bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphoinositide 3-kinase-δ regulates fungus-induced allergic lung inflammation through endoplasmic reticulum stress
Authors: Lee Kyung Sun , Jeong Jae Seok , Kim So Ri , Cho Seong Ho , Kolliputi Narasaiah , Ko Yun Hee , Lee Kyung Bae , Park Suk Chul , Park Hae Jin , Lee Yong Chul 
Published: November 2015

BackgroundSensitisation with Aspergillus fumigatus (Af) is known to be associated with severe allergic lung inflammation, but the mechanism remains to be clarified. Phosphoinositide 3-kinase (PI3K)-δ and endoplasmic reticulum (ER) stress are suggested to be involved in steroid-resistant lung inflammation. We aimed to elucidate the role of PI3K-δ and its relationship with ER stress in fungus-induced allergic lung inflammation.MethodsUsing Af-exposed in vivo and in vitro experimental systems, we examined whether PI3K-δ regulates ER stress, thereby contributing to steroid resistance in fungus-induced allergic lung inflammation. Moreover, we checked expression of an ER stress marker in lung tissues isolated from patients with allergic bronchopulmonary aspergillosis.ResultsAf-exposed mice showed that ER stress markers, unfolded protein response (UPR)-related proteins, phosphorylated Akt, generation of mitochondrial reactive oxygen species (mtROS), eosinophilic allergic inflammation, and airway hyperresponsiveness (AHR) were increased in the lung. Similarly, glucose-regulated protein 78 was increased in lung tissues of patients with ABPA. A PI3K-δ inhibitor reduced Af-induced increases in ER stress markers, UPR-related proteins, allergic inflammation and AHR in mice. However, dexamethasone failed to reduce Af-induced allergic inflammation, AHR and elevation of ER stress. Administration of an ER stress inhibitor or a mtROS scavenger improved Af-induced allergic inflammation. The PI3K-δ inhibitor reduced Af-induced mtROS generation and the mtROS scavenger ameliorated ER stress. In primary cultured tracheal epithelial cells, Af-induced ER stress was inhibited by blockade of PI3K-δ.ConclusionsThese findings suggest that PI3K-δ regulates Af-induced steroid-resistant eosinophilic allergic lung inflammation through ER stress.
Jumping Grammars
Authors: Křivka Zbyněk , Meduna Alexander 
Published: November 2015

This paper introduces and studies jumping grammars, which represent a grammatical counterpart to the recently introduced jumping automata. These grammars are conceptualized just like classical grammars except that during the applications of their productions, they can jump over symbols in either direction within the rewritten strings. More precisely, a jumping grammar rewrites a string z according to a rule x → y in such a way that it selects an occurrence of x in z, erases it, and inserts y anywhere in the rewritten string, so this insertion may occur at a different position than the erasure of x. The paper concentrates its attention on investigating the generative power of jumping grammars. More specifically, it compares this power with that of jumping automata and that of classical grammars. A special attention is paid to various context-free versions of jumping grammars, such as regular, right-linear, linear, and context-free grammars of finite index. In addition, we study the semilinearity of context-free, context-sensitive, and monotonous jumping grammars. We also demonstrate that the general versions of jumping grammars characterize the family of recursively enumerable languages. In its conclusion, the paper formulates several open problems and suggests future investigation areas.
Naturally Occurring Isothiocyanates Exert Anticancer Effects by Inhibiting Deubiquitinating Enzymes
Authors: Lawson Ann P. , Long Marcus J.C. , Coffey Rory T. , Qian Yu , Weerapana Eranthie , El Oualid Farid , Hedstrom Lizbeth 
Published: November 2015

