bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues
Authors: Adamczyk Barbara , Jin Chunsheng , Polom Karol , Muñoz Pedro , Rojas- Macias Miguel A. , Zeeberg David , Borén Mats , Roviello Franco , Karlsson Niclas G. 
Published: January 2018

AbstractSample collection, handling and storage are the most critical steps for ensuring the highest preservation of specimens. Pre-analytical variability can influence the results as protein signatures alter rapidly after tissue excision or during long-term storage. Hence, we evaluated current state-of-the-art biobank preservation methods from a glycomics perspective and analyzed O-glycan alterations occurring in the gastric cancer tissues. Paired tumor and adjacent normal tissue samples were obtained from six patients undergoing gastric cancer surgery. Collected samples (n = 24) were either snap-frozen or heat stabilized and then homogenized. Glycans were released from extracted glycoproteins and analyzed by LC-MS/MS. In total, the relative abundance of 83 O-glycans and 17 derived structural features were used for comparison. There was no statistically significant difference found in variables between snap frozen and heat-stabilized samples, which indicated the two preservation methods were comparable. The data also showed significant changes between normal and cancerous tissue. In addition to a shift from high sialylation in the cancer area towards blood group ABO in the normal area, we also detected that the LacdiNAc epitope (N,N’-diacetyllactosamine) was significantly decreased in cancer samples. The O-glycan alterations that are presented here may provide predictive power for the detection and prognosis of gastric cancer.
Downregulation of Heat Shock Protein 70 Impairs Osteogenic and Chondrogenic Differentiation in Human Mesenchymal Stem Cells
Authors: Li Chenghai , Sunderic Kristifor , Nicoll Steven B. , Wang Sihong 
Published: January 2018

AbstractHuman mesenchymal stem cells (hMSCs) show promise for bone and cartilage regeneration. Our previous studies demonstrated that hMSCs with periodic mild heating had enhanced osteogenic and chondrogenic differentiation with significantly upregulated heat shock protein 70 (HSP70). However, the role of HSP70 in adult tissue regeneration is not well studied. Here, we revealed an essential regulatory mechanism of HSP70 in osteogenesis and chondrogenesis using adult hMSCs stably transfected with specific shRNAs to knockdown HSP70. Periodic heating at 39 °C was applied to hMSCs for up to 26 days. HSP70 knockdown resulted in significant reductions of alkaline phosphatase activity, calcium deposition, and gene expression of Runx2 and Osterix during osteogenesis. In addition, knockdown of HSP70 led to significant decreases of collagens II and X during chondrogenesis. Thus, downregulation of HSP70 impaired hMSC osteogenic and chondrogenic differentiation as well as the enhancement of these processes by thermal treatment. Taken together, these findings suggest a putative mechanism of thermal-enhanced bone and cartilage formation and underscore the importance of HSP70 in adult bone and cartilage differentiation.
Loss of A20 in BM-MSCs regulates the Th17/Treg balance in Rheumatoid Arthritis
Authors: Feng Zhuan , Zhai Yue , Zheng Zhaohui , Yang Lijie , Luo Xing , Dong Xiwen , Han Qing , Jin Jin , Chen Zhi-Nan , Zhu Ping 
Published: January 2018

AbstractMesenchymal stem cells (MSCs) are multi-potent cells that are self-renewable and possess the potential to differentiate into multiple lineages. Several studies demonstrated that MSCs could regulate a Th17/Treg balance and could be a potential therapeutic target for Rheumatoid Arthritis (RA). A20 is highly expressed in many cell types after the stimulation of TNF-α, where it may inhibit pro-inflammatory cytokine secretion. However, the expression of A20 in BM-MSCs in RA is not fully understood. In our study, we found that A20 was decreased in RA patients’ bone marrow MSCs (BM-MSCs), and with more IL-6 secretion, the balance of Th17/Treg was broken. In CIA mice, we found a moderate A20 decrease in mice MSCs as compared with those of control group in mRNA and protein levels. However, the IL-6 expression was increased. After umbilical cord MSCs treatment, A20 and IL-6 expressions were equal to the control group. Thus, our study indicates that loss of A20 in MSCs regulates the Th17/Treg balance in RA and the regulatory role of A20 in pro-inflammatory IL-6 production could be a potential target for the transfer of MSCs in RA adoptive therapy.
Integrated sequencing of exome and mRNA of large-sized single cells
Authors: Wang Lily Yan , Guo Jiajie , Cao Wei , Zhang Meng , He Jiankui , Li Zhoufang 
Published: January 2018

