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1. CDR3 Variants of the TXB2 Shuttle with Increased TfR1 Association Rate and Enhanced Brain Penetration

Author: Pawel Stocki, Jaroslaw Szary, Mykhaylo Demydchuk, Leandra Northall, Charlotte L. M. Rasmussen, Diana Bahu Logan, Aziz Gauhar, Laura Thei, Shu-Fen Coker, Torben Moos, Frank S. Walsh, and J. Lynn Rutkowski
Subjects: blood–brain barrier (BBB), transferrin receptor 1 (TfR1), transcytosis, brain delivery, variable domain of new antigen receptor (VNAR), Pharmacy and materia medica, RS1-441
Abstract: Since the delivery of biologic drugs to the brain is greatly hampered by the existence of the blood–brain barrier (BBB), brain shuttles are being developed to enhance therapeutic efficacy. As we have previously shown, efficient and selective brain delivery was achieved with TXB2, a cross-species reactive, anti-TfR1 VNAR antibody. To further explore the limits of brain penetration, we conducted restricted randomization of the CDR3 loop, followed by phage display to identify improved TXB2 variants. The variants were screened for brain penetration in mice using a 25 nmol/kg (1.875 mg/kg) dose and a single 18 h timepoint. A higher kinetic association rate to TfR1 correlated with improved brain penetration in vivo. The most potent variant, TXB4, showed a 3.6-fold improvement over TXB2, which had on average 14-fold higher brain levels when compared to an isotype control. Like TXB2, TXB4 retained brain specificity with parenchymal penetration and no accumulation in other organs. When fused with a neurotensin (NT) payload, it led to a rapid drop in body temperature upon transport across the BBB. We also showed that fusion of TXB4 to four therapeutic antibodies (anti-CD20, anti-EGFRvIII, anti-PD-L1 and anti-BACE1) improved their brain exposure between 14- to 30-fold. In summary, we enhanced the potency of parental TXB2 brain shuttle and gained a critical mechanistic understanding of brain delivery mediated by the VNAR anti-TfR1 antibody.
Published: 2023
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2. Chromosome arm aneuploidies shape tumour evolution and drug response

Author: Ankit Shukla, Thu H. M. Nguyen, Sarat B. Moka, Jonathan J. Ellis, John P. Grady, Harald Oey, Alexandre S. Cristino, Kum Kum Khanna, Dirk P. Kroese, Lutz Krause, Eloise Dray, J. Lynn Fink, and Pascal H. G. Duijf
Subjects: Science
Abstract: Chromosome arm-level aneuploidies (CAAs) are frequently observed in cancer. Here, the authors analyse CAA landscapes across different tumour types, relating these chromosome arm gains and losses to tumour evolution, metastasis, patient survival and response to a range of anti-cancer therapies.
Published: 2020
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3. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

Author: Longqi Liu, Chuanyu Liu, Andrés Quintero, Liang Wu, Yue Yuan, Mingyue Wang, Mengnan Cheng, Lizhi Leng, Liqin Xu, Guoyi Dong, Rui Li, Yang Liu, Xiaoyu Wei, Jiangshan Xu, Xiaowei Chen, Haorong Lu, Dongsheng Chen, Quanlei Wang, Qing Zhou, Xinxin Lin, Guibo Li, Shiping Liu, Qi Wang, Hongru Wang, J. Lynn Fink, Zhengliang Gao, Xin Liu, Yong Hou, Shida Zhu, Huanming Yang, Yunming Ye, Ge Lin, Fang Chen, Carl Herrmann, Roland Eils, Zhouchun Shang, and Xun Xu
Subjects: Science
Abstract: Heterogeneity in gene expression and epigenetic states exists across individual cells. Here, the authors develop scCAT-seq, a technique for simultaneously performing ATAC-seq and RNA-seq within the same single cell.
Published: 2019
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4. Regional Variation in Epidermal Susceptibility to UV-Induced Carcinogenesis Reflects Proliferative Activity of Epidermal Progenitors

Author: Edwige Roy, Ho Yi Wong, Rehan Villani, Thomas Rouille, Basit Salik, Seen Ling Sim, Valentine Murigneux, Mitchell S. Stark, J. Lynn Fink, H. Peter Soyer, Graeme Walker, J. Guy Lyons, Nicholas Saunders, and Kiarash Khosrotehrani
Subjects: multicolor lineage tracing, basal cell carcinoma, non-melanoma skin cancer, ultra-violet radiation, hair follicles, field carcinogenesis, Biology (General), QH301-705.5
Abstract: Summary: To better understand the influence of ultraviolet (UV) irradiation on the initial steps of skin carcinogenesis, we examine patches of labeled keratinocytes as a proxy for clones in the interfollicular epidermis (IFE) and measure their size variation upon UVB irradiation. Multicolor lineage tracing reveals that in chronically irradiated skin, patches near hair follicles (HFs) increase in size, whereas those far from follicles do not change. This is explained by proliferation of basal epidermal cells within 60 μm of HF openings. Upon interruption of UVB, patch size near HFs regresses significantly. These anatomical differences in proliferative behavior have significant consequences for the cell of origin of basal cell carcinomas (BCCs). Indeed, a UV-inducible murine BCC model shows that BCC patches are more frequent, larger, and more invasive near HFs. These findings have major implications for the prevention of field cancerization in the epidermis.
Published: 2020
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5. Why we continually Misinterpret Classical Tragedy: Ancient Greek Law within the Tragic Tradition

Author: J. Lynn Adams
Subjects: History of scholarship and learning. The humanities, AZ20-999, Fine Arts
Abstract: Literature has long been "seen as a field of activity set apart from ordinary life." But, this modern approach betrays the rich heritage from which tragic theatre arose. Contrary to this view, Greek tragedy, like the law itself, is "not a world of authoritarian clarity, ... but a world of deep uncertainty and openness, of tension and conflict and argument, a world where reasons do not harmonize but oppose one another." It is a world that was firmly connected to "Aristotelian" concepts of justice, a theory of equity and voluntariness largely understood only by academia and the legal community. Great efforts have been made within the United States and Great Britain since the 1970ʼs to rediscover the connections between law and literature. However, outside the work of classics professors, the study of law and classical Greek literature almost exclusively has been conducted in law schools. Yet, of all American Bar Association approved law schools, only twenty-one percent of schools have indicated that they offer a course in law and literature. Those that do use classical literature have focused upon Aeschylusʼs Oresteia and Sophoclesʼs "Antigone" and "Oedipus the King." But, even then, only "Antigone" was listed in more than one syllabus. And, most of these courses have often ignored the actual cultural, historical, and legal context in which the surviving Greek tragedies were written.
Published: 2018
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6. Erythrocyte microRNA sequencing reveals differential expression in relapsing-remitting multiple sclerosis