Abstract
The anticancer properties of cruciferous vegetables are well known and attributed to an abundance of isothiocyanates such as benzyl isothiocyanate (BITC) and phenethyl isothiocyanate (PEITC). While many potential targets of isothiocyanates have been proposed, a full understanding of the mechanisms underlying their anticancer activity has remained elusive. Here we report that BITC and PEITC effectively inhibit deubiquitinating enzymes (DUB), including the enzymes USP9x and UCH37, which are associated with tumorigenesis, at physiologically relevant concentrations and time scales. USP9x protects the antiapoptotic protein Mcl-1 from degradation, and cells dependent on Mcl-1 were especially sensitive to BITC and PEITC. These isothiocyanates increased Mcl-1 ubiquitination and either isothiocyanate treatment, or RNAi-mediated silencing of USP9x decreased Mcl-1 levels, consistent with the notion that USP9x is a primary target of isothiocyanate activity. These isothiocyanates also increased ubiquitination of the oncogenic fusion protein Bcr-Abl, resulting in degradation under low isothiocyanate concentrations and aggregation under high isothiocyanate concentrations. USP9x inhibition paralleled the decrease in Bcr-Abl levels induced by isothiocyanate treatment, and USP9x silencing was sufficient to decrease Bcr-Abl levels, further suggesting that Bcr-Abl is a USP9x substrate. Overall, our findings suggest that USP9x targeting is critical to the mechanism underpinning the well-established anticancer activity of isothiocyanate. We propose that the isothiocyanate-induced inhibition of DUBs may also explain how isothiocyanates affect inflammatory and DNA repair processes, thus offering a unifying theme in understanding the function and useful application of isothiocyanates to treat cancer as well as a variety of other pathologic conditions. Cancer Res; 75(23); 5130–42. ©2015 AACR.
DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer
Authors: Nygård Sune Boris , Vainer Ben , Nielsen Signe Lykke , Bosman Fred , Tejpar Sabine , Roth Arnaud , Delorenzi Mauro , Brünner Nils , Budinska Eva 
Published: November 2015

Abstract
Purpose: Prospective–retrospective assessment of the TOP1 gene copy number and TOP1 mRNA expression as predictive biomarkers for adjuvant irinotecan in stage II/III colon cancer.
Experimental Design: Formalin-fixed, paraffin-embedded tissue microarrays were obtained from an adjuvant colon cancer trial (PETACC3) where patients were randomized to 5-fluorouracil/folinic acid with or without additional irinotecan. TOP1 copy number status was analyzed by fluorescence in situ hybridization (FISH) using a TOP1/CEN20 dual-probe combination. TOP1 mRNA data were available from previous analyses.
Results: TOP1 FISH and follow-up data were obtained from 534 patients. TOP1 gain was identified in 27% using a single-probe enumeration strategy (≥4 TOP1 signals per cell) and in 31% when defined by a TOP1/CEN20 ratio ≥ 1.5. The effect of additional irinotecan was not dependent on TOP1 FISH status. TOP1 mRNA data were available from 580 patients with stage III disease. Benefit of irinotecan was restricted to patients characterized by TOP1 mRNA expression ≥ third quartile (RFS: HRadjusted, 0.59; P = 0.09; OS: HRadjusted, 0.44; P = 0.03). The treatment by TOP1 mRNA interaction was not statistically significant, but in exploratory multivariable fractional polynomial interaction analysis, increasing TOP1 mRNA values appeared to be associated with increasing benefit of irinotecan.
Conclusions: In contrast to the TOP1 copy number, a trend was demonstrated for a predictive property of TOP1 mRNA expression. On the basis of TOP1 mRNA, it might be possible to identify a subgroup of patients where an irinotecan doublet is a clinically relevant option in the adjuvant setting of colon cancer. Clin Cancer Res; 22(7); 1621–31. ©2015 AACR.
Novel Pathways of Apolipoprotein A-I Metabolism in High-Density Lipoprotein of Different Sizes in Humans
Authors: Mendivil Carlos O. , Furtado Jeremy , Morton Allyson M. , Wang Liyun , Sacks Frank M. 
Published: November 2015

Objective—
A prevailing concept is that high-density lipoprotein (HDL) is secreted into the systemic circulation as a small mainly discoidal particle, which expands progressively and becomes spherical by uptake and esterification of cellular cholesterol and then contracts by cholesterol ester delivery to the liver, a process known as reverse cholesterol transport, thought to be impaired in people with low HDL cholesterol (HDLc). This metabolic framework has not been established in humans.

Approach and Results—
We studied the metabolism of apolipoprotein A-I in 4 standard HDL sizes by endogenous isotopic labeling in 6 overweight adults with low HDLc and in 6 adults with normal body weight with high plasma HDLc. Contrary to expectation, HDL was secreted into the circulation in its entire size distribution from very small to very large similarly in both groups. Very small (prebeta) HDL comprised only 8% of total apolipoprotein A-I secretion. Each HDL subfraction circulated mostly within its secreted size range for 1 to 4 days and then was cleared. Enlargement of very small and medium to large and very large HDL and generation of very small from medium HDL were minor metabolic pathways. Prebeta HDL was cleared slower, whereas medium, large, and very large HDL were cleared faster in the low HDLc group.

