315 results on '"Kruszka P"'
Search Results
2. Structural basis of pH-dependent activation in a CLC transporter
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Fortea, Eva, Lee, Sangyun, Chadda, Rahul, Argyros, Yiorgos, Sandal, Priyanka, Mahoney-Kruszka, Robyn, Ciftci, Hatice Didar, Falzone, Maria E., Huysmans, Gerard, Robertson, Janice L., Boudker, Olga, and Accardi, Alessio
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- 2024
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3. Parameters of 150 temperate and boreal tree species and provenances for an individual-based forest landscape and disturbance model
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Dominik Thom, Werner Rammer, Katharina Albrich, Kristin H. Braziunas, Laura Dobor, Christina Dollinger, Winslow D. Hansen, Brian J. Harvey, Tomáš Hlásny, Tyler J. Hoecker, Juha Honkaniemi, William S. Keeton, Yuta Kobayashi, Sofia Saenz Kruszka, Akira Mori, Jenna E. Morris, Stephen Peters-Collaer, Zak Ratajczak, Trond Simensen, Ilié Storms, Kureha F. Suzuki, Anthony R. Taylor, Monica G. Turner, Susan Willis, and Rupert Seidl
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iLand ,Simulation modeling ,Species parameters ,Wind parameters ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Science (General) ,Q1-390 - Abstract
Understanding the impacts of changing climate and disturbance regimes on forest ecosystems is greatly aided by the use of process-based models. Such models simulate processes based on first principles of ecology, which requires parameterization. Parameterization is an important step in model development and application, defining the characteristics of trees and their responses to the environment, i.e., their traits. For species-specific models, parameterization is usually done at the level of individual species. Parameterization is indispensable for accurately modeling demographic processes, including growth, mortality, and regeneration of trees, along with their intra- and inter-specific interactions. As it is time-demanding to compile the parameters required to simulate forest ecosystems in complex models, simulations are often restricted to the most common tree species, genera, or plant-functional types. Yet, as tree species composition might change in the future, it is important to account for a broad range of species and their individual responses to drivers of change explicitly in simulations. Thus, species-specific parameterization is a critical task for making accurate projections about future forest trajectories, yet species parameters often remain poorly documented in simulation studies.We compiled and harmonized all existing tree species parameters available for the individual-based forest landscape and disturbance model (iLand). Since its first publication in 2012, iLand has been applied in 50 peer-reviewed publications across three continents throughout the Northern Hemisphere (i.e., Europe, North America, and Asia). The model operates at individual-tree level and simulates ecosystem processes at multiple spatial scales, making it a capable process-based model for studying forest change. However, the extensive number of processes and their interactions as well as the wide range of spatio-temporal scales considered in iLand require intensive parameterization, with tree species characterized by 66 unique parameters in the model. The database presented here includes parameters for 150 temperate and boreal tree species and provenances (i.e., regional variations). Excluding missing values, the database includes a total of 9,249 individual parameter entries. In addition, we provide parameters for the individual susceptibility of tree species to wind disturbance (five parameters) for a subset of 104 tree species and provenances (498 parameter entries). To guide further model parameterization efforts, we provide an estimate of uncertainty for each species based on how thoroughly simulations with the respective parameters were evaluated against independent data.Our dataset aids the future parameterization and application of iLand, and sets a new standard in documenting parameters used in process-based forest simulations. This dataset will support model application in previously unstudied areas and can facilitate the investigation of new tree species being introduced to well-studied systems (e.g., simulating assisted migration in the context of rapid climate change). Given that many process-based models rely on similar underlying processes our harmonized parameter set will be of relevance beyond the iLand community. Our work could catalyze further research into improving the parameterization of process-based forest models, increasing the robustness of projections of climate change impacts and adaptation strategies.
