bluuebunny/crossref_metadata_2025_split huggingface dataset:
8000-year monsoonal record from Himalaya revealing reinforcement of tropical and global climate systems since mid-Holocene
Authors: Srivastava Pradeep , Agnihotri Rajesh , Sharma Deepti , Meena Narendra , Sundriyal Y. P. , Saxena Anju , Bhushan Ravi , Sawlani R. , Banerji Upasana S. , Sharma C. , Bisht P. , Rana N. , Jayangondaperumal R. 
Published: October 2017

AbstractWe provide the first continuous Indian Summer Monsoon (ISM) climate record for the higher Himalayas (Kedarnath, India) by analyzing a 14C-dated peat sequence covering the last ~8000 years, with ~50 years temporal resolution. The ISM variability inferred using various proxies reveal striking similarity with the Greenland ice core (GISP2) temperature record and rapid denitrification changes recorded in the sediments off Peru. The Kedarnath record provides compelling evidence for a reorganization of the global climate system taking place at ~5.5 ka BP possibly after sea level stabilization and the advent of inter-annual climate variability governed by the modern ENSO phenomenon. The ISM record also captures warm-wet and cold-dry conditions during the Medieval Climate Anomaly and Little Ice Age, respectively.
Neuroprotective effect of Ruminococcus albus on oxidatively stressed SH-SY5Y cells and animals
Authors: Park Jieun , Lee Jiyun , Yeom Zia , Heo Donghyuk , Lim Young-Hee 
Published: October 2017

AbstractRecent evidence shows that the gut microbiota has an important role in gut-brain crosstalk and is linked to neuronal disorders. The aim of this study was to investigate the effects of intestinal Ruminococcus albus with probiotic potential on neuroprotection in oxidatively stressed SH-SY5Y neuroblastoma cells and animals. To investigate these effects, conditioned medium was prepared using Caco-2 cells cultured with heat-killed R. albus (CRA-CM). Caco-2 cells cultured with heat-killed R. albus showed increased BDNF expression and BDNF protein levels increased in CRA-CM. CRA-CM up-regulated the protein expression levels of SRF, C-fos and CDK2. In addition, CRA-CM protected SH-SY5Y cells from H2O2-induced cell death. CRA-CM significantly decreased the Bax/Bcl-2 ratio in oxidatively stressed SH-SY5Y cells. Animal experiments showed that oral administration of heat-killed R. albus for 15 days attenuated the oxidative stress induced by sodium arsenate. Treatment with heat-killed R. albus reduced the level of ROS, and the levels of SOD and GSH increased in oxidatively stressed brains. In conclusion, the secretome prepared from Caco-2 cells cultured with heat-killed R. albus might promote neuronal proliferation through the activation of cell proliferation-related proteins, and heat-killed R. albus protects neurons from oxidative damage by reducing ROS levels and increasing SOD and GSH levels.
Knockdown of amyloid precursor protein increases calcium levels in the endoplasmic reticulum
Authors: Gazda Kinga , Kuznicki Jacek , Wegierski Tomasz 
Published: October 2017

AbstractFamilial Alzheimer’s disease (AD) is caused by mutations in the genes that encode amyloid precursor protein (APP) and presenilins. Disturbances in calcium homeostasis have been observed in various cellular and animal models of AD and are proposed to underlie the pathogenesis of the disease. Furthermore, wildtype presenilins were shown to regulate endoplasmic reticulum (ER) calcium homeostasis, although their precise mechanism of action remains controversial. To investigate whether APP also affects ER calcium levels, we used RNA interference to target the APP gene in cultured T84 cells in combination with two types of ER calcium sensors. Using a genetically encoded calcium indicator, GEM-CEPIA1er, we found that APP-deficient cells exhibited elevated resting calcium levels in the ER and prolonged emptying of ER calcium stores upon the cyclopiazonic acid-induced inhibition of sarco-endoplasmic reticulum calcium-ATPase. These effects could be ascribed to lower ER calcium leakage rates. Consistent with these results, translocation of the endogenous ER calcium sensor STIM1 to its target channel Orai1 was delayed following ER calcium store depletion. Our data suggest a physiological function of APP in the regulation of ER calcium levels.
A robust single-beam optical trap for a gram-scale mechanical oscillator
Authors: Altin P. A. , Nguyen T. T.-H. , Slagmolen B. J. J. , Ward R. L. , Shaddock D. A. , McClelland D. E. 
Published: October 2017