Conclusions—
A new model is proposed from these results in which HDL is metabolized in plasma mainly within several discrete, stable sizes across the common range of HDLc concentrations.
Effect of Short-Term Steroid Therapy on Early Recurrence During the Blanking Period After Catheter Ablation of Atrial Fibrillation
Authors: Kim Yoo Ri , Nam Gi-Byoung , Han Seungbong , Kim Sung-Hwan , Kim Ki-Hun , Lee Sulhee , Kim Jun , Choi Kee-Joon , Kim You-Ho 
Published: November 2015

Background—
Early recurrence (ER) of atrial tachyarrhythmias during the first 3 months (blanking period) after atrial fibrillation ablation can be highly symptomatic, often requiring emergency treatment. Short-term steroid therapy may suppress ER during the blanking period.

Methods and Results—

We prospectively enrolled 138 patients who were randomly assigned to 2 groups (steroid group and control group). An intravenous bolus of 0.5 mg/kg of methylprednisolone for 2 days followed by 12 mg daily of oral methylprednisolone for 4 days was given to the steroid group patients. The primary end point was ER during the blanking period (3 months post ablation). During the blanking period, 51 of the 138 (37.0%) patients experienced ER after atrial fibrillation ablation. The steroid group had a lower rate of ER than the control group (15/64 [23.4%] versus 36/74 [48.6%],
P
=0.003). There was no difference between the 2 groups about late recurrence during a 24-month follow-up (log-rank test,
P
=0.918). In a multivariate analysis, short-term steroid therapy was independently associated with a lower rate of ER during the blanking period (adjusted OR, 0.45; 95% confidence interval, 0.25–0.83;
P
=0.01).

Conclusions—
Periprocedural short-term moderate intensity steroid therapy reduces ER (≈3 months) after catheter ablation of atrial fibrillation. It is not effective in preventing late (3≈24 m) atrial fibrillation recurrence.

Clinical Trial Registration—

URL:
www.who.int/ictrp
; Unique identifier: KCT0000107.
Time‐Course Analysis of Flow Mediated Dilation for the Evaluation of Endothelial Function After a High‐Fat Meal in African Americans
Authors: Marinos Alejandro , Celedonio Jorge E. , Ramirez Claudia E. , Gottlieb JoAnn , Gamboa Alfredo , Hui Nian , Yu Chang , Michael Stein C. , Biaggioni Italo , Shibao Cyndya A. 
Published: November 2015

Background

Flow‐mediated dilation (
FMD
) is used to assess endothelial function through changes in vascular diameter after hyperemia. High‐fat meal (
HFM
) has been shown to induce endothelial dysfunction; recent studies, however, reported conflicting results in obese African American women (
AAW
). Differences in the method used to analyze
FMD
may explain these discrepancies.

Methods and Results

In protocol 1, we assessed the time course of
FMD
and compared the repeatability of
FMD
using the individual maximum peak dilation (
FMD
peak
) and the dilation at 60 seconds (
FMD
60
). Sixteen
AAW
(age, 42±10.4 years; body mass index [
BMI],
39±5.8 kg/m
2
) were studied on 2 occasions, 4 weeks apart, under fasting conditions (study 1 and study 2). In protocol 2, we used the most repeatable measurement from protocol 1 to assess changes in endothelial function after an
HFM
in 17
AAW
(agen 42±11.1 years;
BMIn
38±5.6 kg/m
2
). We found that
FMD
peak
was the most repeatable measurement (N=16; study 1, 5.31±3.12% and study 2, 5.80±2.91%;
r
=0.94). After an
HFM
, the baseline brachial artery diameter significantly increased at 2 hours (0.10 mm; 95% confidence interval [
CI
], 0.01–0.18;
P
=0.03) and at 4 hours (0.17 mm; 95%
CI
, 0.09–0.25;
P
<0.001). At 2 hours, the
FMD
peak
decreased compared with pre‐
HFM
(−1.76; 95%
CI
, −3.55–0.02;
P≤
0.05).

Conclusions

The individual's maximum peak dilation after hyperemia is the most consistent measure to assess the effect of an
HFM
on endothelial function. Endothelial dysfunction occurred at 2 hours after an
HFM
in
AAW
.

