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https://www.readbyqxmd.com/read/28821539/what-motivates-biology-instructors-to-engage-and-persist-in-teaching-professional-development
#1
Jill S McCourt, Tessa C Andrews, Jennifer K Knight, John E Merrill, Ross H Nehm, Karen N Pelletreau, Luanna B Prevost, Michelle K Smith, Mark Urban-Lurain, Paula P Lemons
We conducted a study of 19 biology instructors participating in small, local groups at six research-intensive universities connected to the Automated Analysis of Constructed Response (AACR) project (www.msu.edu/∼aacr). Our aim was to uncover participants' motivation to persist in a long-term teaching professional development effort, a topic that is understudied in discipline-based educational research. We interviewed each participant twice over a 2-year period and conducted qualitative analyses on the data, using expectancy-value theory as a framework for considering motivation...
2017: CBE Life Sciences Education
https://www.readbyqxmd.com/read/28821228/sg-adviser-mtdna-a-web-server-for-mitochondrial-dna-annotation-with-data-from-200-samples-of-a-healthy-aging-cohort
#2
Manuel Rueda, Ali Torkamani
BACKGROUND: Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians...
August 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28819428/development-of-a-new-analog-of-sgk1-inhibitor-and-its-evaluation-as-a-therapeutic-molecule-of-colorectal-cancer
#3
Xuchun Liang, Chunling Lan, Jinzhe Zhou, Wencheng Fu, Xuesha Long, Yu An, Guanming Jiao, Kejin Wang, Yongqin Li, Jiahong Xu, Qi Huang, Bin Xu, Junjie Xiao
Colorectal cancer (CRC) is one of the most leading causes of cancer-related death worldwide. The serum and glucocorticoid inducible kinase SGK1 is highly expressed and involved in several tumors. GSK650394, a SGK1 inhibitor, has been proved to be effective in impeding tumor growth in vitro. In this study, we developed a novel analog of GSK650394, and evaluated its effects on CRC cells and tumor growth both in vitro and in vivo. HCT116 cells were treated with a concentration gradient of new developed compounds and cholecystokinin octapeptide (CCK-8) assay was used to calculate the IC50 value of every analog...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28812439/evaluating-disease-prediction-models-using-a-cohort-whose-covariate-distribution-differs-from-that-of-the-target-population
#4
Scott Powers, Valerie McGuire, Leslie Bernstein, Alison J Canchola, Alice S Whittemore
Personal predictive models for disease development play important roles in chronic disease prevention. The performance of these models is evaluated by applying them to the baseline covariates of participants in external cohort studies, with model predictions compared to subjects' subsequent disease incidence. However, the covariate distribution among participants in a validation cohort may differ from that of the population for which the model will be used. Since estimates of predictive model performance depend on the distribution of covariates among the subjects to which it is applied, such differences can cause misleading estimates of model performance in the target population...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28810905/omni-polya-a-method-and-tool-for-accurate-recognition-of-poly-a-signals-in-human-genomic-dna
#5
Arturo Magana-Mora, Manal Kalkatawi, Vladimir B Bajic
BACKGROUND: Polyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3'-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810249/knockdown-of-cxcl10-inhibits-mesangial-cell-proliferation-in-murine-habu-nephritis-via-erk-signaling
#6
Jie Gao, Lingling Wu, Yong Wang, Shaoyuan Cui, Shuwei Duan, Zheyi Dong, Zhe Feng, Xiangmei Chen
BACKGROUND/AIMS: IFN-γ-inducible protein 10 (IP-10, CXCL10) has been widely demonstrated to be involved in chemotaxis, cell growth regulation and angiogenesis inhibition. It has been reported that CXCL10 expression is significantly increased in patients with MesPGN (Mesangial proliferative glomerulonephritis). However, the underlying mechanism of CXCL10 in MesPGN reminds unclear. METHODS: Wildtype (Cxcl10+/+) mice and Cxcl10-deficient (Cxcl10-/-) mice were used to generate a murine model of MesPGN...
August 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28810144/integrated-genomic-characterization-of-pancreatic-ductal-adenocarcinoma
#7
(no author information available yet)
We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28809675/jointly-learning-deep-features-deformable-parts-occlusion-and-classification-for-pedestrian-detection
#8
Wanli Ouyang, Hui Zhou, Hongsheng Li, Quanquan Li, Junjie Yan, Xiaogang Wang
Feature extraction, deformation handling, occlusion handling, and classification are four important components in pedestrian detection. Existing methods learn or design these components either individually or sequentially. The interaction among these components is not yet well explored. This paper proposes that they should be jointly learned in order to maximize their strengths through cooperation. We formulate these four components into a joint deep learning framework and propose a new deep network architecture (Code available on www...