AbstractPrecise optical control of microscopic particles has been mastered over the past three decades, with atoms, molecules and nano-particles now routinely trapped and cooled with extraordinary precision, enabling rapid progress in the study of quantum phenomena. Achieving the same level of control over macroscopic objects is expected to bring further advances in precision measurement, quantum information processing and fundamental tests of quantum mechanics. However, cavity optomechanical systems dominated by radiation pressure – so-called ‘optical springs’ – are inherently unstable due to the delayed dynamical response of the cavity. Here we demonstrate a fully stable, single-beam optical trap for a gram-scale mechanical oscillator. The interaction of radiation pressure with thermo-optic feedback generates damping that exceeds the mechanical loss by four orders of magnitude. The stability of the resultant spring is robust to changes in laser power and detuning, and allows purely passive self-locking of the cavity. Our results open up a new way of trapping and cooling macroscopic objects for optomechanical experiments.
Prevalence and factors associated with chronic kidney disease and end-stage renal disease in HIV-1-infected Asian patients in Tokyo
Authors: Nishijima Takeshi , Kawasaki Yohei , Mutoh Yoshikazu , Tomonari Kiyomi , Tsukada Kunihisa , Kikuchi Yoshimi , Gatanaga Hiroyuki , Oka Shinichi 
Published: October 2017

AbstractThis single-center cross-sectional study determined the prevalence and factors associated with chronic kidney disease (CKD) and end-stage renal disease (ESRD) in HIV-1-infected Asian patients at the largest HIV clinic in Japan. HIV-1-infected patients who visited the clinic between September and December 2016 were analyzed. CKD was defined as estimated glomerular filtration rate of <60 ml/min/1.73 m2 or proteinuria ≥1+, observed at least over three months. A logistic regression model was used to estimate the effects of various variables on CKD. The study included 1,990 patients; with 97% Asians, 34% aged of ≥50 years, and 94% had HIV-1 load <50 copies/ml. The median time from HIV-1 diagnosis to study enrollment and duration of ART were 9.1 years (IQR4.8–14.2) and 7.35 years (IQR3.28–12), respectively. CKD and ESRD were diagnosed in 256 (13%) and 9 (0.5%) patients, respectively. The prevalence of CKD was 18.6% for age 50–59, 28.5% for 60–69, and 47% for over 70. Older age, heavier body weight, diabetes mellitus, hypertension, and longer duration of ART, but not duration of TDF exposure, were associated with CKD. The traditional risk factors, rather than HIV-1-related variables, were associated with CKD, suggesting the importance of management of such comorbidities in maintenance of renal function.
Selectivity of Cobalt Corrole for CO vs. O2 and N2 in Indoor Pollution
Authors: Sheng Xia , Zhao Hailiang , Du Lin 
Published: October 2017

AbstractCoal combustion causes indoor pollution of CO. In this work, DFT calculations on cobalt corrole (Co(Cor)) with three most common indoor gas molecules (N2, O2 and CO) were performed. The Mulliken spin densities show that the ground states of Co(N2)(Cor), Co(CO)(Cor) and Co(OC)(Cor) have an anti-ferromagnetic coupling fashion of the electrons on the Co 3d
z
2 orbital and the π orbital of the corrole ring. However, Co(O2)(Cor) has a triplet ground state. With the spin contamination corrections, the Co(N2)(Cor) binding energy was obtained at −50.6 kcal mol−1 (B3LYP-D3). While CO can interact with Co(Cor) in two different ways, and their binding energies were −22.8 and −10.9 kcal mol−1 (B3LYP-D3) for Co(CO)(Cor) and Co(OC)(Cor), respectively. The natural bond orbital charges on the axial ligands (NO, CO, OC) are increased upon the chemical bond formation. These are the cause of the shorten metal-ligand bond and the increase of the wavenumber of the metal-ligand bond vibrational transitions. While the charges for O2 are decreased, leading to bond elongation as well as the decrease of the wavenumber upon complexation. Overall, O2 was found to be hardly coordinated with Co(Cor). This study provides a detailed molecular understanding of interactions between a gas sensor and gaseous indoor air-pollutants.
Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets
Authors: Barupal Dinesh Kumar , Fiehn Oliver 
Published: October 2017