Author: Kira Groen, Vicki E. Maltby, Rodney A. Lea, Katherine A. Sanders, J. Lynn Fink, Rodney J. Scott, Lotti Tajouri, and Jeannette Lechner-Scott
Subjects: Erythrocytes, microRNA, Relapsing-remitting multiple sclerosis, Next-generation sequencing, Internal medicine, RC31-1245, Genetics, QH426-470
Abstract: Abstract Background There is a paucity of knowledge concerning erythrocytes in the aetiology of Multiple Sclerosis (MS) despite their potential to contribute to disease through impaired antioxidant capacity and altered haemorheological features. Several studies have identified an abundance of erythrocyte miRNAs and variable profiles associated with disease states, such as sickle cell disease and malaria. The aim of this study was to compare the erythrocyte miRNA profile of relapsing-remitting MS (RRMS) patients to healthy sex- and age-matched controls. Methods Erythrocytes were purified by density-gradient centrifugation and RNA was extracted. Following library preparation, samples were run on a HiSeq4000 Illumina instrument (paired-end 100 bp sequencing). Sequenced erythrocyte miRNA profiles (9 patients and 9 controls) were analysed by DESeq2. Differentially expressed miRNAs were validated by RT-qPCR using miR-152-3p as an endogenous control and replicated in a larger cohort (20 patients and 18 controls). After logarithmic transformation, differential expression was determined by two-tailed unpaired t-tests. Logistic regression analysis was carried out and receiver operating characteristic (ROC) curves were generated to determine biomarker potential. Results A total of 236 erythrocyte miRNAs were identified. Of twelve differentially expressed miRNAs in RRMS two showed increased expression (adj. p
Published: 2018
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7. Inherited BRCA1 and RNF43 pathogenic variants in a familial colorectal cancer type X family

Author: Chan, James M., Clendenning, Mark, Joseland, Sharelle, Georgeson, Peter, Mahmood, Khalid, Joo, Jihoon E., Walker, Romy, Como, Julia, Preston, Susan, Chai, Shuyi Marci, Chu, Yen Lin, Meyers, Aaron L., Pope, Bernard J., Duggan, David, Fink, J. Lynn, Macrae, Finlay A., Rosty, Christophe, Winship, Ingrid M., Jenkins, Mark A., and Buchanan, Daniel D.
Published: 2024
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8. A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing

Author: Kelly Quek, Katia Nones, Ann-Marie Patch, J. Lynn Fink, Felicity Newell, Nicole Cloonan, David Miller, Muhammad Z. H. Fadlullah, Karin Kassahn, Angelika N. Christ, Timothy J. C. Bruxner, Suzanne Manning, Ivon Harliwong, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Shivangi Wani, Anita Steptoe, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Qinying Xu, Peter Wilson, Andrew V. Biankin, John V. Pearson, Nic Waddell, and Sean M. Grimmond
Subjects: next-generation sequencing, cancer, chromosome breakpoints, structural variation, verification, high-throughput, Biology (General), QH301-705.5
Abstract: Somatic rearrangements, which are commonly found in human cancer genomes, contribute to the progression and maintenance of cancers. Conventionally, the verification of somatic rearrangements comprises many manual steps and Sanger sequencing. This is labor intensive when verifying a large number of rearrangements in a large cohort. To increase the verification throughput, we devised a high-throughput workflow that utilizes benchtop next-generation sequencing and in-house bioinformatics tools to link the laboratory processes. In the proposed workflow, primers are automatically designed. PCR and an optional gel electrophoresis step to confirm the somatic nature of the rearrangements are performed. PCR products of somatic events are pooled for Ion Torrent PGM and/or Illumina MiSeq sequencing, the resulting sequence reads are assembled into consensus contigs by a consensus assembler, and an automated BLAT is used to resolve the breakpoints to base level. We compared sequences and breakpoints of verified somatic rearrangements between the conventional and high-throughput workflow. The results showed that next-generation sequencing methods are comparable to conventional Sanger sequencing. The identified breakpoints obtained from next-generation sequencing methods were highly accurate and reproducible. Furthermore, the proposed workflow allows hundreds of events to be processed in a shorter time frame compared with the conventional workflow.
Published: 2014
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9. Encouraging general practitioners to complete the four‐year‐old Healthy Kids Check and provide healthy eating and physical activity messages

Author: A. Colin Bell, Elizabeth Campbell, J. Lynn Francis, and John Wiggers
Subjects: general practice, brief advice, nutrition and physical activity, children, obesity prevention and management, Public aspects of medicine, RA1-1270
Abstract: Abstract Objective: To describe the impact of a training and support intervention to encourage completion of the Healthy Kids Check (HKC) by general practitioners (GP) or practice nurses (PN) and provision of brief advice on diet and physical activity. Methods: The intervention (June 2008 to July 2010) was delivered by Divisions of General Practice (DGP) in the Hunter New England (HNE) region of NSW, Australia, to members in 300 practices. Intervention impact was evaluated using Medicare data on the number of HKCs completed and a post‐intervention telephone survey of randomly selected parents in HNE and rest of NSW. Results: Training reached 31% of GPs (n∼ 216/700) and 71% of PNs (n∼320/450); 31% of four‐year‐olds received a HKC in HNE compared to 15% in NSW; 27% of HNE parents (n=162) reported a GP or PN had provided advice during their child's vaccinations visit compared to 15% of parents (n=154) in NSW (p=0.002). There was no significant difference in proportion of children who had weight or height assessed (55.6% in HNE and 54.6% in NSW). Conclusions: Boosting HKC claims and healthy eating and physical activity messages in general practice is feasible. More intensive strategies are required if obesity prevention and management benefits are to be achieved. Implications: General practice is an important but under‐utilised source of advice for parents and data for policy makers on childhood obesity in Australia.
Published: 2014
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10. Fatal Accelerated Cirrhosis after Imported HEV Genotype 4 Infection

Author: Ryan B. Perumpail, Aijaz Ahmed, John P. Higgins, Samuel K. So, J. Lynn Cochran, Jan Drobeniuc, Tonya R. Mixson-Hayden, and Chong-Gee Teo
Subjects: hepatitis E, HEV, genotype 4, chronic liver disease, acute liver disease, cirrhosis, Medicine, Infectious and parasitic diseases, RC109-216
Published: 2015
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11. Luminosity determination in pp collisions at $\sqrt{s} = 7$ TeV using the ATLAS detector at the LHC