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- 2024
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4. Evaluation of Cytotoxic Activity of Cell Biomass from Eryngium planum and Lychnis flos-cuculi on Melanoma Cancer Cell
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Anastasia Aliesa Hermosaningtyas, Ewa Totoń, Natalia Lisiak, Dariusz Kruszka, Anna Budzianowska, and Małgorzata Kikowska
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melanoma cell ,cytotoxic activity ,flat sea holly ,ragged robin ,callus ,plant cell cultures ,Organic chemistry ,QD241-441 - Abstract
Melanoma is a malignant neoplasm of melanocytes in the skin, and its occurrence is increasing annually. Plant-based products contain active compounds with low toxicity and are accessible alternatives for melanoma cancer treatment. The biotechnology approach for obtaining plant-based products provides continuity and allows the high-yield production of phytochemically uniform biomass. The callus biomass of Eryngium planum L. and Lychnis flos-cuculi L. was induced on Murashige and Skoog (MS) medium supplemented with growth regulators. A combination of 3.0 mg/L of 3,6-dichloro-2-methoxybenzoic acid (dicamba) and 0.3 mg/L of 1-phenyl-3-(1,2,3-thiadiazol-5-yl)urea—(thidiazuron) was used to obtain E. planum callus. Meanwhile, the callus of L. flos-cuculi was cultivated on MS medium with 2.0 mg/L of 2,4-dichlorophenoxyacetic acid (2,4-D). Methanolic extracts (EpME and LFcME), including 40% MeOH fractions (Ep40MF and LFc40MF) and 80% MeOH fractions (Ep80MF and LFc80MF), of E. planum and L. flos-cuculi cell biomass were prepared. Their cytotoxicity activity was assessed in human fibroblast cells (MRC-5) and human melanoma cells (MeWo) by direct cell counting and 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay. Qualitative analyses using thin-layer chromatography and UPLC-HRMS/MS chromatograms showed the presence of phenolic acids and saponins within the extracts and fractions of both cell biomasses. LFc80MF and Ep80MF showed the strongest toxicity against the MeWo cell line, with IC50 values of 47 ± 0.5 and 52 ± 4 μg/mL after 72 h of treatment. EpME and LFcME had IC50 values of 103 ± 4 and 147 ± 4 µg/mL, respectively. On the other hand, Ep40MF and LFc40MF were less toxic against the MeWo cell line compared to the extracts and 80% MeOH fractions, with IC50 values of 145 ± 10 and 172 ± 7 µg/mL. This study suggests that the obtained extracts and fractions of E. planum and L. flos-cuculi cell biomass potentially possess significant cytotoxic activity against MeWo cells, which work in a time and dose-dependent manner. Although the extracts and 80% MeOH fractions were more potent, the 40% MeOH was shown to be more selective against the MeWo than the control MRC-5 cells.
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- 2024
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5. Author Correction: Structural basis of pH-dependent activation in a CLC transporter
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Fortea, Eva, Lee, Sangyun, Chadda, Rahul, Argyros, Yiorgos, Sandal, Priyanka, Mahoney-Kruszka, Robyn, Ciftci, Hatice Didar, Falzone, Maria E., Huysmans, Gerard, Robertson, Janice L., Boudker, Olga, and Accardi, Alessio
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- 2024
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6. P014: Multiple cases of mosaic X-linked adrenoleukodystrophy in males identified through newborn screening
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Alexandra Keefe, Dana Jensen, Renee Bend, Michelle Morrow, Paul Kruszka, Lauren O'Grady, Florian Eichler, Angela Sun, and James Bennett
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Genetics ,QH426-470 ,Medicine - Published
- 2024
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7. P149: Exome sequencing vs chromosomal microarray for copy number variant detection
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Kirsty McWalter, Ganka Douglas, Amanda Lindy, Jane Juusola, and Paul Kruszka
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Genetics ,QH426-470 ,Medicine - Published
- 2024
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8. P194: SeqFirst mitigates race-based disparities in access to a precise genetic diagnosis in hospitalized neonates