AbstractMetabolomics answers a fundamental question in biology: How does metabolism respond to genetic, environmental or phenotypic perturbations? Combining several metabolomics assays can yield datasets for more than 800 structurally identified metabolites. However, biological interpretations of metabolic regulation in these datasets are hindered by inherent limits of pathway enrichment statistics. We have developed ChemRICH, a statistical enrichment approach that is based on chemical similarity rather than sparse biochemical knowledge annotations. ChemRICH utilizes structure similarity and chemical ontologies to map all known metabolites and name metabolic modules. Unlike pathway mapping, this strategy yields study-specific, non-overlapping sets of all identified metabolites. Subsequent enrichment statistics is superior to pathway enrichments because ChemRICH sets have a self-contained size where p-values do not rely on the size of a background database. We demonstrate ChemRICH’s efficiency on a public metabolomics data set discerning the development of type 1 diabetes in a non-obese diabetic mouse model. ChemRICH is available at www.chemrich.fiehnlab.ucdavis.edu
Cytotoxicity of Aconitum alkaloid and its interaction with calf thymus DNA by multi-spectroscopic techniques
Authors: Liu Fei , Tan Xiaoxin , Han Xu , Li Xiang , Li Nan , Kang Weijun 
Published: October 2017

AbstractThe cytotoxicities of three aconitum alkaloids- aconitine, hypaconitine and mesaconitine, and their abilities to bind DNA have been explored. Rat myocardial cells H9c2 were treated with aconitum alkaloids and assessed the cytotoxicities by using MTT assay and flow cytometry. Apoptosis was evidenced by the results of the annexin V/propidium iodide (PI) assay. Aconitine was found to be the most toxic in rat myocardial cells H9c2 in three aconitum alkaloids. At the same time, DNA adducts were isolated and then analyzed by UV-Vis spectroscopy after exposure to alkaloids, which indicated that three alkaloids could bind to DNA in rat myocardial cells H9c2. Furthermore, their binding modes were investigated by UV-Visible, fluorescence, DNA melting studies and ionic strength effect. Results indicated that the interaction between three alkaloids and DNA were intercalation coupled with electrostatic effect. The estimated binding constants were between 4.83 × 105 M−1 to 9.85 × 105 M−1 for three alkaloids at 298 K.
Safety of Nonporous Silica Nanoparticles in Human Corneal Endothelial Cells
Authors: Kim Ja-Yeon , Park Joo-Hee , Kim Martha , Jeong Hyejoong , Hong Jinkee , Chuck Roy S. , Park Choul Yong 
Published: October 2017

AbstractNonporous silica nanoparticles (SiNPs) are promising drug carrier platforms for intraocular drug delivery. In this study, we investigated the safety of three different sizes of SiNPs (50, 100, and 150 nm) in a human corneal endothelial cell (HCEC) line, B4G12. The HCECs were exposed to different concentrations (0, 25, 50, and 100 µg/ml) of three sizes of SiNPs for up to 48 h. Cellular viability, autophagy, lactate dehydrogenase (LDH) assay, and mammalian target of rapamycin (mTOR) pathway activation were evaluated. Intracellular distribution of the SiNPs was evaluated with transmission electron microscopy (TEM). TEM revealed that the SiNPs were up-taken by the HCECs inside cytoplasmic vacuoles. No mitochondrial structural damage was observed. Both cellular viability and LDH level remained unchanged with up to 100 µg/mL of SiNP treatment. Autophagy showed a significant dose-dependent activation with 50, 100, and 150 nm SiNPs. However, the mTOR activation remained unchanged. Human corneal tissue culture with 100 µg/ml concentrations of SiNPs for 72 h revealed no significant endothelial toxicity. In vivo corneal safety of the SiNPs (0.05 ml intracameral injection, 200 mg/ml concentration) was also verified in rabbit models. These findings suggested that 50, 100, and 150 nm SiNPs did not induce acute significant cytotoxicity in corneal endothelial cells at concentrations up to 100 µg/mL. However, long-term toxicity of SiNPs remains unknown.
Ultra-broadband Asymmetric Light Transmission and Absorption Through The Use of Metal Free Multilayer Capped Dielectric Microsphere Resonator
Authors: Ghobadi Amir , Dereshgi Sina Abedini , Butun Bayram , Ozbay Ekmel 
Published: October 2017