AbstractCurrent approaches of single cell DNA-RNA integrated sequencing are difficult to call SNPs, because a large amount of DNA and RNA is lost during DNA-RNA separation. Here, we performed simultaneous single-cell exome and transcriptome sequencing on individual mouse oocytes. Using microinjection, we kept the nuclei intact to avoid DNA loss, while retaining the cytoplasm inside the cell membrane, to maximize the amount of DNA and RNA captured from the single cell. We then conducted exome-sequencing on the isolated nuclei and mRNA-sequencing on the enucleated cytoplasm. For single oocytes, exome-seq can cover up to 92% of exome region with an average sequencing depth of 10+, while mRNA-sequencing reveals more than 10,000 expressed genes in enucleated cytoplasm, with similar performance for intact oocytes. This approach provides unprecedented opportunities to study DNA-RNA regulation, such as RNA editing at single nucleotide level in oocytes. In future, this method can also be applied to other large cells, including neurons, large dendritic cells and large tumour cells for integrated exome and transcriptome sequencing.
Effects of metformin on colorectal cancer stem cells depend on alterations in glutamine metabolism
Authors: Kim Jae Hyun , Lee Kyoung Jin , Seo Yoojeong , Kwon Ji-Hee , Yoon Jae Pil , Kang Jo Yeon , Lee Hyun Jung , Park Soo Jung , Hong Sung Pil , Cheon Jae Hee , Kim Won Ho , Il Kim Tae 
Published: January 2018

AbstractMetformin has been known to suppress cancer stem cells (CSCs) in some cancers. However, the differential effects of metformin on CSCs and their mechanisms have not been reported. Herein, metformin induced pAMPK activation and pS6 suppression in metformin-sensitive (HT29) cells, but not in metformin-resistant (SW620) cells. The oxygen consumption rate was higher in HT29 cells than in SW620 cells and showed a prominent decrease after metformin treatment in HT29 cells. In glutamine-depleted medium, but not in low-glucose medium, SW620 cells became sensitive to the CSC-suppressing effect of metformin. A combination of metformin and glutaminase C inhibitor (compound 968) suppressed CSCs in SW620 cells and enhanced that effect in HT29 cells. SW620 cells showed higher expression of glutaminase 1 and glutamine transporter (ASCT2) than HT29 cells, especially ASCT2 in CSCs. Knockdown of glutaminase 1, ASCT2, and c-Myc induced significant CSC-suppression and enhanced CSC-suppressing effect of metformin and compound 968. In xenografts and human cancer organoids, combined treatment with metformin and compound 968 showed the same results as those shown in vitro. In conclusion, the effect of metformin on CSCs varies depending on the AMPK-mTOR and glutamine metabolism. The inhibition of glutamine pathway could enhance the CSC-suppressing effect of metformin, overcoming metformin resistance.
Unravelling the effects of mechanical physiological conditioning on cardiac adipose tissue-derived progenitor cells in vitro and in silico
Authors: Llucià-Valldeperas Aida , Bragós Ramon , Soler-Botija Carolina , Roura Santiago , Gálvez-Montón Carolina , Prat-Vidal Cristina , Perea-Gil Isaac , Bayes-Genis Antoni 
Published: January 2018

AbstractMechanical conditioning is incompletely characterized for stimulating therapeutic cells within the physiological range. We sought to unravel the mechanism of action underlying mechanical conditioning of adipose tissue-derived progenitor cells (ATDPCs), both in vitro and in silico. Cardiac ATDPCs, grown on 3 different patterned surfaces, were mechanically stretched for 7 days at 1 Hz. A custom-designed, magnet-based, mechanical stimulator device was developed to apply ~10% mechanical stretching to monolayer cell cultures. Gene and protein analyses were performed for each cell type and condition. Cell supernatants were also collected to analyze secreted proteins and construct an artificial neural network. Gene and protein modulations were different for each surface pattern. After mechanostimulation, cardiac ATDPCs increased the expression of structural genes and there was a rising trend on cardiac transcription factors. Finally, secretome analyses revealed upregulation of proteins associated with both myocardial infarction and cardiac regeneration, such as regulators of the immune response, angiogenesis or cell adhesion. To conclude, mechanical conditioning of cardiac ATDPCs enhanced the expression of early and late cardiac genes in vitro. Additionally, in silico analyses of secreted proteins showed that mechanical stimulation of cardiac ATDPCs was highly associated with myocardial infarction and repair.
Mice deficient in the Shmt2 gene have mitochondrial respiration defects and are embryonic lethal
Authors: Tani Haruna , Ohnishi Sakiko , Shitara Hiroshi , Mito Takayuki , Yamaguchi Midori , Yonekawa Hiromichi , Hashizume Osamu , Ishikawa Kaori , Nakada Kazuto , Hayashi Jun-Ichi 
Published: January 2018