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Tara Wenger, Alexandra Keefe, Lukas Kruidenier, Megan Sikes, Abbey Scott, Joon-Ho Yu, Kate MacDuffie, Kailyn Anderson, Olivia Sommers, Heidi Gildersleeve, Kati Buckingham, Jessica Chong, Katrina Dipple, David Veenstra, Dan Doherty, Daniel Miller, Deborah Copenheaver, Jane Juusola, Amy Snook, Chayna Davis, Kirsty McWalter, Paul Kruszka, and Michael Bamshad
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Genetics ,QH426-470 ,Medicine - Published
- 2024
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9. P214: SeqFirst DDi: Early whole genome sequencing improves access to early precise genetic diagnosis for children with developmental differences
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Katrina Dipple, Daniel Doherty, Kailyn Anderson, Olivia Sommers, Tara Wenger, Kate MacDuffie, Alexandra Keefe, Abbey Scott, Lukas Kruidenier, Jamie Love-Nichols, Heidi Gildersleeve, Chayna Davis, Kati Buckingham, Jessica Chong, David Veenstra, Danny Miller, Deborah Copenheaver, Jane Juusola, Kyle Retterer, Kirsty McWalter, Paul Kruszka, Joon-Ho Yu, and Michael Bamshad
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Genetics ,QH426-470 ,Medicine - Published
- 2024
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10. P293: Long read sequencing analysis of 120 samples with known and challenging-to-detect clinical variants
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Joseph Devaney, Jessica Noya, April Berlyoung, Aaron Johnson, Julianna Spangler, Rhonda Brandon, Kathleen Hruska, Lucas Lochovsky, Egor Dolzhenko, Xiao Chen, Michael Eberle, Alexander Robertson, Paul Kruszka, Gustavo Stolovitzky, and Scott Newman
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Genetics ,QH426-470 ,Medicine - Published
- 2024
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11. O35: Feasibility of expanded newborn screening using genome sequencing for early actionable conditions in a diverse city
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Wendy Chung, Alban Ziegler, Carrie Koval-Burt, Denise Kay, Sharon Suchy, Amber Bergtrup, Katherine Langley, Laura Amendola, Brenna Boyd, Jennifer Bradley, Tracy Brandt, Lilian Cohen, Alison Coffey, Joseph Devaney, Beata Dygulska, Bethany Friedman, Ramsey Fuleihan, Awura Gyimah, Rebecca Hernan, Sean Hofherr, Kathleen Hruska, Zhanzhi Hu, Mederic Jeanne, Guanjun Jin, Aaron Johnson, Haluk Kavus, Rudolph Leibel, Kirsty McWalter, Kristin Monaghan, Nicole Pimentel Soler, Yeyson Quevedo, Samantha Ratner, Kyle Retterer, Natasha Shapiro, Robert Sicko, Samuel Storm, Rebecca Torene, Olatundun Williams, Julia Wynn, Ryan Taft, Paul Kruszka, and Michele Caggana
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Genetics ,QH426-470 ,Medicine - Published
- 2024
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12. Revealing the transitory and local effect of zebularine on development and on proteome dynamics of Salix purpurea
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Andrea Pagano, Carolina Gomes, Evy Timmerman, Paweł Sulima, Jerzy Andrzej Przyborowski, Dariusz Kruszka, Francis Impens, and Jorge Almiro Pinto Paiva
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purple willow ,cytidine analogue ,DNA methylation ,plant development ,proteomic ,Plant culture ,SB1-1110 - Abstract
IntroductionDNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for woody species, DNA methylation constitutes a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes.MethodsThe present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach was adopted to highlight the effects of zebularine on proteomic dynamics, revealing age-specific (3 weeks of in vitro culture and 1 month of growth in soil) and tissue-specific (stem and root) effects.Results and discussionAfter 3 weeks of recovery from zebularine treatment, a decrease of 5-mC levels was observed in different genomic contexts in the roots of explants that were exposed to zebularine, whereas a functionally heterogeneous subset of protein entries was differentially accumulated in stem samples, including entries related to cell wall biosynthesis, tissue morphogenesis, and hormonal regulation. Significant proteomic remodeling was revealed in the development from in vitro to in-soil culture, but no significant changes in 5-mC levels were observed. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation and proteome in early plant development in willow species. Proteomic data are available via ProteomeXchange with identifier PXD045653. WGBS data are available under BioProject accession PRJNA889596.