August 11, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28801420/protocol-study-for-a-randomised-controlled-double-blind-clinical-trial-involving-virtual-reality-and-anodal-transcranial-direct-current-stimulation-for-the-improvement-of-upper-limb-motor-function-in-children-with-down-syndrome
#9
Jamile Benite Palma Lopes, Luanda André Collange Grecco, Renata Calhes Franco de Moura, Roberta Delasta Lazzari, Natalia de Almeida Carvalho Duarte, Isabela Miziara, Gileno Edu Lameira de Melo, Arislander Jonathan Lopes Dumont, Manuela Galli, Claudia Santos Oliveira
INTRODUCTION: Down syndrome results in neuromotor impairment that affects selective motor control, compromising the acquisition of motor skills and functional independence. The aim of the proposed study is to evaluate and compare the effects of multiple-monopolar anodal transcranial direct current stimulation and sham stimulation over the primary motor cortex during upper limb motor training involving virtual reality on motor control, muscle activity, cerebral activity and functional independence...
August 11, 2017: BMJ Open
https://www.readbyqxmd.com/read/28796801/long-noncoding-rnas-are-dynamically-regulated-during-%C3%AE-cell-mass-expansion-in-mouse-pregnancy-and-control-%C3%AE-cell-proliferation-in-vitro
#10
Giorgia Sisino, Alex-Xianghua Zhou, Niklas Dahr, Alan Sabirsh, Mangala M Soundarapandian, Ranjan Perera, Erik Larsson-Lekholm, Maria Chiara Magnone, Magnus Althage, Björn Tyrberg
Pregnancy is associated with increased β-cell proliferation driven by prolactin. Long noncoding RNAs (lncRNA) are the most abundant RNA species in the mammalian genome, yet, their functional importance is mainly elusive. AIMS/HYPOTHESIS: This study tests the hypothesis that lncRNAs regulate β-cell proliferation in response to prolactin in the context of β-cell mass compensation in pregnancy. METHODS: The expression profile of lncRNAs in mouse islets at day 14...
2017: PloS One
https://www.readbyqxmd.com/read/28781712/trom-a-testing-based-method-for-finding-transcriptomic-similarity-of-biological-samples
#11
Wei Vivian Li, Yiling Chen, Jingyi Jessica Li
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and divergence of biological processes in different species. We propose a testing-based method TROM (Transcriptome Overlap Measure) for comparing transcriptomes within or between different species, and provide a different perspective, in contrast to traditional correlation analyses, about capturing transcriptomic similarity...
June 2017: Statistics in Biosciences
https://www.readbyqxmd.com/read/28780735/rna-folding-kinetics-using-monte-carlo-and-gillespie-algorithms
#12
Peter Clote, Amir H Bayegan
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm...
August 5, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28780378/homblocks-a-multiple-alignment-construction-pipeline-for-organelle-phylogenomics-based-on-locally-collinear-block-searching
#13
Guiqi Bi, Yunxiang Mao, Qikun Xing, Min Cao
Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multi-gene alignments. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multi-gene alignment in a few hours...
August 2, 2017: Genomics
https://www.readbyqxmd.com/read/28778024/a-combination-of-radiation-and-the-hypoxia-activated-prodrug-evofosfamide-th-302-is-efficacious-against-a-human-orthotopic-pancreatic-tumor-model
#14
Carla Hajj, James Russell, Charles P Hart, Karyn A Goodman, Maeve A Lowery, Adriana Haimovitz-Friedman, Joseph O Deasy, John L Humm
This study was designed to investigate the effect of single-dose radiation therapy (RT) in combination with evofosfamide (TH-302), a hypoxia-activated prodrug, in a pre-clinical model of pancreatic cancer. AsPC1 tumors were implanted orthotopically in the pancreas of nude mice. Tumors were treated with 15 Gy of RT, using a 1 cm diameter field, and delivered as a continuous arc. Image-guidance to center the field on the tumor was based on CT imaging with intraperitoneal contrast. Evofosfamide (100 mg/kg, i.p...
July 21, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28777851/-analysis-of-genomic-copy-number-variations-in-36-fetuses-with-heart-malformations-using-next-generation-sequencing
#15
Ming Gao, Hong Pang, Yanhui Zhao, Jesse Li-Ling
OBJECTIVE: To explore the implications of copy number variations (CNVs) for congenital heart diseases (CHD) in fetuses. METHODS: G-banding karyotype analysis and next-generation sequencing (NGS) technology were performed on cord blood samples derived from 36 fetuses with CHD. Pathological implication of the CNVs was explored through comparison against the International Genomic Polymorphism Database (http://www.ebi.ac.uk/dgva/), Phenotype Database (http://decipher...