AbstractAccumulation of somatic mutations in mitochondrial DNA (mtDNA) has been proposed to be responsible for human aging and age-associated mitochondrial respiration defects. However, our previous findings suggested an alternative hypothesis of human aging—that epigenetic changes but not mutations regulate age-associated mitochondrial respiration defects, and that epigenetic downregulation of nuclear-coded genes responsible for mitochondrial translation [e.g., glycine C-acetyltransferase (GCAT), serine hydroxymethyltransferase 2 (SHMT2)] is related to age-associated respiration defects. To examine our hypothesis, here we generated mice deficient in Gcat or Shmt2 and investigated whether they have respiration defects and premature aging phenotypes. Gcat-deficient mice showed no macroscopic abnormalities including premature aging phenotypes for up to 9 months after birth. In contrast, Shmt2-deficient mice showed embryonic lethality after 13.5 days post coitum (dpc), and fibroblasts obtained from 12.5-dpc Shmt2-deficient embryos had respiration defects and retardation of cell growth. Because Shmt2 substantially controls production of N-formylmethionine-tRNA (fMet-tRNA) in mitochondria, its suppression would reduce mitochondrial translation, resulting in expression of the respiration defects in fibroblasts from Shmt2-deficient embryos. These findings support our hypothesis that age-associated respiration defects in fibroblasts of elderly humans are caused not by mtDNA mutations but by epigenetic regulation of nuclear genes including SHMT2.
Thickness Control of the Spin-Polarized Two-Dimensional Electron Gas in LaAlO3/BaTiO3 Superlattices
Authors: Chen Chen , Fang Le , Zhang Jihua , Zhao Guodong , Ren Wei 
Published: January 2018

AbstractWe explored the possibility of increasing the interfacial carrier quantum confinement, mobility and conductivity in the (LaAlO3)n/(BaTiO3)n superlattices by thickness regulation using the first-principles electronic structure calculations. Through constructing two different interfacial types of LaAlO3/BaTiO3 superlattices, we discovered that the LaO/TiO2 interface is preferred from cleavage energy consideration. We then studied the electronic characteristics of two-dimensional electron gas (2DEG) produced at the LaO/TiO2 interface in the LaAlO3/BaTiO3 superlattices via spin-polarized density functional theory calculations. The charge carrier density of 2DEG has a magnitude of 1014 cm−2 (larger than the traditional system LaAlO3/SrTiO3), which is mainly provided by the interfacial Ti 3dxy orbitals when the thicknesses of LaAlO3 and BaTiO3 layers are over 4.5 unit cells. We have also revealed the interfacial electronic characteristics of the LaAlO3/BaTiO3 system, by showing the completely spin-polarized 2DEG mostly confined at the superlattice interface. The interfacial charge carrier mobility and conductivity are found to be converged beyond the critical thickness. Therefore, we can regulate the interfacial confinement for the spin-polarized 2DEG and quantum transport properties in LaAlO3/BaTiO3 superlattice via controlling the thicknesses of the LaAlO3 and BaTiO3 layers.
Abnormally Low or High Ankle-Brachial Index Is Associated With the Development of Diabetic Retinopathy in Type 2 Diabetes Mellitus
Authors: Lee Mei-Yueh , Hsiao Pi-Jung , Huang Jiun-Chi , Hsu Wei-Hao , Chen Szu-Chia , Chang Jer-Ming , Shin Shyi–Jang 
Published: January 2018