Author: The ATLAS Collaboration, G. Aad, B. Abbott, J. Abdallah, A. A. Abdelalim, A. Abdesselam, O. Abdinov, B. Abi, M. Abolins, H. Abramowicz, H. Abreu, E. Acerbi, B. S. Acharya, M. Ackers, D. L. Adams, T. N. Addy, J. Adelman, M. Aderholz, S. Adomeit, P. Adragna, T. Adye, S. Aefsky, J. A. Aguilar-Saavedra, M. Aharrouche, S. P. Ahlen, F. Ahles, A. Ahmad, H. Ahmed, M. Ahsan, G. Aielli, T. Akdogan, T. P. A. Åkesson, G. Akimoto, A. V. Akimov, M. S. Alam, M. A. Alam, S. Albrand, M. Aleksa, I. N. Aleksandrov, M. Aleppo, F. Alessandria, C. Alexa, G. Alexander, G. Alexandre, T. Alexopoulos, M. Alhroob, M. Aliev, G. Alimonti, J. Alison, M. Aliyev, P. P. Allport, S. E. Allwood-Spiers, J. Almond, A. Aloisio, R. Alon, A. Alonso, J. Alonso, M. G. Alviggi, K. Amako, P. Amaral, C. Amelung, V. V. Ammosov, A. Amorim, G. Amorós, N. Amram, C. Anastopoulos, T. Andeen, C. F. Anders, K. J. Anderson, A. Andreazza, V. Andrei, M.-L. Andrieux, X. S. Anduaga, A. Angerami, F. Anghinolfi, N. Anjos, A. Annovi, A. Antonaki, M. Antonelli, S. Antonelli, J. Antos, F. Anulli, S. Aoun, L. Aperio Bella, R. Apolle, G. Arabidze, I. Aracena, Y. Arai, A. T. H. Arce, J. P. Archambault, S. Arfaoui, J.-F. Arguin, E. Arik, M. Arik, A. J. Armbruster, K. E. Arms, S. R. Armstrong, O. Arnaez, C. Arnault, A. Artamonov, G. Artoni, D. Arutinov, S. Asai, R. Asfandiyarov, S. Ask, B. Åsman, L. Asquith, K. Assamagan, A. Astbury, A. Astvatsatourov, G. Atoian, B. Aubert, B. Auerbach, E. Auge, K. Augsten, M. Aurousseau, N. Austin, R. Avramidou, D. Axen, C. Ay, G. Azuelos, Y. Azuma, M. A. Baak, G. Baccaglioni, C. Bacci, A. M. Bach, H. Bachacou, K. Bachas, G. Bachy, M. Backes, E. Badescu, P. Bagnaia, S. Bahinipati, Y. Bai, D. C. Bailey, T. Bain, J. T. Baines, O. K. Baker, S. Baker, F. Baltasar Dos Santos Pedrosa, E. Banas, P. Banerjee, Sw. Banerjee, D. Banfi, A. Bangert, V. Bansal, H. S. Bansil, L. Barak, S. P. Baranov, A. Barashkou, A. Barbaro Galtieri, T. Barber, E. L. Barberio, D. Barberis, M. Barbero, D. Y. Bardin, T. Barillari, M. Barisonzi, T. Barklow, N. Barlow, B. M. Barnett, R. M. Barnett, A. Baroncelli, A. J. Barr, F. Barreiro, J. Barreiro Guimar aes da Costa, P. Barrillon, R. Bartoldus, A. E. Barton, D. Bartsch, R. L. Bates, L. Batkova, J. R. Batley, A. Battaglia, M. Battistin, G. Battistoni, F. Bauer, H. S. Bawa, B. Beare, T. Beau, P. H. Beauchemin, R. Beccherle, P. Bechtle, H. P. Beck, M. Beckingham, K. H. Becks, A. J. Beddall, A. Beddall, V. A. Bednyakov, C. Bee, M. Begel, S. Behar Harpaz, P. K. Behera, M. Beimforde, C. Belanger-Champagne, B. Belhorma, P. J. Bell, W. H. Bell, G. Bella, L. Bellagamba, F. Bellina, G. Bellomo, M. Bellomo, A. Belloni, K. Belotskiy, O. Beltramello, S. Ben Ami, O. Benary, D. Benchekroun, C. Benchouk, M. Bendel, B. H. Benedict, N. Benekos, Y. Benhammou, D. P. Benjamin, M. Benoit, J. R. Bensinger, K. Benslama, S. Bentvelsen, D. Berge, E. Bergeaas Kuutmann, N. Berger, F. Berghaus, E. Berglund, J. Beringer, K. Bernardet, P. Bernat, R. Bernhard, C. Bernius, T. Berry, A. Bertin, F. Bertinelli, F. Bertolucci, M. I. Besana, N. Besson, S. Bethke, W. Bhimji, R. M. Bianchi, M. Bianco, O. Biebel, J. Biesiada, M. Biglietti, H. Bilokon, M. Bindi, A. Bingul, C. Bini, C. Biscarat, R. Bischof, U. Bitenc, K. M. Black, R. E. Blair, J.-B. Blanchard, G. Blanchot, C. Blocker, J. Blocki, A. Blondel, W. Blum, U. Blumenschein, C. Boaretto, G. J. Bobbink, V. B. Bobrovnikov, A. Bocci, R. Bock, C. R. Boddy, M. Boehler, J. Boek, N. Boelaert, S. Böser, J. A. Bogaerts, A. Bogdanchikov, A. Bogouch, C. Bohm, V. Boisvert, T. Bold, V. Boldea, M. Boonekamp, G. Boorman, C. N. Booth, P. Booth, J. R. A. Booth, S. Bordoni, C. Borer, A. Borisov, G. Borissov, I. Borjanovic, S. Borroni, K. Bos, D. Boscherini, M. Bosman, H. Boterenbrood, D. Botterill, J. Bouchami, J. Boudreau, E. V. Bouhova-Thacker, C. Boulahouache, C. Bourdarios, N. Bousson, A. Boveia, J. Boyd, I. R. Boyko, N. I. Bozhko, I. Bozovic-Jelisavcic, S. Braccini, J. Bracinik, A. Braem, E. Brambilla, P. Branchini, G. W. Brandenburg, A. Brandt, G. Brandt, O. Brandt, U. Bratzler, B. Brau, J. E. Brau, H. M. Braun, B. Brelier, J. Bremer, R. Brenner, S. Bressler, D. Breton, N. D. Brett, P. G. Bright-Thomas, D. Britton, F. M. Brochu, I. Brock, R. Brock, T. J. Brodbeck, E. Brodet, F. Broggi, C. Bromberg, G. Brooijmans, W. K. Brooks, G. Brown, E. Brubaker, P. A. Bruckman de Renstrom, D. Bruncko, R. Bruneliere, S. Brunet, A. Bruni, G. Bruni, M. Bruschi, T. Buanes, F. Bucci, J. Buchanan, N. J. Buchanan, P. Buchholz, R. M. Buckingham, A. G. Buckley, S. I. Buda, I. A. Budagov, B. Budick, V. Büscher, L. Bugge, D. Buira-Clark, E. J. Buis, O. Bulekov, M. Bunse, T. Buran, H. Burckhart, S. Burdin, T. Burgess, S. Burke, E. Busato, P. Bussey, C. P. Buszello, F. Butin, B. Butler, J. M. Butler, C. M. Buttar, J. M. Butterworth, W. Buttinger, T. Byatt, S. Cabrera Urbán, M. Caccia, D. Caforio, O. Cakir, P. Calafiura, G. Calderini, P. Calfayan, R. Calkins, L. P. Caloba, R. Caloi, D. Calvet, S. Calvet, A. Camard, P. Camarri, M. Cambiaghi, D. Cameron, J. Cammin, S. Campana, M. Campanelli, V. Canale, F. Canelli, A. Canepa, J. Cantero, L. Capasso, M. D. M. Capeans Garrido, I. Caprini, M. Caprini, M. Caprio, D. Capriotti, M. Capua, R. Caputo, C. Caramarcu, R. Cardarelli, T. Carli, G. Carlino, L. Carminati, B. Caron, S. Caron, C. Carpentieri, G. D. Carrillo Montoya, S. Carron Montero, A. A. Carter, J. R. Carter, J. Carvalho, D. Casadei, M. P. Casado, M. Cascella, C. Caso, A. M. Castaneda Hernandez, E. Castaneda-Miranda, V. Castillo Gimenez, N. F. Castro, G. Cataldi, F. Cataneo, A. Catinaccio, J. R. Catmore, A. Cattai, G. Cattani, S. Caughron, A. Cavallari, P. Cavalleri, D. Cavalli, M. Cavalli-Sforza, V. Cavasinni, A. Cazzato, F. Ceradini, C. Cerna, A. S. Cerqueira, A. Cerri, L. Cerrito, F. Cerutti, M. Cervetto, S. A. Cetin, F. Cevenini, A. Chafaq, D. Chakraborty, K. Chan, B. Chapleau, J. D. Chapman, J. W. Chapman, E. Chareyre, D. G. Charlton, V. Chavda, S. Cheatham, S. Chekanov, S. V. Chekulaev, G. A. Chelkov, H. Chen, L. Chen, S. Chen, T. Chen, X. Chen, S. Cheng, A. Cheplakov, V. F. Chepurnov, R. Cherkaoui El Moursli, V. Chernyatin, E. Cheu, S. L. Cheung, L. Chevalier, F. Chevallier, G. Chiefari, L. Chikovani, J. T. Childers, A. Chilingarov, G. Chiodini, M. V. Chizhov, G. Choudalakis, S. Chouridou, I. A. Christidi, A. Christov, D. Chromek-Burckhart, M. L. Chu, J. Chudoba, G. Ciapetti, A. K. Ciftci, R. Ciftci, D. Cinca, V. Cindro, M. D. Ciobotaru, C. Ciocca, A. Ciocio, M. Cirilli, A. Clark, P. J. Clark, W. Cleland, J. C. Clemens, B. Clement, C. Clement, R. W. Clifft, Y. Coadou, M. Cobal, A. Coccaro, J. Cochran, P. Coe, J. G. Cogan, J. Coggeshall, E. Cogneras, C. D. Cojocaru, J. Colas, A. P. Colijn, C. Collard, N. J. Collins, C. Collins-Tooth, J. Collot, G. Colon, R. Coluccia, G. Comune, P. Conde Mui no, E. Coniavitis, M. C. Conidi, M. Consonni, S. Constantinescu, C. Conta, F. Conventi, J. Cook, M. Cooke, B. D. Cooper, A. M. Cooper-Sarkar, N. J. Cooper-Smith, K. Copic, T. Cornelissen, M. Corradi, S. Correard, F. Corriveau, A. Cortes-Gonzalez, G. Cortiana, G. Costa, M. J. Costa, D. Costanzo, T. Costin, D. Côté, R. Coura Torres, L. Courneyea, G. Cowan, C. Cowden, B. E. Cox, K. Cranmer, M. Cristinziani, G. Crosetti, R. Crupi, S. Crépé-Renaudin, C. Cuenca Almenar, T. Cuhadar Donszelmann, S. Cuneo, M. Curatolo, C. J. Curtis, P. Cwetanski, H. Czirr, Z. Czyczula, S. D’Auria, M. D’Onofrio, A. D’Orazio, A. Da Rocha Gesualdi Mello, P. V. M. Da Silva, C. Da Via, W. Dabrowski, A. Dahlhoff, T. Dai, C. Dallapiccola, S. J. Dallison, M. Dam, M. Dameri, D. S. Damiani, H. O. Danielsson, R. Dankers, D. Dannheim, V. Dao, G. Darbo, G. L. Darlea, C. Daum, J. P. Dauvergne, W. Davey, T. Davidek, N. Davidson, R. Davidson, M. Davies, A. R. Davison, E. Dawe, I. Dawson, J. W. Dawson, R. K. Daya, K. De, R. de Asmundis, S. De Castro, S. De Cecco, J. de Graat, N. De Groot, P. de Jong, E. De La Cruz-Burelo, C. De La Taille, B. De Lotto, L. De Mora, L. De Nooij, M. De Oliveira Branco, D. De Pedis, P. de Saintignon, A. De Salvo, U. De Sanctis, A. De Santo, J. B. De Vivie De Regie, S. Dean, G. Dedes, D. V. Dedovich, J. Degenhardt, M. Dehchar, M. Deile, C. Del Papa, J. Del Peso, T. Del Prete, A. Dell’Acqua, L. Dell’Asta, M. Della Pietra, D. della Volpe, M. Delmastro, P. Delpierre, N. Delruelle, P. A. Delsart, C. Deluca, S. Demers, M. Demichev, B. Demirkoz, J. Deng, S. P. Denisov, C. Dennis, D. Derendarz, J. E. Derkaoui, F. Derue, P. Dervan, K. Desch, E. Devetak, P. O. Deviveiros, A. Dewhurst, B. DeWilde, S. Dhaliwal, R. Dhullipudi, A. Di Ciaccio, L. Di Ciaccio, A. Di Girolamo, B. Di Girolamo, S. Di Luise, A. Di Mattia, R. Di Nardo, A. Di Simone, R. Di Sipio, M. A. Diaz, M. M. Diaz Gomez, F. Diblen, E. B. Diehl, H. Dietl, J. Dietrich, T. A. Dietzsch, S. Diglio, K. Dindar Yagci, J. Dingfelder, C. Dionisi, P. Dita, S. Dita, F. Dittus, F. Djama, R. Djilkibaev, T. Djobava, M. A. B. do Vale, A. Do Valle Wemans, T. K. O. Doan, M. Dobbs, R. Dobinson, D. Dobos, E. Dobson, M. Dobson, J. Dodd, O. B. Dogan, C. Doglioni, T. Doherty, Y. Doi, J. Dolejsi, I. Dolenc, Z. Dolezal, B. A. Dolgoshein, T. Dohmae, M. Donadelli, M. Donega, J. Donini, J. Dopke, A. Doria, A. Dos Anjos, M. Dosil, A. Dotti, M. T. Dova, J. D. Dowell, A. D. Doxiadis, A. T. Doyle, Z. Drasal, J. Drees, N. Dressnandt, H. Drevermann, C. Driouichi, M. Dris, J. G. Drohan, J. Dubbert, T. Dubbs, S. Dube, E. Duchovni, G. Duckeck, A. Dudarev, F. Dudziak, M. Dührssen, I. P. Duerdoth, L. Duflot, M.-A. Dufour, M. Dunford, H. Duran Yildiz, R. Duxfield, M. Dwuznik, F. Dydak, D. Dzahini, M. Düren, J. Ebke, S. Eckert, S. Eckweiler, K. Edmonds, C. A. Edwards, I. Efthymiopoulos, W. Ehrenfeld, T. Ehrich, T. Eifert, G. Eigen, K. Einsweiler, E. Eisenhandler, T. Ekelof, M. El Kacimi, M. Ellert, S. Elles, F. Ellinghaus, K. Ellis, N. Ellis, J. Elmsheuser, M. Elsing, R. Ely, D. Emeliyanov, R. Engelmann, A. Engl, B. Epp, A. Eppig, J. Erdmann, A. Ereditato, D. Eriksson, J. Ernst, M. Ernst, J. 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Yang, U. K. Yang, Y. Yang, Z. Yang, S. Yanush, W.-M. Yao, Y. Yao, Y. Yasu, J. Ye, S. Ye, M. Yilmaz, R. Yoosoofmiya, K. Yorita, R. Yoshida, C. Young, S. Youssef, D. Yu, J. Yu, L. Yuan, A. Yurkewicz, V. G. Zaets, R. Zaidan, A. M. Zaitsev, Z. Zajacova, Yo. K. Zalite, L. Zanello, P. Zarzhitsky, A. Zaytsev, M. Zdrazil, C. Zeitnitz, M. Zeller, P. F. Zema, A. Zemla, C. Zendler, A. V. Zenin, O. Zenin, T. Ženiš, Z. Zenonos, S. Zenz, D. Zerwas, G. Zevi della Porta, Z. Zhan, D. Zhang, H. Zhang, J. Zhang, X. Zhang, Z. Zhang, L. Zhao, T. Zhao, Z. Zhao, A. Zhemchugov, S. Zheng, J. Zhong, B. Zhou, N. Zhou, Y. Zhou, C. G. Zhu, H. Zhu, Y. Zhu, X. Zhuang, V. Zhuravlov, D. Zieminska, B. Zilka, R. Zimmermann, S. Zimmermann, M. Ziolkowski, R. Zitoun, L. Živković, V. V. Zmouchko, G. Zobernig, A. Zoccoli, Y. Zolnierowski, A. Zsenei, M. zur Nedden, V. Zutshi, and L. Zwalinski
Subjects: Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract Measurements of luminosity obtained using the ATLAS detector during early running of the Large Hadron Collider (LHC) at $\sqrt{s} = 7$ TeV are presented. The luminosity is independently determined using several detectors and multiple algorithms, each having different acceptances, systematic uncertainties and sensitivity to background. The ratios of the luminosities obtained from these methods are monitored as a function of time and of μ, the average number of inelastic interactions per bunch crossing. Residual time- and μ-dependence between the methods is less than 2% for 0
Published: 2011
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12. Translocation Breakpoints Preferentially Occur in Euchromatin and Acrocentric Chromosomes

