bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cytosolic carbonic anhydrase molecular switch occurs in the gills of metamorphic sea lamprey
Authors: Ferreira-Martins D. , McCormick S. D. , Campos A. , Lopes-Marques M. , Osório H. , Coimbra J. , Castro L. F. C. , Wilson J. M. 
Published: October 2016

AbstractCarbonic anhydrase plays a key role in CO2 transport, acid-base and ion regulation and metabolic processes in vertebrates. While several carbonic anhydrase isoforms have been identified in numerous vertebrate species, basal lineages such as the cyclostomes have remained largely unexamined. Here we investigate the repertoire of cytoplasmic carbonic anhydrases in the sea lamprey (Petromyzon marinus), that has a complex life history marked by a dramatic metamorphosis from a benthic filter-feeding ammocoete larvae into a parasitic juvenile which migrates from freshwater to seawater. We have identified a novel carbonic anhydrase gene (ca19) beyond the single carbonic anhydrase gene (ca18) that was known previously. Phylogenetic analysis and synteny studies suggest that both carbonic anhydrase genes form one or two independent gene lineages and are most likely duplicates retained uniquely in cyclostomes. Quantitative PCR of ca19 and ca18 and protein expression in gill across metamorphosis show that the ca19 levels are highest in ammocoetes and decrease during metamorphosis while ca18 shows the opposite pattern with the highest levels in post-metamorphic juveniles. We propose that a unique molecular switch occurs during lamprey metamorphosis resulting in distinct gill carbonic anhydrases reflecting the contrasting life modes and habitats of these life-history stages.
A key process controlling the wet removal of aerosols: new observational evidence
Authors: Ohata Sho , Moteki Nobuhiro , Mori Tatsuhiro , Koike Makoto , Kondo Yutaka 
Published: October 2016

AbstractThe lifetime and spatial distributions of accumulation-mode aerosols in a size range of approximately 0.05–1 μm and thus their global and regional climate impacts, are primarily constrained by their removal via cloud and precipitation (wet removal). However, the microphysical process that predominantly controls the removal efficiency remains unidentified because of observational difficulties. Here, we demonstrate that the activation of aerosols to cloud droplets (nucleation scavenging) predominantly controls the wet removal efficiency of accumulation-mode aerosols, using water-insoluble black carbon as an observable particle tracer during the removal process. From simultaneous ground-based observations of black carbon in air (prior to removal) and in rainwater (after removal) in Tokyo, Japan, we found that the wet removal efficiency depends strongly on particle size and the size dependence can be explained quantitatively by the observed size-dependent cloud-nucleating ability. Furthermore, our observational method provides an estimate of the effective supersaturation of water vapour in precipitating cloud clusters, a key parameter controlling nucleation scavenging. These novel data firmly indicate the importance of quantitative numerical simulations of the nucleation scavenging process to improve the model’s ability to predict the atmospheric aerosol burden and the resultant climate forcings and enable a new validation of such simulations.
The antenna of horse stomach bot flies: morphology and phylogenetic implications (Oestridae, Gasterophilinae: Gasterophilus Leach)
Authors: Zhang Dong , Li Xinyu , Liu Xianhui , Wang Qike , Pape Thomas 
Published: October 2016

AbstractAntennae are among the most elaborate sensory organs in adult flies, and they provide rich information for phylogenic studies. The antennae of five out of eight species of Gasterophilus Leach (G. haemorrhoidalis (Linnaeus), G. intestinalis (De Geer), G. nasalis (Linnaeus), G. nigricornis (Loew) and G. pecorum (Fabricius)), were examined using scanning electron microscopy. The general morphology, including distribution, type, size, and ultrastructure of antennal sensilla were presented, and the definition of auriculate sensilla and sensory pits were updated and clarified. Eighteen antennal characters were selected to construct the first species-level phylogeny of this genus. The monophyly of Gasterophilus was supported by the presence of coeloconic sensilla III on the antennal arista. The species-level cladogram showed G. pecorum branching off at the base, and the remaining species forming the topology (G. intestinalis+ (G. haemorrhoidalis+ (G. nasalis+ G. nigricornis))). Our research shows the importance of the antennal ultrastructure as a reliable source for phylogenetic analysis.
Deficiency in Toll-interacting protein (Tollip) skews inflamed yet incompetent innate leukocytes in vivo during DSS-induced septic colitis
Authors: Diao Na , Zhang Yao , Chen Keqiang , Yuan Ruoxi , Lee Christina , Geng Shuo , Kowalski Elizabeth , Guo Wen , Xiong Huabao , Li Mingsong , Li Liwu 
Published: October 2016