AbstractIn this paper, we propose a simple design with an excellent performance to obtain high contrast in transmission asymmetry based on dielectric microspheres. Initially, we scrutinize the impact of the sphere radius on forward and backward transmissions. Afterward, by introducing a capping layer on top of the sphere, transmission response for the backward illuminated light will be blocked. In the next step, in order to replace the reflecting metal cap with a metal free absorbing design, we adopt a modeling approach based on the transfer matrix method (TMM) to explore an ideal material to achieve metal free perfect absorption in a multilayer configuration of material-insulator-material-insulator (MIMI). As a result of our investigations, it is found that Titanium Nitride (TiN) is an excellent alternative to replace metal in a MIMI multilayer stack. Setting this stack as the top capping coating, we obtain a high contrast between forward and backward light transmission where in an ultra-broadband range of 400 nm–1000 nm, forward transmission is above 0.85 while its backward response stays below 0.2. Moreover, due to the existence of multilayer stack, a high asymmetry is also observed for absorption profiles. This design has a relatively simple and large scale compatible fabrication route.
SIM2l attenuates resistance to hypoxia and tumor growth by transcriptional suppression of HIF1A in uterine cervical squamous cell carcinoma
Authors: Nakamura Kanako , Komatsu Masayuki , Chiwaki Fumiko , Takeda Takashi , Kobayashi Yusuke , Banno Kouji , Aoki Daisuke , Yoshida Teruhiko , Sasaki Hiroki 
Published: October 2017

AbstractDespite chemoradiotherapy being one of the most important modalities in advanced cervical cancer, there is a lack of both usable biomarkers to predict treatment outcome and of knowledge about the mechanism of refractoriness to the therapy. Here we identified a transcriptional factor Single-minded homolog 2 (SIM2) as an independent predictive biomarker for uterine cervical squamous cell carcinoma (CvSCC). The retrospective study showed that high expression level of SIM2 was correlated to good survival in CvSCC patients. SIM2 knockdown in CvSCC cell lines showed resistance to hypoxia with increased expression of HIF1A and its target genes. Loss of SIM2 also caused growth promotion, resistance to ROS, and radiation in 3D culture. Furthermore, SIM2 knockdown suppressed tumor growth with increased HIF-1α expression and angiogenesis in vivo. On the other hand, SIM2 long isoform (SIM2l)-overexpressed cells had contrary results, indicating the long isoform plays a key role for maintenance of these phenotypes. These data indicated that SIM2l has a potential to be precision medicine for CvSCC patients and that anti-angiogenesis therapy might be usable for SIM2lLow poor survivors.
mir-355 Functions as An Important Link between p38 MAPK Signaling and Insulin Signaling in the Regulation of Innate Immunity
Authors: Zhi Lingtong , Yu Yonglin , Jiang Zhixia , Wang Dayong 
Published: October 2017

AbstractWe performed a systematic identification of microRNAs (miRNAs) involved in the control of innate immunity. We identified 7 novel miRNA mutants with altered survival, colony forming in the body, and expression pattern of putative antimicrobial genes afterPseudomonas aeruginosainfection. Loss-of-function mutation ofmir-45, mir-75, mir-246, mir-256, ormir-355induced resistance toP. aeruginosainfection, whereas loss-of-function mutation ofmir-63ormir-360induced susceptibility toP. aeruginosainfection. DAF-2 in the insulin signaling pathway acted as a target for intestinalmir-355to regulate innate immunity.mir-355functioned as an important link between p38 MAPK signaling pathway and insulin signaling pathway in the regulation of innate immunity. Our results provide an important molecular basis for further elucidation of the functions of various miRNAs in the regulation of innate immunity.
The cell-type specific transcriptome in human adipose tissue and influence of obesity on adipocyte progenitors
Authors: Ehrlund Anna , Acosta Juan R. , Björk Christel , Hedén Per , Douagi Iyadh , Arner Peter , Laurencikiene Jurga 
Published: October 2017

AbstractObesity affects gene expression and metabolism of white adipose tissue (WAT), which results in insulin resistance (IR) and type 2 diabetes. However, WAT is a heterogeneous organ containing many cell types that might respond differently to obesity-induced changes. We performed flow cytometry sorting and RNA expression profiling by microarray of major WAT cell types (adipocytes, CD45−/CD31−/CD34+ progenitors, CD45+/CD14+ monocytes/ macrophages, CD45+/CD14− leukocytes), which allowed us to identify genes enriched in specific cell fractions. Additionally, we included adipocytes and adipocyte progenitor cells obtained from lean and obese individuals. Taken together, we provide a detailed gene expression atlas of major human adipose tissue resident cell types for clinical/basic research and using this dataset provide lists of cell-type specific genes that are of interest for metabolic research.
Randomized Controlled Trial of a Novel Device for Tinnitus Sound Therapy During Sleep
Authors: Theodoroff Sarah M. , McMillan Garnett P. , Zaugg Tara L. , Cheslock Megan , Roberts Chan , Henry James A. 
Published: October 2017

Purpose
The aim of this study was to determine if a customized stimulus from the Otoharmonics Levo System reduces tinnitus perceptions and reactions for people with bothersome tinnitus.

