forecasts are performed with a detailed sectional model, the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC). Within GSI, forward AOD and adjoint sensitivities are performed using Mie computations from the WRF-Chem optical properties module, providing consistency with the forecast. GSI tools such as recursive filters and weak constraints are used to provide correlation within aerosol size bins and upper and lower bounds for the optimization. The system is used to perform assimilation experiments with fine vertical structure and no data thinning or re-gridding on a 12 km horizontal grid over the region of California, USA, where improvements on analyses and forecasts is demonstrated. A first set of simulations was performed, comparing the assimilation impacts of using the operational MODIS (Moderate Resolution Imaging Spectroradiometer) dark target retrievals to those using observationally constrained ones, i.e., calibrated with AERONET (Aerosol RObotic NETwork) data. It was found that using the observationally constrained retrievals produced the best results when evaluated against ground based monitors, with the error in PM2.5 predictions reduced at over 90% of the stations and AOD errors reduced at 100% of the monitors, along with larger overall error reductions when grouping all sites. A second set of experiments reveals that the use of fine mode fraction AOD and ocean multi-wavelength retrievals can improve the representation of the aerosol size distribution, while assimilating only 550 nm AOD retrievals produces no or at times degraded impact. While assimilation of multi-wavelength AOD shows positive impacts on all analyses performed, future work is needed to generate observationally constrained multi-wavelength retrievals, which when assimilated will generate size distributions more consistent with AERONET data and will provide better aerosol estimates.
Laboratory and field measurements of enantiomeric monoterpene emissions as a function of chemotype, light and temperature
Authors: Song W. , Staudt M. , Bourgeois I. , Williams J.
Published: October 2013

Abstract. Plants emit significant amounts of monoterpenes into the Earth's atmosphere where they react rapidly to form a multitude of gas phase species and particles. Many monoterpenes exist in mirror images forms or enantiomers. In this study the enantiomeric monoterpene profile for several representative plants (Quercus ilex L., Rosmarinus officinalis L., and Pinus halepensis Mill.) was investigated as a function of chemotype, light and temperature both in the laboratory and in the field. Analysis of enantiomeric monoterpenes from 19 Quercus ilex individuals from Southern France and Spain revealed four regiospecific chemotypes (genetically fixed emission patterns). In agreement with previous work, only Quercus ilex emissions increased strongly with light. However, for all three plant species no consistent enantiomeric variation was observed as a function of light, and the enantiomeric ratio of α-pinene was found vary by less than 20% from 100 and 1000 μmol m–2 s–1 PAR. The rate of monoterpene emission increased with temperature from all three plant species, but little variation in the enantiomeric distribution of α-pinene was observed with temperature. There was more enantiomeric variability between individuals of the same species than could be induced by either light or temperature. Field measurements of α-pinene enantiomer mixing ratios in the air taken at a Quercus ilex forest in Southern France, and several other previously reported field enantiomeric ratio diel cycle profiles are compared. All show smoothly varying diel cycles (some positive and some negative) even over changing wind directions. This is surprising in comparison with variations of enantiomeric emission patterns shown by individuals of the same species.
Development of two-moment cloud microphysics for liquid and ice within the NASA Goddard earth observing system model (GEOS-5)
Authors: Barahona D. , Molod A. , Bacmeister J. , Nenes A. , Gettelman A. , Morrison H. , Phillips V. , Eichmann A.
Published: October 2013

Abstract. This work presents the development of a two-moment cloud microphysics scheme within the version 5 of the NASA Goddard Earth Observing System (GEOS-5). The scheme includes the implementation of a comprehensive stratiform microphysics module, a new cloud coverage scheme that allows ice supersaturation and a new microphysics module embedded within the moist convection parameterization of GEOS-5. Comprehensive physically-based descriptions of ice nucleation, including homogeneous and heterogeneous freezing, and liquid droplet activation are implemented to describe the formation of cloud particles in stratiform clouds and convective cumulus. The effect of preexisting ice crystals on the formation of cirrus clouds is also accounted for. A new parameterization of the subgrid scale vertical velocity distribution accounting for turbulence and gravity wave motion is developed. The implementation of the new microphysics significantly improves the representation of liquid water and ice in GEOS-5. Evaluation of the model shows agreement of the simulated droplet and ice crystal effective and volumetric radius with satellite retrievals and in situ observations. The simulated global distribution of supersaturation is also in agreement with observations. It was found that when using the new microphysics the fraction of condensate that remains as liquid follows a sigmoidal increase with temperature which differs from the linear increase assumed in most models and is in better agreement with available observations. The performance of the new microphysics in reproducing the observed total cloud fraction, longwave and shortwave cloud forcing, and total precipitation is similar to the operational version of GEOS-5 and in agreement with satellite retrievals. However the new microphysics tends to underestimate the coverage of persistent low level stratocumulus. Sensitivity studies showed that the simulated cloud properties are robust to moderate variation in cloud microphysical parameters. However significant sensitivity in ice cloud properties was found to variation in the dispersion of the ice crystal size distribution and the critical size for ice autoconversion. The implementation of the new microphysics leads to a more realistic representation of cloud processes in GEOS-5 and allows the linkage of cloud properties to aerosol emissions.
The influence of conceptual model structure on model performance: a comparative study for 237 French catchments
Authors: van Esse W. R. , Perrin C. , Booij M. J. , Augustijn D. C. M. , Fenicia F. , Kavetski D. , Lobligeois F.
Published: October 2013