Author: Cheng-Yu Lin, Ankit Shukla, John P. Grady, J. Lynn Fink, Eloise Dray, and Pascal H.G. Duijf
Subjects: translocations, DNA double strand breaks, DNA repair, leukemia, lymphoma, V(D)J recombination, CTCF, cohesin, nucleolus, acrocentric chromosomes, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract: Chromosomal translocations drive the development of many hematological and some solid cancers. Several factors have been identified to explain the non-random occurrence of translocation breakpoints in the genome. These include chromatin density, gene density and CCCTC-binding factor (CTCF)/cohesin binding site density. However, such factors are at least partially interdependent. Using 13,844 and 1563 karyotypes from human blood and solid cancers, respectively, our multiple regression analysis only identified chromatin density as the primary statistically significant predictor. Specifically, translocation breakpoints preferentially occur in open chromatin. Also, blood and solid tumors show markedly distinct translocation signatures. Strikingly, translocation breakpoints occur significantly more frequently in acrocentric chromosomes than in non-acrocentric chromosomes. Thus, translocations are probably often generated around nucleoli in the inner nucleoplasm, away from the nuclear envelope. Importantly, our findings remain true both in multivariate analyses and after removal of highly recurrent translocations. Finally, we applied pairwise probabilistic co-occurrence modeling. In addition to well-known highly prevalent translocations, such as those resulting in BCR-ABL1 (BCR-ABL) and RUNX1-RUNX1T1 (AML1-ETO) fusion genes, we identified significantly underrepresented translocations with putative fusion genes, which are probably subject to strong negative selection during tumor evolution. Taken together, our findings provide novel insights into the generation and selection of translocations during cancer development.
Published: 2018
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13. Basic Compatibility of Albugo candida in Arabidopsis thaliana and Brassica juncea Causes Broad-Spectrum Suppression of Innate Immunity