Method
Sixty participants were randomized to 1 of 3 groups that used sound therapy devices during sleep that differed in their acoustic stimulus: (a) tinnitus-matched (TM), (b) noise stimulus (NS), and (c) bedside sound generator (BSG). Outcome measures were the Tinnitus Functional Index (TFI), numeric rating scale of tinnitus loudness, and tinnitus loudness match. A Bayesian hierarchical model was fit to estimate the differences in treatment efficacy among groups.

Results
Average tinnitus reactions and perceptions improved across treatment groups. We are at least 87% certain that treatment with TM or NS reduces mean TFI compared to treatment with BSG, with an estimated relative efficacy of 4.5–5 points greater reduction. We are at least 95% certain that treatment with TM results in greater reduction in mean numeric rating scale (NRS) of tinnitus loudness compared to the other groups, with an estimated relative efficacy of about 0.75 points greater reduction.

Conclusions
This study offers some support for greater average improvement in reactions to tinnitus with TM or NS devices compared to the BSG device. The TM group, compared to the BSG and NS groups, showed a greater reduction in ratings of tinnitus loudness on the NRS on average.

Supplemental Material

https://doi.org/10.23641/asha.5545759
Using the Delphi Technique to Explore Complex Concepts in Speech-Language Pathology: An Illustrative Example From Children's Social Communication
Authors: Izaryk Kristen , Skarakis-Doyle Elizabeth 
Published: October 2017

PurposeIn recent years, there has been an increasing interest in expanding the research approaches that speech-language pathologists utilize, particularly for addressing complex questions. Consensus-building techniques can be useful for addressing such questions. The Delphi technique is a consensus-building process involving structured communication among members of an expert panel via independent responses to iterative rounds of questionnaires. The purpose of this research note is to describe and demonstrate the Delphi technique using an application to a complex problem in speech-language pathology, that is, the bases of social communication and pragmatics.MethodThe Delphi technique was described and illustrated via the following study: 10 expert speech-language pathologists participated in a 3-round Delphi study. Participants were asked to list the key features of social communication and pragmatics in Round 1. Questions for Rounds 2 and 3 were developed on the basis of the participants' responses to previous rounds.ResultsThe Delphi technique was useful in bringing participants to consensus on the key features of social communication and pragmatics and offered a starting point for the continued exploration of this complex problem.ConclusionA discussion of the benefits and limitations of the technique is included, highlighting the utility of the technique to the field of speech-language pathology.
Self-Ratings of Vocal Status in Daily Life: Reliability and Validity for Patients With Vocal Hyperfunction and a Normative Group
Authors: Van Stan Jarrad H. , Maffei Marc , Masson Maria Lúcia Vaz , Mehta Daryush D. , Burns James A. , Hillman Robert E. 
Published: October 2017

Purpose
The aim of this study was to establish reliability and validity for self-ratings of vocal status obtained during the daily activities of patients with vocal hyperfunction (VH) and matched controls.

Method
Eight-four patients with VH and 74 participants with normal voices answered 3 vocal status questions—difficulty producing soft, high-pitched phonation (D-SHP); discomfort; and fatigue—on an ambulatory voice monitor at the beginning, 5-hr intervals, and the end of each day (7 total days). Two subsets of the patient group answered the questions during a 2nd week after voice therapy (29 patients) or laryngeal surgery (16 patients).

Results

High reliability resulted for patients (Cronbach's α = .88) and controls (α = .95). Patients reported higher D-SHP, discomfort, and fatigue (Cohen's
d
= 1.62–1.92) compared with controls. Patients posttherapy and postsurgery reported significantly improved self-ratings of vocal status relative to their pretreatment ratings (
d
= 0.70–1.13). Within-subject changes in self-ratings greater than 20 points were considered clinically meaningful.

Conclusions
Ratings of D-SHP, discomfort, and fatigue have adequate reliability and validity for tracking vocal status throughout daily life in patients with VH and vocally healthy individuals. These questions could help investigate the relationship between vocal symptom variability and putative contributing factors (e.g., voice use/rest, emotions).