AbstractFunctionally compromised neutrophils contribute to adverse clinical outcomes in patients with severe inflammation and injury such as colitis and sepsis. However, the ontogeny of dysfunctional neutrophil during septic colitis remain poorly understood. We report that the dysfunctional neutrophil may be derived by the suppression of Toll-interacting-protein (Tollip). We observed that Tollip deficient neutrophils had compromised migratory capacity toward bacterial product fMLF due to reduced activity of AKT and reduction of FPR2, reduced potential to generate bacterial-killing neutrophil extra-cellular trap (NET), and compromised bacterial killing activity. On the other hand, Tollip deficient neutrophils had elevated levels of CCR5, responsible for their homing to sterile inflamed tissues. The inflamed and incompetent neutrophil phenotype was also observed in vivo in Tollip deficient mice subjected to DSS-induced colitis. We observed that TUDCA, a compound capable of restoring Tollip cellular function, can potently alleviate the severity of DSS-induced colitis. In humans, we observed significantly reduced Tollip levels in peripheral blood collected from human colitis patients as compared to blood samples from healthy donors. Collectively, our data reveal a novel mechanism in Tollip alteration that underlies the inflamed and incompetent polarization of neutrophils leading to severe outcomes of colitis.
Directional and monochromatic thermal emitter from epsilon-near-zero conditions in semiconductor hyperbolic metamaterials
Authors: Campione Salvatore , Marquier Francois , Hugonin Jean-Paul , Ellis A. Robert , Klem John F. , Sinclair Michael B. , Luk Ting S. 
Published: October 2016

AbstractThe development of novel thermal sources that control the emission spectrum and the angular emission pattern is of fundamental importance. In this paper, we investigate the thermal emission properties of semiconductor hyperbolic metamaterials (SHMs). Our structure does not require the use of any periodic corrugation to provide monochromatic and directional emission properties. We show that these properties arise because of epsilon-near-zero conditions in SHMs. The thermal emission is dominated by the epsilon-near-zero effect in the doped quantum wells composing the SHM. Furthermore, different properties are observed for s and p polarizations, following the characteristics of the strong anisotropy of hyperbolic metamaterials.
Feature Subset Selection for Cancer Classification Using Weight Local Modularity
Authors: Zhao Guodong , Wu Yan 
Published: October 2016

AbstractMicroarray is recently becoming an important tool for profiling the global gene expression patterns of tissues. Gene selection is a popular technology for cancer classification that aims to identify a small number of informative genes from thousands of genes that may contribute to the occurrence of cancers to obtain a high predictive accuracy. This technique has been extensively studied in recent years. This study develops a novel feature selection (FS) method for gene subset selection by utilizing the Weight Local Modularity (WLM) in a complex network, called the WLMGS. In the proposed method, the discriminative power of gene subset is evaluated by using the weight local modularity of a weighted sample graph in the gene subset where the intra-class distance is small and the inter-class distance is large. A higher local modularity of the gene subset corresponds to a greater discriminative of the gene subset. With the use of forward search strategy, a more informative gene subset as a group can be selected for the classification process. Computational experiments show that the proposed algorithm can select a small subset of the predictive gene as a group while preserving classification accuracy.
Gallic acid prevents isoproterenol-induced cardiac hypertrophy and fibrosis through regulation of JNK2 signaling and Smad3 binding activity
Authors: Ryu Yuhee , Jin Li , Kee Hae Jin , Piao Zhe Hao , Cho Jae Yeong , Kim Gwi Ran , Choi Sin Young , Lin Ming Quan , Jeong Myung Ho 
Published: October 2016