Author: A. J. Cooper, A. O. Latunde-Dada, A. Woods-Tör, J. Lynn, J. A. Lucas, I. R. Crute, and E. B. Holub
Subjects: oilseed mustard, Microbiology, QR1-502, Botany, QK1-989
Abstract: A biotrophic parasite often depends on an intrinsic ability to suppress host defenses in a manner that will enable it to infect and successfully colonize a susceptible host. If the suppressed defenses otherwise would have been effective against alternative pathogens, it follows that primary infection by the “suppressive” biotroph potentially could enhance susceptibility of the host to secondary infection by avirulent pathogens. This phenomenon previously has been attributed to true fungi such as rust (basidiomycete) and powdery mildew (ascomycete) pathogens. In our study, we observed broad-spectrum suppression of host defense by the oomycete Albugo candida (white blister rust) in the wild crucifer Arabidopsis thaliana and a domesticated relative, Brassica juncea. A. candida subsp. arabidopsis suppressed the “runaway cell death” phenotype of the lesion mimic mutant lsd1 in Arabidopsis thaliana in a sustained manner even after subsequent inoculation with avirulent Hyaloperonospora arabidopsis (Arabidopsis thaliana downy mildew). In sequential inoculation experiments, we show that preinfection by virulent Albugo candida can suppress disease resistance in cotyledons to several downy mildew pathogens, including contrasting examples of genotype resistance to H. arabidopsis in Arabidopsis thaliana that differ in the R protein and modes of defense signaling used to confer the resistance; genotype specific resistance in B. juncea to H. parasitica (Brassica downy mildew; isolates derived from B. juncea); species level (nonhost) resistance in both crucifers to Bremia lactucae (lettuce downy mildew) and an isolate of the H. parasitica race derived from Brassica oleracea; and nonhost resistance in B. juncea to H. arabidopsis. Broad-spectrum powdery mildew resistance conferred by RPW8 also was suppressed in Arabidopsis thaliana to two morphotypes of Erysiphe spp. following pre-infection with A. candida subsp. arabidopsis.
Published: 2008
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14. The Effects of a Single Night of Sleep Deprivation on Fluency and Prefrontal Cortex Function during Divergent Thinking

Author: Oshin eVartanian, Fethi eBouak, J. Lynn eCaldwell, Bob eCheung, Gerald eCupchik, Marie-Eve eJobidon, Quan eLam, Ann eNakashima, Michel ePaul, Henry ePeng, Paul J. Silvia, and Ingrid eSmith
Subjects: Executive Function, Fatigue, Sleep, divergent thinking, fluency, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: The dorsal and ventral aspects of the prefrontal cortex (PFC) are the two regions most consistently recruited in divergent thinking tasks. Given that frontal tasks have been shown to be vulnerable to sleep loss, we explored the impact of a single night of sleep deprivation on fluency (i.e., number of generated responses) and PFC function during divergent thinking. Participants underwent functional magnetic resonance imaging (fMRI) scanning twice while engaged in the Alternate Uses Task (AUT)—once following a single night of sleep deprivation and once following a night of normal sleep. They also wore wrist activity monitors, which enabled us to quantify daily sleep and model cognitive effectiveness. The intervention was effective, producing greater levels of fatigue and sleepiness. Modelled cognitive effectiveness and fluency were impaired following sleep deprivation, and sleep deprivation was associated with greater activation in the left inferior frontal gyrus during AUT. The results suggest that an intervention known to temporarily compromise frontal function can impair fluency, and that this effect is instantiated in the form of an increased haemodynamic response in the left inferior frontal gyrus.
Published: 2014
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15. Virtual Spaces: Employing a Synchronous Online Classroom to Facilitate Student Engagement in Online Learning

Author: J. Lynn McBrien, Rui Cheng, and Phyllis Jones
Subjects: Distance learning, synchronous online learning, transactional distance theory, virtual classroom, Special aspects of education, LC8-6691
Abstract: This research study is a collaborative project between faculty in social foundations, special education, and instructional technology in which we analyze student data from six undergraduate and graduate courses related to the use of a virtual classroom space. Transactional distance theory (Moore & Kearsley, 1996) operates as our theoretical framework as we explore the role of a virtual classroom in distance education and analyze the ways in which a synchronous learning environment affects students’ learning experiences. Elluminate Live! was the software employed in the virtual classroom. In this analysis, particular themes emerged related to dialogue, structure, and learner autonomy. In addition, students rated convenience, technical issues, and pedagogical preferences as important elements in their learning experiences. The article discusses these themes as a contribution to reducing the “distance” that students experience in online learning and to developing quality distance education experiences for students in higher education.
Published: 2009