August 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28770966/inhibition-of-mir-221-influences-bladder-cancer-cell-proliferation-and-apoptosis
#16
H Liu, J-K Chang, J-Q Hou, Z-H Zhao, L-D Zhang
OBJECTIVE: Janus kinase (JAK) - signal transducer and activator of transcription (STAT) signaling pathway participate in cell proliferation and apoptosis. Suppressors of cytokine signaling 3 (SOCS3) are negative regulators of JAK-STAT3. SOCS3 was found significantly declined, while microRNA-221 (miR-221) obviously up-regulated in bladder cancer tissue. Bioinformatics analysis revealed the complementary binding site between miR-221 and 3'-UTR of SOCS3. This study investigated the role of miR-221 in regulating SOCS3/JAK-STAT3 signaling pathway and bladder cancer cell proliferation and apoptosis...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28766075/protein-binding-hot-spots-prediction-from-sequence-only-by-a-new-ensemble-learning-method
#17
Shan-Shan Hu, Peng Chen, Bing Wang, Jinyan Li
Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods have been widely used for hot spot prediction through sequence or structure characterization. As the structural information of proteins is not always solved, and thus hot spot identification from amino acid sequences only is more useful for real-life applications. This work proposes a new sequence-based model that combines physicochemical features with the relative accessible surface area of amino acid sequences for hot spot prediction...
August 1, 2017: Amino Acids
https://www.readbyqxmd.com/read/28764703/anti-tumor-and-anti-angiogenic-effects-of-fucoidan-on-prostate-cancer-possible-jak-stat3-pathway
#18
Xin Rui, Hua-Feng Pan, Si-Liang Shao, Xiao-Ming Xu
BACKGROUND: Prostate cancer is the most common cancer in men in the United States. Fucoidan is a bioactive polysaccharide extracted mainly from algae. The aim of this study was to investigate anti-tumor and anti-angiogenic effects of fucoidan in both cell-based assays and mouse xenograft model, as well as to clarify possible role of JAK-STAT3 pathway in the protection. METHODS: DU-145 human prostate cancer cells were treated with 100-1000 μg/mL of fucoidan. Cell viability, proliferation, migration and tube formation were studied using MTT, EdU, Transwell and Matrigel assays, respectively...
August 1, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28763902/-role-of-yes-associated-protein-1-in-angiotensin%C3%A2-induced-pulmonary-fibrosis-in-rats
#19
M X Pan, B B Zheng, N N Sun, Z M Zheng, Q J Yang, Y Meng
Objective: To explore the mechanism of Yes-associated protein 1 (Yap1) in angiotensinⅡ(AngⅡ)-induced pulmonary fibrosis. Methods:In vivo, 18 male Wistar rats were randomly divided into three equal groups with 6 rats in each group, including control group, bleomycin-treated group (BLM), and BLM+ AngⅡ group. 28 days later, the lung tissues in all groups were harvested for the HE and Masson staining as well as the immunohistochemical (IHC) staining for Yap1. In vitro, the isolated fibroblasts were treated with 10(-7) mmol/L AngⅡor the AngⅡ-targeted inhibitor irbesartan for the scheduled time for mRNA and protein expressions of Yap1, PDZ-binding motif (TAZ), and collagen Ⅰusing PCR and Western blot, as well as the translocation test from the nucleus to the cytoplasm of Yap1 and TAZ...
July 25, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28757453/lnc133b-a-novel-long-non-coding-rna-regulates-bovine-skeletal-muscle-satellite-cell-proliferation-and-differentiation-by-mediating-mir-133b
#20
Cong Fei Jin, Yan Li, Xiang Bin Ding, Xin Li, Lin Lin Zhang, Xin Feng Liu, Hong Guo
The proliferation and differentiation of skeletal muscle satellite cells is regulated by multiple regulatory factors including non-coding RNAs. It has been reported that miR-133b regulates myogenesis. In this study, we detected a novel lncRNA, lnc133b, which is completely complemented by mature miR-133b, indicating that lnc133b may regulate the expression of miR-133b by "sponge" miR-133b. A luciferase report assay confirmed that lnc133b interacts with miR-133b in regions complemented by miR-133b. We successfully constructed lnc133b gain/loss-of-function cell models by infecting LV-1nc133b and transfecting si-lnc133b into satellite cells...
July 27, 2017: Gene
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