AbstractGallic acid, a type of phenolic acid, has been shown to have beneficial effects in inflammation, vascular calcification, and metabolic diseases. The present study was aimed at determining the effect and regulatory mechanism of gallic acid in cardiac hypertrophy and fibrosis. Cardiac hypertrophy was induced by isoproterenol (ISP) in mice and primary neonatal cardiomyocytes. Gallic acid pretreatment attenuated concentric cardiac hypertrophy. It downregulated the expression of atrial natriuretic peptide, brain natriuretic peptide, and beta-myosin heavy chain in vivo and in vitro. Moreover, it prevented interstitial collagen deposition and expression of fibrosis-associated genes. Upregulation of collagen type I by Smad3 overexpression was observed in cardiac myoblast H9c2 cells but not in cardiac fibroblasts. Gallic acid reduced the DNA binding activity of phosphorylated Smad3 in Smad binding sites of collagen type I promoter in rat cardiac fibroblasts. Furthermore, it decreased the ISP-induced phosphorylation of c-Jun N-terminal kinase (JNK) and extracellular signal regulated kinase (ERK) protein in mice. JNK2 overexpression reduced collagen type I and Smad3 expression as well as GATA4 expression in H9c2 cells and cardiac fibroblasts. Gallic acid might be a novel therapeutic agent for the prevention of cardiac hypertrophy and fibrosis by regulating the JNK2 and Smad3 signaling pathway.
Are Scores Reliable in Predicting the Need for Surgery and Mortality in Necrotizing Enterocolitis?
Authors: Arni Delphine , Karam Oliver , Vidal Isabelle , Rimensberger Peter , Hanquinet Sylviane , Wildhaber Barbara 
Published: October 2016

Background Management of children with necrotizing enterocolitis (NEC) remains challenging. Various scores try to facilitate therapeutic decision-making. We aim to assess the agreement of three scores intending to predict the need for surgery and/or mortality in our patient cohort, and analyze agreement between the different scores.
Methods This study is a retrospective analysis of patients with NEC Bell's stage II and III, managed in a single institution (1991–2011). Three existing scores (Metabolic Derangement Acuity score, NEC score, Detroit score) were calculated individually for each patient. The agreement between predicted outcome by scores and real outcome was evaluated with kappa statistic.
Results Of 57 children, 46% presented with NEC stage II, 54% with stage III, 46% were treated with surgery, 54% conservatively, and survival was 58%. The kappa indexes for “need for surgery” were 0.41, 0.13, and 0.12 and kappa indexes for “mortality” were 0.27, 0.04, and 0.1 for the Metabolic Derangement Acuity score, the NEC score, and the Detroit score, respectively.
Conclusion In our cohort, the agreement between the predicted outcomes by scores and the real need for surgery and/or mortality was poor. There was a lack of clinical usefulness of the tested scores. We must continue to better identify parameters to help guide the management of these patients.
Isotopic overprinting of nitrification on denitrification as a ubiquitous and unifying feature of environmental nitrogen cycling
Authors: Granger Julie , Wankel Scott D. 
Published: October 2016

Significance
Stable isotopes of nitrate have long provided a tool for tracking environmental sources and biological transformations. However, divergent interpretations of fundamental nitrate isotope systematics exist among disciplinary divisions. In an effort to transcend disciplinary boundaries of terrestrial and marine biogeochemistry, we use a quantitative model for coupled nitrogen and oxygen isotopes of nitrate founded on benchmarks established from microbial cultures, to reconcile decades of nitrate isotopic measurements in freshwater and seawater and move toward a unified understanding of cycling processes and isotope systematics. Our findings indicate that denitrification operates within the pervasive context of nitrite reoxidation mechanisms, specifically highlighting the relative importance of nitrification in marine denitrifying systems and anammox in groundwater aquifers.
Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression
Authors: Roy Bijoyita , Friesen Westley J. , Tomizawa Yuki , Leszyk John D. , Zhuo Jin , Johnson Briana , Dakka Jumana , Trotta Christopher R. , Xue Xiaojiao , Mutyam Venkateshwar , Keeling Kim M. , Mobley James A. , Rowe Steven M. , Bedwell David M. , Welch Ellen M. , Jacobson Allan 
Published: October 2016

Significance
The drug ataluren restores activity to otherwise nonfunctional nonsense alleles, a capability possibly reflecting the insertion of near-cognate aminoacyl tRNAs at premature termination codons during protein synthesis. Because nonsense alleles comprise a significant fraction of all alleles causing inherited disorders, drugs that promote such nonsense codon readthrough have broad therapeutic potential. However, the effectiveness of therapeutic nonsense suppression depends on the nature of the amino acids inserted at each of the three nonsense codons. Here we demonstrate that ataluren does indeed promote insertion of near-cognate tRNAs at nonsense codons, that the latter process yields functional proteins, and that specific codon:anticodon base pairings are critical to this process. These results should enable predictions of better clinical outcomes with therapeutic nonsense suppression.
Predictability and hierarchy in
Drosophila
behavior
Authors: Berman Gordon J. , Bialek William , Shaevitz Joshua W. 
Published: October 2016