Clinical Trial Registration

URL
:
https://clinicaltrials.gov/
Unique identifiers:
NCT
01334554 and
NCT
02126735.
Watch out or relax: conspecifics affect vigilance in wild spider monkeys (Ateles geoffroyi)
Authors: Busia Laura , Schaffner Colleen M. , Aureli Filippo 
Published: November 2015

In most animal species, predation risk is considered the main factor affecting vigilance, and an individual is expected to spend less time vigilant in larger than in smaller groups. However, vigilance patterns in primates appear to differ, with no consistency in group-size effects. As individuals in highly gregarious species such as diurnal primates face frequent threats from group members, there may be increased vigilance in larger groups to monitor conspecifics rather than or in addition to predators. We tested this hypothesis in wild spider monkeys, which live in communities but fission and fuse in subgroups of variable size and membership throughout the same day. We found no overall effect of subgroup size, as traditionally measured, on vigilance. However, a possible explanation is that vigilance may be effectively shared only with individuals in close proximity, rather than with all subgroup members. We found that a larger number of neighbours (i.e., subgroup members within 5 m) was associated with a lower proportion of time individuals spent vigilant, which is similar to findings in other studies. Another social factor that may affect individuals’ vigilance is the possibility of between-community encounters. Higher levels of vigilance can be expected in areas closer to the boundary of the home range, where between-community encounters are more likely to occur compared with non-boundary areas. We found that location in terms of boundary vs. non-boundary areas had a significant effect on the time individuals spent vigilant in the expected direction. We also found that location modulated the effect of subgroup size on vigilance: only in the boundary areas did larger subgroup sizes result in less individual vigilance time. We concluded that conspecifics affect vigilance of wild spider monkeys in multiple ways.
Molecular cloning, characterization, and immune response against white spot syndrome virus and Taura syndrome virus infections of peroxiredoxin in Litopenaeus vannamei and its antioxidant activity
Authors: Zeng Digang , Peng Min , Chen Xiuli , Yang Chunling , Chen Xiaohan , Li Yongmei , Zhao Yongzhen 
Published: November 2015

Peroxiredoxin (Prx) is an important peroxidase that can protect organisms against various oxidative stresses. In this study, a member of Prx family, designated LvPrx, was cloned fromLitopenaeus vannamei. Sequence and phylogenetic analyses indicated that LvPrx belongs to the 2-Cys Prx (Prx IV) isoform. The recombinant LvPrx protein was constructed and expressed inEscherichia coli, and the purified LvPrx proteins were shown to reduce H2O2in vitro in the presence of dithiothreitol, indicating that LvPrx is a functional peroxiredoxin. Using qRT-PCR, the mRNA expression levels of LvPrx were determined in the haemocytes ofL. vannameiat different stages after being challenged with WSSV and TSV at different doses. The results showed that the expression levels of LvPrx were significantly up-regulated () during 4-24 h after both WSSV and TSV challenge, suggesting that LvPrx may participate in the shrimp’s immune response to viral infection.
All Sonic Anemometers Need to Correct for Transducer and Structural Shadowing in Their Velocity Measurements
Authors: Frank John M. , Massman William J. , Swiatek Edward , Zimmerman Herb A. , Ewers Brent E. 
Published: November 2015

AbstractSonic anemometry is fundamental to all eddy-covariance studies of surface energy and ecosystem carbon and water balance. Recent studies have shown that some nonorthogonal anemometers underestimate vertical wind. Here it is hypothesized that this is due to a lack of transducer and structural shadowing correction. This is tested with a replicated intercomparison experiment between orthogonal (K-probe, Applied Technologies, Inc.) and nonorthogonal (A-probe, Applied Technologies, Inc.; and CSAT3 and CSAT3V, Campbell Scientific, Inc.) anemometer designs. For each of the 12 weeks, five randomly selected and located anemometers were mounted both vertically and horizontally. Bayesian analysis was used to test differences between half-hourly anemometer measurements of the standard deviation of wind (σu, συ, and σw) and temperature, turbulent kinetic energy (TKE), the ratio between vertical/horizontal TKE (VHTKE), and sensible heat flux (H). Datasets were analyzed with various applications of transducer shadow correction. Using the manufacturer’s current recommendations, orthogonal anemometers partitioned higher VHTKE and measured about 8%–9% higher σw and ~10% higher H. This difference can be mitigated by adding shadow correction to nonorthogonal anemometers. The horizontal manipulation challenged each anemometer to measure the three dimensions consistently, which allowed for testing two hypotheses explaining the underestimate in vertical wind. While measurements were essentially unchanged when the orthogonal anemometers were mounted sideways, the nonorthogonal anemometers changed substantially and confirmed the lack of shadow correction. Considering the ubiquity of nonorthogonal anemometers, these results are consequential across flux networks and could potentially explain half of the ~20% missing energy that is typical at most flux sites.
Diagnosing Model Errors from Time-Averaged Tendencies in the Weather Research and Forecasting (WRF) Model
Authors: Cavallo Steven M. , Berner Judith , Snyder Chris 
Published: November 2015