Abstract. Models with a fixed structure are widely used in hydrological studies and operational applications. For various reasons, these models do not always perform well. As an alternative, flexible modelling approaches allow the identification and refinement of the model structure as part of the modelling process. In this study, twelve different conceptual model structures from the SUPERFLEX framework are compared with the fixed model structure GR4H, using a large set of 237 French catchments and discharge-based performance metrics. The results show that, in general, the flexible approach performs better than the fixed approach. However, the flexible approach has a higher chance of inconsistent results when calibrated on two different periods. When analysing the subset of 116 catchments where the two approaches produce consistent performance over multiple time periods, their average performance relative to each other is almost equivalent. From the point of view of developing a well-performing fixed model structure, the findings favour models with parallel reservoirs and a power function to describe the reservoir outflow. In general, conceptual hydrological models perform better on larger and/or wetter catchments than on smaller and/or drier catchments. The model structures performed poorly when there were large climatic differences between the calibration and validation periods, in catchments with flashy flows, and in catchments with unexplained variations in low flow measurements.
Development of a method of robust rain gauge network optimization based on intensity-duration-frequency results
Authors: Chebbi A. , Bargaoui Z. K. , da Conceição Cunha M.
Published: October 2013

Abstract. Based on rainfall intensity-duration-frequency (IDF) curves, fitted in several locations of a given area, a robust optimization approach is proposed to identify the best locations to install new rain gauges. The advantage of robust optimization is that the resulting design solutions yield networks which behave acceptably under hydrological variability. Robust optimization can overcome the problem of selecting representative rainfall events when building the optimization process. This paper reports an original approach based on Montana IDF model parameters. The latter are assumed to be geostatistical variables, and their spatial interdependence is taken into account through the adoption of cross-variograms in the kriging process. The problem of optimally locating a fixed number of new monitoring stations based on an existing rain gauge network is addressed. The objective function is based on the mean spatial kriging variance and rainfall variogram structure using a variance-reduction method. Hydrological variability was taken into account by considering and implementing several return periods to define the robust objective function. Variance minimization is performed using a simulated annealing algorithm. In addition, knowledge of the time horizon is needed for the computation of the robust objective function. A short- and a long-term horizon were studied, and optimal networks are identified for each. The method developed is applied to north Tunisia (area = 21 000 km2). Data inputs for the variogram analysis were IDF curves provided by the hydrological bureau and available for 14 tipping bucket type rain gauges. The recording period was from 1962 to 2001, depending on the station. The study concerns an imaginary network augmentation based on the network configuration in 1973, which is a very significant year in Tunisia because there was an exceptional regional flood event in March 1973. This network consisted of 13 stations and did not meet World Meteorological Organization (WMO) recommendations for the minimum spatial density. Therefore, it is proposed to augment it by 25, 50, 100 and 160% virtually, which is the rate that would meet WMO requirements. Results suggest that for a given augmentation robust networks remain stable overall for the two time horizons.
A controlled‐source seismic and gravity study of the High Lava Plains (HLP) of Eastern Oregon
Authors: Cox Catherine , Keller G. Randy , Harder Steven H.
Published: October 2013

This study employs data collected during the High Lava Plains (HLP) controlled‐source seismic experiment conducted in September 2008. In this experiment, 2612 short‐period seismic recorders and 120 3‐component recorders were deployed across eastern Oregon and adjacent parts of Nevada and Idaho to record 15 seismic sources. Seismic and gravity data were integrated to create 2‐D crustal scale P‐wave velocity and density models for the ∼400 km long NW‐SE and N‐S profiles to provide a better understanding of the crustal and upper mantle structure and ultimately the magmatic and tectonic evolution of the region. These models are the first high‐resolution images beneath the path of migratory, bi‐modal volcanism that dotted the High Lava Plains beginning at 16 Ma. Our models show that the crustal structure across the HLP region is similar to that of the northern Basin and Range which has experienced extension since ∼35 Ma but with moderate magmatic modification of the crust. A thick layer (5–7 km) of sediments and volcanics extends over most of the area and is thickest in the Harney Basin area. We interpret denser/faster material in the lower to middle crust under the southern Harney Basin area to be mafic intraplating. We have also identified a region of denser/faster material in the upper crust in the vicinity of Oregon‐Idaho border. The crust thickens from 34 to 37 km, and the lower crust increases in density (2.8–2.85 g/cm3), from west to east across eastern Oregon in close proximity to the interpreted position of the 0.706 Sr isotope line, suggesting a decrease in extension. In the lowermost crust below the southeastern HLP, there is relatively high velocity (7.2–7.4 km/s) and density (2.95 g/cm3) that suggests the presence of underplating. The HLP region has undergone moderate extension, and the average crustal velocity is somewhat higher than in the adjacent Basin and Range, suggesting some magmatic modification in the lower crust, but not as much as might be expected given the voluminous surface volcanism.
Thermal evolution of the North Atlantic lithosphere: New constraints from magnetic anomaly inversion with a fractal magnetization model
Authors: Li Chun‐Feng , Wang Jian , Lin Jian , Wang Tingting
Published: October 2013