Significance
How an animal chooses to order its activities—moving, grooming, resting, and so on—is essential to its ability to survive, adapt, and reproduce. Here we investigate the temporal pattern of behaviors performed by fruit flies, finding that their movements are organized in a hierarchical manner that exhibits long time scales. This organization is likely advantageous for adaptability and ease of neural representation and provides hints as to the form of the fly’s internal representations of behavioral programs.
Hypoxia-activated cytotoxic agent tirapazamine enhances hepatic artery ligation-induced killing of liver tumor in HBx transgenic mice
Authors: Lin Wei-Hsiang , Yeh Shiou-Hwei , Yeh Kun-Huei , Chen Kai-Wei , Cheng Ya-Wen , Su Tung-Hung , Jao Ping , Ni Lin-Chun , Chen Pei-Jer , Chen Ding-Shinn 
Published: October 2016

Significance
The development of more effective arterial embolization therapy is one of the major challenges of hepatocellular carcinoma (HCC). We showed that the addition of tirapazamine, a cytotoxic agent that can be activated by sublethal hypoxia, greatly improved the efficacy of arterial embolization in killing HCC developed in hepatitis B virus X protein transgenic mice. Nearly complete tumor necrosis was identified in most HCCs shortly after combination treatment. This preclinical study showed that the combination of tirapazamine and arterial embolization is a regimen that improved the liver tumor-killing activity, but spared the normal hepatocytes. These results form the basis for the ongoing clinical phase I trial to determine whether this treatment can be an effective therapy for intermediate stage HCC.
The safety and tolerability of inhaled treprostinil in patients with pulmonary hypertension and chronic obstructive pulmonary disease
Authors: Bajwa Abubakr A. , Shujaat Adil , Patel Minal , Thomas Colleen , Rahaghi Franck , Burger Charles D. 
Published: October 2016

The primary aim was to explore the safety and tolerability of inhaled treprostinil when used in patients with pulmonary hypertension (PH) with concomitant chronic obstructive pulmonary disease (COPD). Patients with a diagnosis of pre‐capillary PH (defined as pulmonary artery mean pressure of ≥ 25 mmHg and pulmonary artery wedge pressure or left ventricular end diastolic pressure of ≤ 15 mmHg) who were being initiated on inhaled treprostinil and had concomitant COPD (defined as FEV1/FVC ratio ≤ 70% with FEV1 ≥ 40% predicted) were considered for inclusion in this pilot study. Assessments included adverse events, physical exam, World Health Organization (WHO) functional class, 6‐minute walk test (6MWT), modified Borg dyspnea score, and concomitant medication. At baseline and week 16 St. George’s Respiratory Questionnaire (SGRQ), arterial blood gas (ABG), and pulmonary function test (PFT) were assessed. The median age was 65 years (age range, 56–80 years) and five patients (56%) were men. Among the nine patients, a majority had an increase in 6MWT from baseline to week 16 (median change, 19 m). Only three of the nine patients (33%) had an increase in A‐a gradient at week 16 (median change, –7). There was no difference in any of the following: arterial blood gases, WHO functional class, 6MWT results, or SGRQ scores from baseline to week 16. There was a statistically significant decline in several of the PFT measures, including FEV1 (median change, –0.18 L; P = 0.004; median change, –7% of predicted; P = 0.016), FVC (median change, –0.23 L; P = 0.027), and diffusion capacity for carbon monoxide (DLCO) (median change, –5% of predicted; P = 0.023). The small number of patients limits firm conclusions; however, inhaled treprostinil did not seem to adversely impact oxygenation in the majority of the study patients with pre‐capillary PH and COPD. While there may have an adverse impact on some pulmonary function parameters, the clinical significance is unclear.
Sleep to Lower Elevated Blood Pressure: A Randomized Controlled Trial (SLEPT)
Authors: McGrath Emer R. , Espie Colin A. , Power Alice , Murphy Andrew W. , Newell John , Kelly Caroline , Duffy Niamh , Gunning Patricia , Gibson Irene , Bostock Sophie , O’Donnell Martin J. 
Published: October 2016

Abstract

BACKGROUND
Impaired sleep quality is common and associated with an increased risk of cardiovascular disease (CVD), thought to be mediated through adverse effects on established vascular risk factors, particularly hypertension. We determined if a web-delivered sleep intervention (sleep–hygiene education, stimulus control, and cognitive behavioral therapy) reduces blood pressure compared to vascular risk factor education (standard care) alone.