Abstract
Accurate predictions in numerical weather models depend on the ability to accurately represent physical processes across a wide range of scales. This paper evaluates the utility of model time tendencies, averaged over many forecasts at a given lead time, to diagnose systematic forecast biases in the Advanced Research version of the Weather Research and Forecasting (WRF) Model during the 2010 North Atlantic hurricane season using continuously cycled ensemble data assimilation (DA). Erroneously strong low-level heating originates from the planetary boundary layer parameterization as a consequence of using fixed sea surface temperatures, impacting the upward surface sensible heat fluxes. Warm temperature bias is observed with a magnitude 0.5 K in a deep tropospheric layer centered 700 hPa, originating primarily from the Kain–Fritsch convective parameterization.
This study is the first to diagnose systematic forecast bias in a limited-area mesoscale model using its forecast tendencies. Unlike global models where relatively fewer time steps typically encompass a DA cycling period, averaging all short-term forecast tendencies can require potentially large data. It is shown that 30-min averaging intervals can sufficiently represent the systematic model bias in this modeling configuration when initializing forecasts from an ensemble member that is generated using a DA system with an identical model configuration. However, the number of time steps before model error begins to dominate initial condition (IC) errors may vary between modeling configurations. Model and IC error are indistinguishable in short-term forecasts when initialized from the ensemble mean, a global analysis from a different model, and an ensemble member using a different parameterization.
Outcome of surgery in patients with solitary fibrous tumors of the pleura
Authors: Fattahi Masuom Seyed Hossein , Bagheri Reza , Sadrizadeh Ali , Nouri Dalouee Marziyeh , Taherian Ali , Rajaie Zahra 
Published: November 2015

Background Solitary fibrous tumor of the pleura is rare, and the origin is submesothelial tissue. These tumors are seen in lung infrequently, and most are benign. We report our experience in the diagnosis and treatment of patients with solitary fibrous tumors of the pleura. Methods We studied 13 patients (6 men and 7 women, aged 26 to 76 years) with a diagnosis of benign solitary fibrous tumor of the pleura who were operated on from 2001 to 2014. One had a recurrent tumor after 10 years, and the others had primary tumors. Our approach was complete resection in all cases. Results After surgical excision, the most essential characteristic on histopathology was a neoplastic lesion composed of spindle-shaped tumor cells with hyperchromatic nuclei and eosinophilic bands of collagen. On immunohistochemical analysis, the cells were positive for desmin and negative for actin, synaptophysin, chromogranin, and CD117. Conclusions The essential step in the treatment of a patient with a diagnosis of benign solitary fibrous tumor of the pleura is complete resection. These patients should be followed up for a long time because of the possibility of late recurrence. Due to the rarity of these tumors, there has been no systematic assessment of the role of adjuvant therapy for benign solitary fibrous tumor of the pleura.
Diffusion-weighted magnetic resonance imaging in the differentiation of endometriomas from hemorrhagic cysts in the ovary
Authors: Lee Nam Kyung , Kim Suk , Kim Ki Hyung , Suh Dong Soo , Kim Tae Un , Han Ga Jin , Lee Ji Won , Kim Jin You 
Published: November 2015

Background The classic magnetic resonance imaging (MRI) feature of endometriomas is the shading sign, which is characterized by T2-shortening in ovarian cystic lesions that are hyperintense on T1-weighted images. The shading sign is infrequently observed in hemorrhagic ovarian cysts. Purpose To investigate the value of MRI with diffusion-weighted imaging (DWI) for distinguishing endometriomas from hemorrhagic cysts in the ovary. Material and Methods This retrospective study included 91 patients with 98 ovarian endometriomas and 21 hemorrhagic ovarian cysts that were confirmed pathologically, who had undergone MRI with DWI. Two radiologists compared MRI features, including size, bilaterality, multilocularity, the shading sign, the ovarian lesion/muscle signal intensity ratio at T2-weighted images, and T2 dark spots, between endometriomas and hemorrhagic cysts. We also compared the mean ADC value between endometriomas and hemorrhagic cysts, and determined the optimal cutoff ADC value for differentiating endometriomas from hemorrhagic cysts. Results The size and mean ADC values were significantly different between endometriomas and hemorrhagic cysts. The mean ADC values of endometriomas and hemorrhagic cysts were 1.06 ± 0.38 × 10 −3 mm2/s and 0.73 ± 0.29 × 10−3 mm2/s, respectively ( P < 0.002). The optimal cutoff ADC value for differentiating endometriomas from hemorrhagic cysts was 0.849 × 10−3 mm2/s (sensitivity, 77.6%; specificity, 76.2%). Conclusion The addition of DWI could help in differentiating endometriomas from hemorrhagic cysts in the ovary, when conventional MRI is challenging.