AbstractAlthough some studies have reported an association between peripheral artery disease (PAD) and diabetic retinopathy (DR) in patients with diabetes, whether or not a causal relationship exists is unknown. The aim of this study was to investigate whether PAD, as indicated by an abnormally low or high ankle-brachial index (ABI), is associated with the development of DR in patients with type 2 diabetes mellitus (DM) without DR. We enrolled 414 (221 men and 193 women) patients with type 2 DM who underwent ABI measurements at our outpatient clinic. PAD was defined as an abnormally low (<0.9) or high (≥1.3) ABI in either leg, and DR was defined as being non-proliferative or proliferative. Of the enrolled patients, 69 (16.7%) had an ABI <0.9 or ≥1.3. The median follow-up period was 23 (15–40) months, during which 74 (17.9%) patients developed DR. In multivariate analysis, an ABI <0.9 or ≥1.3 was independently associated with the development of DR (vs. ABI ≥0.9 to <1.3; hazard ratio, 2.186; 95% confidence interval, 1.261 to 3.789; p = 0.005). An abnormal ABI was associated with the development of DR in our patients with type 2 DM without DR.
Slower Time estimation in Post-Traumatic Stress Disorder
Authors: Vicario Carmelo M. , Felmingham Kim L. 
Published: January 2018

AbstractCognitive deficits in Posttraumatic Stress Disorder (PTSD) and dissociative symptoms suggest there may be an underlying and persistent problem with temporal processing in PTSD, but this question has not been systematically examined. We investigated the ability of a group of PTSD participants in estimating the duration of supra-second visual stimuli relative to healthy controls. The data of 59 participants with PTSD and 62 healthy controls, collected from the BRID database, have been examined. Overall, our results indicate that PTSD patients overestimate the duration of the displayed stimuli. Moreover, we found that PTSD are more variable in the time estimation compared to the control group. Finally, we found evidence that working memory and attention impairments were associated with time overestimation in PTSD. The finding of time overestimation in PTSD accords with previous reports of time overestimation during stressful experiences associated with fear and arousal, but extends findings to suggest it remains in chronic PTSD populations processing non-emotional stimuli. The evidence of time overestimation in PTSD suggests the potential relevance of this factor as a cognitive marker in assessing the neuropsychological profile of this clinical population.
Rapid Thermal Processing to Enhance Steel Toughness
Authors: Judge V. K. , Speer J. G. , Clarke K. D. , Findley K. O. , Clarke A. J. 
Published: January 2018

AbstractQuenching and Tempering (Q&T) has been utilized for decades to alter steel mechanical properties, particularly strength and toughness. While tempering typically increases toughness, a well-established phenomenon called tempered martensite embrittlement (TME) is known to occur during conventional Q&T. Here we show that short-time, rapid tempering can overcome TME to produce unprecedented property combinations that cannot be attained by conventional Q&T. Toughness is enhanced over 43% at a strength level of 1.7 GPa and strength is improved over 0.5 GPa at an impact toughness of 30 J. We also show that hardness and the tempering parameter (TP), developed by Holloman and Jaffe in 1945 and ubiquitous within the field, is insufficient for characterizing measured strengths, toughnesses, and microstructural conditions after rapid processing. Rapid tempering by energy-saving manufacturing processes like induction heating creates the opportunity for new Q&T steels for energy, defense, and transportation applications.
Phases and rates of iron and magnetism changes during paddy soil development on calcareous marine sediment and acid Quaternary red-clay
Authors: Huang Laiming , Jia Xiaoxu , Shao Ming’an , Chen Liumei , Han Guangzhong , Zhang Ganlin 
Published: January 2018

AbstractDynamic changes in Fe oxides and magnetic properties during natural pedogenesis are well documented, but variations and controls of Fe and magnetism changes during anthropedogenesis of paddy soils strongly affected by human activities remain poorly understood. We investigated temporal changes in different Fe pools and magnetic parameters in soil profiles from two contrasting paddy soil chronosequences developed on calcareous marine sediment and acid Quaternary red clay in Southern China to understand the directions, phases and rates of Fe and magnetism evolution in Anthrosols. Results showed that paddy soil evolution under the influence of artificial submergence and drainage caused changes in soil moisture regimes and redox conditions with both time and depth that controlled Fe transport and redistribution, leading to increasing profile differentiation of Fe oxides, rapid decrease of magnetic parameters, and formation of diagnostic horizons and features, irrespective of the different parent materials. However, the initial parent material characteristics (pH, Fe content and composition, weathering degree and landscape positions) exerted a strong influence on the rates and trajectories of Fe oxides evolution as well as the phases and rates of magnetism changes. This influence diminished with time as prolonged rice cultivation drove paddy soil evolving to common pedogenic features.
Expression of cry2Ah1 and two domain II mutants in transgenic tobacco confers high resistance to susceptible and Cry1Ac-resistant cotton bollworm
Authors: Li Shengyan , Wang Zeyu , Zhou Yiyao , Li Changhui , Wang Guiping , Wang Hai , Zhang Jie , Liang Gemei , Lang Zhihong 
Published: January 2018