16. Deliberate practice to improve interdisciplinary communication: A pilot study

Author: Godsey, Veronica, Gaither, Stacy, Tofil, Nancy M., Norwood, Carrie, Zinkan, J. Lynn, Rahman, AKM Fazlur, Aban, Inmaculada, and Rutledge, Chrystal
Published: 2023
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17. Degradation and Reliability of Organic Materials in Organic Light-Emitting Diodes (OLEDs)

Author: Rountree, Kelley, Davis, J. Lynn, Riter, Karmann C., Kim, Jean, McCombs, Michelle, Pope, Roger, van Driel, Willem Dirk, editor, and Yazdan Mehr, Maryam, editor
Published: 2022
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18. Reliability and Failures in Solid State Lighting Systems

Author: van Driel, W. D., Jacobs, B. J. C., Onushkin, G., Watte, P., Zhao, X., Davis, J. Lynn, van Driel, Willem Dirk, editor, and Yazdan Mehr, Maryam, editor
Published: 2022
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19. The Role of Resilience in Black Men’s Success in STEM Graduate Programs

Author: Gazley, J. Lynn and Campbell, Patricia B.
Published: 2022

20. Insights Gained into Marginalized Students Access Challenges During the COVID-19 Academic Response

Author: Kimble-Hill, Ann C., Rivera-Figueroa, Armando, Chan, Benny C., Lawal, Wasiu A., Gonzalez, Sheryl, Adams, Michael R., Heard, George L., Gazley, J. Lynn, and Fiore-Walker, Benjamin
Abstract: The American Chemical Society (ACS) Committee on Minority Affairs (CMA) endeavors to support all chemistry faculty and staff as they educate all of our students during this pandemic. While the chemistry education community and the ACS have both provided resources as most institutions transitioned to virtual platforms, this pandemic disproportionally affects our students of color, lower socio-economic and rural backgrounds, and students with disabilities. Specifically, these students must overcome hurdles of technology access, environmental disruptions, and cultural pressures in order to be successful. Therefore, CMA has formulated partnerships with both academic and industrial institutions to highlight some best practices to improve future virtual learning experiences of these oftentimes marginalized students. Specifically, the work presented here examines programs and policies at three academic institutions with very different student body demographics and surrounding learning environments (Indiana University Purdue University Indianapolis (IUPUI), The College of New Jersey (TCNJ), and Los Angeles Community College District (LACCD)) with an attempt to identify variables that enhance marginalized student success in chemistry courses. The combination of their results suggests elements such as access to technology, home responsibility, and impostor syndrome, that other learning programs should consider to increase virtual learning success. Furthermore, other stopgap measures implemented at industrial partners give insight as to how these considerations can be implemented during virtual internship programs to meet their learning objectives associated with entering their institutional pipeline.
Published: 2020
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21. Theory of Change to Practice: How Experimentalist Teaching Enabled Faculty to Navigate the COVID-19 Disruption

Author: Chan, Benny C., Baker, Joseph L., Bunagan, Michelle R., Ekanger, Levi A., Gazley, J. Lynn, Hunter, Rebecca A., O'Connor, Abby R., and Triano, Rebecca M.
Abstract: The College of New Jersey's Chemistry Department and School of Science have been strategically transforming our teaching, learning, and mentoring environments for over a decade through programs that are targeted toward "new majority" students: low-income, first generation, and historically marginalized races and ethnicities. Recently, we shifted from programs that target a small number of students to focus on systemic and structural changes to create inclusive excellence. We formalized our work in a Theory of Change (ToC) that emphasizes mechanisms for our faculty to depart from traditional pedagogy to become experimentalist teachers who use evidence-based practices and data to support our student success. The ToC is built on three pillars: (1) gaining empathy and understanding of our students, (2) a changing toolkit of acceptable pedagogical practices, and (3) a process to create shared language and values and an understanding of our responsibilities to our students. By focusing on mechanism, we do not prescribe a single pedagogy but instead are flexible for different course contexts. Department work on the ToC allowed our faculty to pivot instead of panic during the shift to online instruction. The students noted smooth transitions to remote learning, and more importantly, departmental discussions regarding pedagogy helped faculty to support each other with suggestions and sharing of best practices. As a department, we learned a great deal during the pandemic that furthers our collective work toward inclusive excellence and believe our ToC is transferable to other institutions.
Published: 2020
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22. The Role of Resilience in Black Men's Success in STEM Graduate Programs

Author: Gazley, J. Lynn and Campbell, Patricia B.
Abstract: Although significant underrepresentation remains, many Black men successfully complete PhDs in science, accruing resources and deploying resilience strategies to manage stress including the constant stress associated with racism. We explore the role resilience plays in the success of three Black men, using annual interviews collected from beginning graduate school through attaining the PhD. Based on their experiences, we frame resilience as a replenishable resource, where the level of resource at any given moment reflects a history of withdrawal and renewal. In addition, we provide suggestions for ways students can build and deploy resilience resources to help them move toward their goals and point out the critical role graduate institutions play in creating resource-rich contexts for Black students.
Published: 2020
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23. The Role of Resilience in Black Men’s Success in STEM Graduate Programs

Author: Gazley, J. Lynn and Campbell, Patricia B.
Published: 2020
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24. Incidence and Risk Factors of Heterotopic Ossification in the Knee After Reamed Tibial Nailing

Author: Jones, Corey A., primary, Seilern und Aspang, Jesse, additional, Holmes, Jeffrey S., additional, Zamanzadeh, Ryan S., additional, Phen, Huai M., additional, Baker, J.'Lynn L., additional, Hernandez-Irizarry, Roberto C., additional, and Moore, Thomas J., additional
Published: 2024
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25. Subtype-Specific Analyses Reveal Infiltrative Basal Cell Carcinomas Are Highly Interactive with their Environment

Author: Villani, Rehan, Murigneux, Valentine, Alexis, Josue, Sim, Seen-Ling, Wagels, Michael, Saunders, Nicholas, Soyer, H. Peter, Parmentier, Laurent, Nikolaev, Sergey, Fink, J. Lynn, Roy, Edwige, and Khosrotehrani, Kiarash
Published: 2021
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26. AUTONOMOUS AGRICULTURE a premature promise?

Author: FRASER, J. LYNN
Published: 2024

27. Adapting to the unpredictable: Preparing Canadian greenhouses for climate change challenges.

Author: FRASER, J. LYNN
Subjects: GREENHOUSES, CLIMATE change, BUILT environment, TELECOMMUNICATION
Published: 2024

28. CONSUMER TRENDS 2024: Sustainability, health and wellness are major forces in the marketplace.

Author: FRASER, J. LYNN
Subjects: GREENHOUSES, SUSTAINABILITY, CONSUMER attitudes, MARKETPLACES, EMPLOYEE attitudes
Published: 2024

29. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Author: Allison, Sarah, Bailey, Peter J., Bailey, Ulla-Maja, Biankin, Andrew V., Beraldi, Dario, Brunton, Holly, Caligiuri, Giuseppina, Cameron, Euan, Chang, David K., Cooke, Susanna L., Cunningham, Richard, Dreyer, Stephan, Grimwood, Paul, Kelly, Shane, Lampraki, Eirini-Maria, Marshall, John, Martin, Sancha, McDade, Brian, McElroy, Daniel, Musgrove, Elizabeth A., Nourse, Craig, Paulus-Hock, Viola, Ramsay, Donna, Upstill-Goddard, Rosie, Wright, Derek, Jones, Marc D., Evers, Lisa, Rebus, Selma, Rahib, Lola, Serrels, Bryan, Hair, Jane, Jamieson, Nigel B., McKay, Colin J., Westwood, Paul, Williams, Nicola, Duthie, Fraser, Johns, Amber L., Mawson, Amanda, Scarlett, Christopher J., Brancato, Mary-Anne L., Rowe, Sarah J., Simpson, Skye H., Martyn-Smith, Mona, Thomas, Michelle T., Chantrill, Lorraine A., Chin, Venessa T., Chou, Angela, Cowley, Mark J., Humphris, Jeremy L., Mead, R. Scott, Nagrial, Adnan M., Pajic, Marina, Pettit, Jessica, Pinese, Mark, Rooman, Ilse, Wu, Jianmin, Tao, Jiang, DiPietro, Renee, Watson, Clare, Steinmann, Angela, Lee, Hong Ching, Wong, Rachel, Pinho, Andreia V., Giry-Laterriere, Marc, Daly, Roger J., Sutherland, Robert L., Grimmond, Sean M., Waddell, Nicola, Kassahn, Karin S., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, J. Lynn, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity, Pearson, John V., Bailey, Peter, Quinn, Michael, Nagaraj, Shivashankar, Kazakoff, Stephen, Waddell, Nick, Krisnan, Keerthana, Quek, Kelly, Wood, David, Samra, Jaswinder S., Gill, Anthony J., Pavlakis, Nick, Guminski, Alex, Toon, Christopher, Asghari, Ray, Merrett, Neil D., Pavey, Darren, Das, Amitabha, Cosman, Peter H., Ismail, Kasim, O’Connnor, Chelsie, Lam, Vincent W., McLeod, Duncan, Pleass, Henry C., Richardson, Arthur, James, Virginia, Kench, James G., Cooper, Caroline L., Joseph, David, Sandroussi, Charbel, Crawford, Michael, Gallagher, James, Texler, Michael, Forest, Cindy, Laycock, Andrew, Epari, Krishna P., Ballal, Mo, Fletcher, David R., Mukhedkar, Sanjay, Spry, Nigel A., DeBoer, Bastiaan, Chai, Ming, Zeps, Nikolajs, Beilin, Maria, Feeney, Kynan, Nguyen, Nan Q., Ruszkiewicz, Andrew R., Worthley, Chris, Tan, Chuan P., Debrencini, Tamara, Chen, John, Brooke-Smith, Mark E., Papangelis, Virginia, Tang, Henry, Barbour, Andrew P., Clouston, Andrew D., Martin, Patrick, O’Rourke, Thomas J., Chiang, Amy, Fawcett, Jonathan W., Slater, Kellee, Yeung, Shinn, Hatzifotis, Michael, Hodgkinson, Peter, Christophi, Christopher, Nikfarjam, Mehrdad, Mountain, Angela, Biobank, Victorian Cancer, Eshleman, James R., Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Hodgin, Mary, Scarpa, Aldo, Lawlor, Rita T., Beghelli, Stefania, Corbo, Vincenzo, Scardoni, Maria, Bassi, Claudio, Tempero, Margaret A., Graham, Janet S., Dreyer, Stephan B., Paris, Clara, Dray, Eloise, Plenker, Dennis, Galluzzo, Zachary, Tesson, Mathias, Jones, Marc, Moran-Jones, Kim, Wright, Derek W., Oien, Karin, McGregor, Grant A., Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephan, Dziubinski, Michele L., Candido, Juliana, Balkwill, Frances, Barry, Simon T., Grützmann, Robert, Johns, Amber, Froeling, Fieke E.M., Beer, Phillip, Petersen, Gloria M., Ashworth, Alan, Frame, Margaret C., Crawford, Howard C., Simeone, Diane M., Lord, Chris, Mukhopadhyay, Debabrata, Pilarsky, Christian, Tuveson, David A., Morton, Jennifer P., and Sansom, Owen J.
Published: 2021
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30. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Author: Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee 0006, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang 0062, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang 0032, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, and Jorge Zamora
Published: 2020
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31. Inherited BRCA1 and RNF43 pathogenic variants in a familial colorectal cancer type X family

Author: Chan, James M., primary, Clendenning, Mark, additional, Joseland, Sharelle, additional, Georgeson, Peter, additional, Mahmood, Khalid, additional, Joo, Jihoon E., additional, Walker, Romy, additional, Como, Julia, additional, Preston, Susan, additional, Chai, Shuyi Marci, additional, Chu, Yen Lin, additional, Meyers, Aaron L., additional, Pope, Bernard J., additional, Duggan, David, additional, Fink, J. Lynn, additional, Macrae, Finlay A., additional, Rosty, Christophe, additional, Winship, Ingrid M., additional, Jenkins, Mark A., additional, and Buchanan, Daniel D., additional
Published: 2023
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32. Advances in Teaching Inorganic Chemistry Volume 1: Classroom Innovations and Faculty Development

Author: Rebecca M. Jones, Barbara A. Reisner, Joanne L. Stewart, Sabrina G. Sobel, Terrie Salupo-Bryant, Adam R. Johnson, Chip Nataro, Zachary Thammavongsy, Brent J. Hamstra, Sibrina N. Collins, Levi A. Ekanger, Benny C. Chan, J. Lynn Gazley, Abby R. O'Connor, Justin M. Pratt, Jeffrey R. Raker, Jeffrey R. R and Rebecca M. Jones, Barbara A. Reisner, Joanne L. Stewart, Sabrina G. Sobel, Terrie Salupo-Bryant, Adam R. Johnson, Chip Nataro, Zachary Thammavongsy, Brent J. Hamstra, Sibrina N. Collins, Levi A. Ekanger, Benny C. Chan, J. Lynn Gazley, Abby R. O'Connor, Justin M. Pratt, Jeffrey R. Raker, Jeffrey R. R
Published: 2020

33. Virtual Spaces: Employing a Synchronous Online Classroom to Facilitate Student Engagement in Online Learning

Author: McBrien, J. Lynn, Jones, Phyllis, and Cheng, Rui
Abstract: This research study is a collaborative project between faculty in social foundations, special education, and instructional technology in which we analyze student data from six undergraduate and graduate courses related to the use of a virtual classroom space. Transactional distance theory (Moore & Kearsley, 1996) operates as our theoretical framework as we explore the role of a virtual classroom in distance education and analyze the ways in which a synchronous learning environment affects students' learning experiences. Elluminate Live! was the software employed in the virtual classroom. In this analysis, particular themes emerged related to dialogue, structure, and learner autonomy. In addition, students rated convenience, technical issues, and pedagogical preferences as important elements in their learning experiences. The article discusses these themes as a contribution to reducing the "distance" that students experience in online learning and to developing quality distance education experiences for students in higher education. (Contains 7 tables.)
Published: 2009

34. Flipped Active Learning in Your Mathematics Classroom without Videos

Author: Patterson, Brian, McBride, C. Rett, and Gieger, J. Lynn
Abstract: We explored the effectiveness of a flipped active learning pedagogy in a liberal arts mathematics course without video or interactive preparation. In both control and active learning classes, students were required to respond to a reading before class and take a quiz after class. During the active learning class, students worked together in groups on problems instead of listening to a lecture. This modest change in the in-class course structure showed that students were more willing to work with peers and ask questions of the instructor. Sources examined include common grade items as well as pre- and post-course attitude surveys.
Published: 2018
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35. Minimizing Sample Failure Rates for Challenging Clinical Tumor Samples

Author: J. Lynn Fink, Binny Jaradi, Nathan Stone, Lisa Anderson, Paul J. Leo, Mhairi Marshall, Jonathan Ellis, Paul M. Waring, and Kenneth O’Byrne
Subjects: Molecular Medicine, Pathology and Forensic Medicine
Published: 2023

36. Exquisitely Platinum-Sensitive Triple-Negative Breast Cancer, Time for BRCA Methylation Testing?

Author: Tan, Tira J., Fink, J. Lynn, Tay, Timothy K., Jaradi, Binny, Stone, Nathan, Waring, Paul, Koo, Kevin M., Tan, Puay Hoon, Tan, Daniel S., and Dent, Rebecca A.
Published: 2022
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37. Fatigue and its management in the workplace

Author: Caldwell, John A., Caldwell, J. Lynn, Thompson, Lauren A., and Lieberman, Harris R.
Published: 2019
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38. Waste not, want not: Reaping the benefits of waste heat.