Using recently published global magnetic models, we present the first independent constraint on North Atlantic geothermal state and mantle dynamics from magnetic anomaly inversion with a fractal magnetization model. Two theoretical models of radial amplitude spectrum of magnetic anomalies are found almost identical, and both are applicable to detecting Curie depths in using the centroid method based on spectral linearization at certain wave number bands. Theoretical and numerical studies confirm the robustness of this inversion scheme. A fractal exponent of 3.0 in the magnetic susceptibility is found suitable, and Curie depths are well constrained by their known depths near the mid‐Atlantic ridge. While generally increasing with growing ages, North Atlantic Curie depths show large oscillating and heterogeneous patterns related most likely to small‐scale sublithospheric convections, which are found to have an onset time around 40 Ma and a scale of about 500 km, and are in preferred transverse rolls. Hotspots in North Atlantic also contribute to large geothermal and Curie‐depth variations, but they appear to connect more closely to geochemical anomalies or small‐scale convection than to mantle plumes. Curie depths can be correlated to heat flow gridded in a constant 1° interval, which reveals decreasing effective thermal conductivity with depths within the magnetic layer. North Atlantic Curie points are mostly beneath the Moho, suggesting that the uppermost mantle is magnetized from serpentinization and induces long‐wavelength magnetic anomalies. Small‐scale convection and serpentinization together may cause apparent flattening and deviations in heat flow and bathymetry from theoretical cooling models in old oceanic lithosphere.
Velocity‐porosity relationships in smectite‐rich sediments: Shikoku Basin, Japan
Authors: Tudge Joanne , Tobin Harold J.
Published: October 2013

At the Nankai Trough, Japan, smectite‐rich sediments of the Shikoku Basin are both underthrust beneath and frontally accreted to the outer accretionary wedge. To understand the changes that occur in the physical properties of sediments as they are underthrust or incorporated into the accretionary wedge, it is necessary to characterize those physical properties outboard of the deformation front. One key relationship to constrain is between the compressional wave velocity (vp) and porosity (ϕ) in order to estimate pore fluid pressure and determine the strength of fault rocks at depth. Here we investigate how the type of clay minerals and proportions of the different clays may affect the velocity‐porosity relationship, with particular emphasis on the abundance of hydrous smectitic clays. Using data from IODP Sites C0011 and C0012 in the Shikoku Basin, we demonstrate that when the core‐based porosity is corrected for the abundance of smectite, the resultant velocity‐porosity relationship does not fit previously established transforms. Therefore, we propose a new empirical relationship for the smectite‐rich sediments of the Shikoku Basin, and caution against the indiscriminate use of global and/or pre‐existing models in smectite rich formations.
Vertical transport mechanisms of black carbon over East Asia in spring during the A‐FORCE aircraft campaign
Authors: Oshima N. , Koike M. , Kondo Y. , Nakamura H. , Moteki N. , Matsui H. , Takegawa N. , Kita K.
Published: October 2013

Mechanisms of vertical transport of black carbon (BC) aerosols and their three‐dimensional transport pathways over East Asia in spring were examined through numerical simulations for the Aerosol Radiative Forcing in East Asia (A‐FORCE) aircraft campaign in March–April 2009 using a modified version of the Community Multiscale Air Quality (CMAQ) modeling system. The simulations reproduced the spatial distributions of mass concentration of BC and its transport efficiency observed by the A‐FORCE campaign reasonably well, including its vertical and latitudinal gradients and dependency on precipitation amount that air parcels experienced during the transport. During the A‐FORCE period, two types of pronounced upward BC mass fluxes from the planetary boundary layer (PBL) to the free troposphere were found over northeastern and inland‐southern China. Over northeastern China, cyclones with modest precipitation were the primary uplifting mechanism of BC. Over inland‐southern China, both cumulus convection and orographic uplifting along the slopes of the Tibetan Plateau played important roles in the upward transport of BC, despite its efficient wet deposition due to a large amount of precipitation supported by an abundant moisture supply by the low‐level southerlies. In addition to the midlatitude (35–45°N) eastward outflow within the PBL (21% BC removal by precipitation during transport), the uplifting of BC over northeastern and inland‐southern China and the subsequent BC transport by the midlatitude lower tropospheric (50% BC removal) and subtropical (25–35°N) midtropospheric westerlies (67% BC removal), respectively, provided the major transport pathways for BC export from continental East Asia to the Pacific.