AbstractTo improve the novel Bacillus thuringiensis insecticidal gene cry2Ah1 toxicity, two mutants cry2Ah1-vp (V354VP) and cry2Ah1-sp (V354SP) were performed. SWISS-MODEL analysis showed two mutants had a longer loop located between β-4 and β-5 of domain II, resulting in higher binding affinity with brush border membrane vesicles (BBMV) of Helicoverpa armigera comparing with Cry2Ah1. The cry2Ah1, cry2Ah1-vp, and cry2Ah1-sp were optimized codon usage according to plant codon bias, and named mcry2Ah1, mcry2Ah1-vp, and mcry2Ah1-sp. They were transformed into tobacco via Agrobacterium-mediated transformation and a total of 4, 8, and 24 transgenic tobacco plants were obtained, respectively. The molecular detection showed the exogenous gene was integrated into tobacco genome, and successfully expressed at the transcript and translation levels. Cry2Ah1 protein in transgenic tobacco plants varied from 4.41 to 40.28 μg g−1 fresh weight. Insect bioassays indicated that all transgenic tobacco plants were highly toxic to both susceptible and Cry1Ac-resistant cotton bollworm larvae, and the insect resistance efficiency to Cry1Ac-resistant cotton bollworm was highest in mcry2Ah1-sp transgenic tobacco plants. The results demonstrated that cry2Ah1 was a useful Bt insecticidal gene to susceptible and Cry1Ac-resistant cotton bollworm and had potential application for insect biocontrol and as a candidate for pyramid strategy in Bt crops.
The value of narrow band imaging in diagnosis of head and neck cancer: a meta-analysis
Authors: Zhou Hui , Zhang Jing , Guo Linghong , Nie Ji , Zhu Chenjing , Ma Xuelei 
Published: January 2018

AbstractHead and neck cancer is difficult to diagnose early. We aimed to estimate the diagnosis value of narrow band imaging(NBI) in head and neck cancers. We identified relevant studies through a search of PubMed, Embase and the Cochrane Library. We used a random effect model. Subgroup analysis and meta-regression analysis were performed to estimate the factors which may influence the sensitivity and specificity of the NBI. We included 25 studies with total 6187 lesions. The pooled sensitivity, specificity, positive likelihood rate, negative likelihood rate and diagnostic odds ratios of NBI were 88.5%, 95.6%, 12.33, 0.11 and 121.26, respectively. The overall area under the curve of SROC was 96.94%. The location, type of assessment, type of endoscope system and high definition were not significant sources of heterogeneity (P > 0.05). However, magnification may be related to the source of heterogeneity (P = 0.0065). Therefore, NBI may be a promising endoscopic tool in the diagnosis of head and neck cancer.
Author's Rebuttal to Smits et al. (2018), “Comment on ‘Sensitivity of the Speech Intelligibility Index to the Assumed Dynamic Range’ by Jin et al. (2017)”
Authors: Jin In-Ki , Kates James M. , Arehart Kathryn H. 
Published: January 2018

Purpose
The purpose of this letter is to refute the comments written by Smits, Goverts, and Versfeld (2018).

Method

Refutations to each issue including the fixed mathematical relationship between dynamic range (DR) and a fitting constant (
Q
value), deviating results for small DRs, and determination of Speech Intelligibility Index (SII) model parameters are described.

Results
Although Smits et al. (2018) correctly identified several issues, those comments do not diminish the results of the original article (Jin, Kates, & Arehart, 2017) in providing new insights for the SII.

Conclusions
Jin et al. (2017) clearly provided the impact of languages and DR on the SII, which was the main result of the study.
Endoscopic Management of Developmental Anomalies of the Skull Base
Authors: Wilson Meghan , Snyderman Carl 
Published: January 2018

AbstractDevelopmental anomalies of the skull base may present in childhood or as an adult. The most common pathologies include dermoid, encephalocele, and glioma. Encephaloceles may present as part of a syndrome. Other entities include infantile hemangiomas and teratoma. Endoscopic techniques provide a less invasive and morbid option for treatment. Proper evaluation and treatment is necessary to prevent complications such as meningitis.