Author: FRASER, J. LYNN
Subjects: WASTE heat, REVERSIBLE work (Mechanics), SUSTAINABLE development, AGRICULTURAL wastes, PLANT species
Published: 2024

39. The Impact of a 9-Month Booster Training Using Rapid Cycle Deliberate Practice on Pediatric Resident PALS Skills

Author: Surapa Raju, Sai, Tofil, Nancy M., Gaither, Stacy L., Norwood, Carrie, Zinkan, J. Lynn, Godsey, Veronica, Aban, Inmaculada, Xue, Yumo, and Rutledge, Chrystal
Published: 2021
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40. Bear-Human Relationships in Native Eastern North America

Author: Waselkov, Gregory A., primary and Funkhouser, J. Lynn, additional
Published: 2020
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41. Genome‐wide exploration reveals distinctive northern and southern variants of Clonorchis sinensis in the Far East

Author: Liina Kinkar, Pasi K. Korhonen, Urmas Saarma, Tao Wang, Xing‐Quan Zhu, Ivon Harliwong, Bicheng Yang, J. Lynn Fink, Daxi Wang, Bill C. H. Chang, Galina N. Chelomina, Anson V. Koehler, Neil D. Young, and Robin B. Gasser
Subjects: Genetics, Ecology, Evolution, Behavior and Systematics, Biotechnology
Published: 2023

42. Understanding chromaticity shifts in LED devices through analytical models

Author: Davis, J. Lynn, Mills, Karmann C., Bobashev, Georgiy, Rountree, Kelley J., Lamvik, Michael, Yaga, Robert, and Johnson, Cortina
Published: 2018
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43. Computational approaches to identify functional genetic variants in cancer genomes

Author: Gonzalez-Perez, Abel, Mustonen, Ville, Reva, Boris, Ritchie, Graham RS, Creixell, Pau, Karchin, Rachel, Vazquez, Miguel, Fink, J Lynn, Kassahn, Karin S, Pearson, John V, Bader, Gary D, Boutros, Paul C, Muthuswamy, Lakshmi, Ouellette, BF Francis, Reimand, Jueri, Linding, Rune, Shibata, Tatsuhiro, Valencia, Alfonso, Butler, Adam, Dronov, Serge, Flicek, Paul, Shannon, Nick B, Carter, Hannah, Ding, Li, Sander, Chris, Stuart, Josh M, Stein, Lincoln D, and Lopez-Bigas, Nuria
Subjects: Cancer, Computational Biology, Genetic Variation, Genome, Human, Humans, Mutation, Neoplasms, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract: The International Cancer Genome Consortium (ICGC) aims to catalog genomic abnormalities in tumors from 50 different cancer types. Genome sequencing reveals hundreds to thousands of somatic mutations in each tumor but only a minority of these drive tumor progression. We present the result of discussions within the ICGC on how to address the challenge of identifying mutations that contribute to oncogenesis, tumor maintenance or response to therapy, and recommend computational techniques to annotate somatic variants and predict their impact on cancer phenotype.
Published: 2013

44. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Author: M. Sivade Dumousseau, Diego Alonso-López, Mais G. Ammari, Glyn Bradley, Nancy H. Campbell, Arnaud Céol, Gianni Cesareni, Colin W. Combe, Javier De Las Rivas, Noemi del-Toro, Joshua Heimbach, Henning Hermjakob, Igor Jurisica, Maximilian Koch, Luana Licata, Ruth C. Lovering, David J. Lynn, Birgit H. M. Meldal, Gos Micklem, Simona Panni, Pablo Porras, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwínski, Anjali Shrivastava, Julie M. Sullivan, Nicolas Thierry-Mieg, Yo Yehudi, Kim Van Roey, and Sandra E. Orchard
Published: 2018
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45. Understanding chromaticity shifts in LED devices through analytical models.

Author: J. Lynn Davis, Karmann C. Mills, Georgiy V. Bobashev, Kelley J. Rountree, Michael Lamvik, Robert Yaga, and Cortina Johnson
Published: 2018
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46. Subclonal evolution in disease progression from MGUS/SMM to multiple myeloma is characterised by clonal stability

Author: Dutta, Ankit K., Fink, J. Lynn, Grady, John P., Morgan, Gareth J., Mullighan, Charles G., To, Luen B., Hewett, Duncan R., and Zannettino, Andrew C. W.
Published: 2019
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47. Adding the 'US' in FNA: Pearls for starting a pathologist-performed ultrasound-guided fine needle aspiration service (USG FNA)

Author: Terrance J. Lynn and Sara E. Monaco
Subjects: Pathologists, Image-Guided Biopsy, Biopsy, Fine-Needle, Humans, Laboratories, Ultrasonography, Interventional, Pathology and Forensic Medicine
Abstract: Ultrasound-guided fine needle aspiration (USG-FNA) biopsies have traditionally been performed in the radiology department, with radiologists performing the procurement with or without on-site cytotechnologists or pathologists to provide adequacy or diagnostic evaluation of the specimen. However, more recently, these image-guided biopsies have been performed by endocrinologists and now cytopathologists. Starting an USG-FNA service is a big task that requires consideration of multiple factors, including training, certification, privileges, equipment, documentation, information technology (IT) issues, and the overall business plan or financial component. In this review, the issues confronted when bringing on an USG-FNA service are discussed in detail in an effort to highlight the issues and challenges that many cytopathology laboratories are facing when implementing this new service.
Published: 2022

48. Educational Needs and Barriers for Refugee Students in the United States: A Review of the Literature

Author: McBrien, J. Lynn
Published: 2005

49. Decrease in Anogenital Distance among Male Infants with Prenatal Phthalate Exposure

Author: Swan, Shanna H., Main, Katharina M., Liu, Fan, Stewart, Sara L., Kruse, Robin L., Calafat, Antonia M., Mao, Catherine S., Redmon, J. Bruce, Ternand, Christine L., Sullivan, Shannon, and Teague, J. Lynn
Published: 2005

50. Minimizing Sample Failure Rates for Challenging Clinical Tumor Samples

Author: Fink, J. Lynn, primary, Jaradi, Binny, additional, Stone, Nathan, additional, Anderson, Lisa, additional, Leo, Paul J., additional, Marshall, Mhairi, additional, Ellis, Jonathan, additional, Waring, Paul M., additional, and O’Byrne, Kenneth, additional
Published: 2023
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