METHODS
Phase II randomized, blinded, controlled trial of 134 participants without CVD with mild sleep impairment and blood pressure 130–160/&lt;110 mm Hg. The primary outcome was the difference in the mean change in 24-hour ambulatory systolic blood pressure (SBP) over 8 weeks between intervention and control groups. Secondary outcomes included measures of sleep quality and psychosocial health, namely Insomnia Severity Index (ISI), Pittsburgh Sleep Quality Index (PSQI), Beck Depression Inventory (BDI), and Beck Anxiety Inventory (BAI).

RESULTS
Participants in the sleep intervention group showed significantly greater improvements in sleep quality, including ISI [difference in mean improvement 2.8; 95% confidence interval (CI), 1.3–4.4], PSQI (1.1; 95% CI, 0.1–2.2), sleep condition indicator (0.8; 95% CI, 0.2–1.4), and psychosocial health, including BDI (2.0; 95% CI, 0.3–3.7) and BAI (1.4; 95% CI, 0.02–2.8). The mean improvement in 24-hour ambulatory SBP did not differ between the sleep intervention (0.9 mm Hg) and control (0.8 mm Hg) arms, (difference in mean improvement 0.1; 95% CI, −3.4 to 3.2).

CONCLUSION
A simple, low-cost, web-delivered sleep intervention is feasible and significantly improves sleep quality and measures of psychosocial health in individuals with mild sleep impairment but does not result in short-term improvements in blood pressure.
Greatest Challenges of Rectal Cancer Survivors: Results of a Population-Based Survey
Authors: McMullen Carmit K. , Bulkley Joanna E. , Altschuler Andrea , Wendel Christopher S. , Grant Marcia , Hornbrook Mark C. , Sun Virginia , Krouse Robert S. 
Published: October 2016

BACKGROUND:
Eliciting the priorities of cancer survivors is essential to address the specific needs of cancer survivor subgroups.

OBJECTIVE:
The purpose of this study was to describe the greatest challenges related to treatment for long-term rectal cancer survivors.

DESIGN:
This was an observational study with a cross-sectional survey.

SETTINGS:
The study included members of Kaiser Permanente Northern California and Northwest health plans.

PATIENTS:
A survey was mailed to long-term (≥5 years postdiagnosis) survivors of rectal cancer who had an anastomosis, temporary ostomy, or permanent ostomy.

MAIN OUTCOME MEASURES:
The main outcome was measured with an open-ended question about the greatest challenge related to cancer surgery. We categorized responses using a grounded theory approach with double coding for reliability. Bonferroni-adjusted χ2 values were used to assess differences in the proportions of subgroups who mentioned challenges within each response category.

RESULTS:
The survey completion rate was 61% (577/953); 76% (440/577) of participants responded to the greatest challenge question. The greatest challenges for respondents were bowel/ostomy management (reported by 44%), negative psychosocial effects (37%), late effects of treatment (21%), comorbidities and aging (13%), postoperative recovery (5%), and negative healthcare experiences (5%). Survivors with temporary ostomy or anastomosis were more likely than survivors with permanent ostomy to report late effects (p < 0.0001 and p = 0.01). Survivors with anastomosis were less likely than survivors with permanent ostomy to report negative psychosocial impacts (p = 0.0001).

LIMITATIONS:
Generalizability is restricted by the lack of ethnically and racially diverse, uninsured (non-Medicare–eligible population), and non-English–speaking participants. Because the survey was cross-sectional and included respondents at different times since diagnosis, we could not adequately address changes in the greatest challenges over time.

CONCLUSIONS:
Our results reveal the need for bowel/ostomy management, psychosocial services, and surveillance for late effects in survivorship and supportive care services for all survivors of rectal cancer, regardless of ostomy status. The perspective of long-term survivors with anastomosis reveals challenges that may not be anticipated during decision making for treatment (see Video, Supplemental Digital Content 1, http://links.lww.com/DCR/A254).