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- 2024
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13. The human Y and inactive X chromosomes similarly modulate autosomal gene expression
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Adrianna K. San Roman, Helen Skaletsky, Alexander K. Godfrey, Neha V. Bokil, Levi Teitz, Isani Singh, Laura V. Blanton, Daniel W. Bellott, Tatyana Pyntikova, Julian Lange, Natalia Koutseva, Jennifer F. Hughes, Laura Brown, Sidaly Phou, Ashley Buscetta, Paul Kruszka, Nicole Banks, Amalia Dutra, Evgenia Pak, Patricia C. Lasutschinkow, Colleen Keen, Shanlee M. Davis, Angela E. Lin, Nicole R. Tartaglia, Carole Samango-Sprouse, Maximilian Muenke, and David C. Page
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sex chromosomes ,sex differences ,X chromosome inactivation ,aneuploidy ,Turner syndrome ,Klinefelter syndrome ,Genetics ,QH426-470 ,Internal medicine ,RC31-1245 - Abstract
Summary: Somatic cells of human males and females have 45 chromosomes in common, including the “active” X chromosome. In males the 46th chromosome is a Y; in females it is an “inactive” X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors—ZFX and ZFY—encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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- 2024
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14. Loss-of-Function Variants in PPP1R12A: From Isolated Sex Reversal to Holoprosencephaly Spectrum and Urogenital Malformations.
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Hughes, Joel, Alkhunaizi, Ebba, Kruszka, Paul, Pyle, Louise, Grange, Dorothy, Berger, Seth, Payne, Katelyn, Masser-Frye, Diane, Hu, Tommy, Christie, Michelle, Clegg, Nancy, Everson, Joshua, Martinez, Ariel, Walsh, Laurence, Bedoukian, Emma, Jones, Marilyn, Harris, Catharine, Riedhammer, Korbinian, Choukair, Daniela, Fechner, Patricia, Rutter, Meilan, Hufnagel, Sophia, Roifman, Maian, Kletter, Gad, Delot, Emmanuele, Vilain, Eric, Lipinski, Robert, Vezina, Chad, Muenke, Maximilian, and Chitayat, David
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MYPT1 ,PPP1R12A ,disorders of sex development ,embryogenesis ,encephalocele ,facial dysmorphism ,forebrain ,holoprosencephaly ,hypospadias ,omphalocele ,Abnormalities ,Multiple ,Adolescent ,Child ,Child ,Preschool ,Disorders of Sex Development ,Female ,Gestational Age ,Holoprosencephaly ,Humans ,Male ,Mutation ,Myosin-Light-Chain Phosphatase ,Phenotype ,Pregnancy ,Urogenital Abnormalities - Abstract
In two independent ongoing next-generation sequencing projects for individuals with holoprosencephaly and individuals with disorders of sex development, and through international research collaboration, we identified twelve individuals with de novo loss-of-function (LoF) variants in protein phosphatase 1, regulatory subunit 12a (PPP1R12A), an important developmental gene involved in cell migration, adhesion, and morphogenesis. This gene has not been previously reported in association with human disease, and it has intolerance to LoF as illustrated by a very low observed-to-expected ratio of LoF variants in gnomAD. Of the twelve individuals, midline brain malformations were found in five, urogenital anomalies in nine, and a combination of both phenotypes in two. Other congenital anomalies identified included omphalocele, jejunal, and ileal atresia with aberrant mesenteric blood supply, and syndactyly. Six individuals had stop gain variants, five had a deletion or duplication resulting in a frameshift, and one had a canonical splice acceptor site loss. Murine and human in situ hybridization and immunostaining revealed PPP1R12A expression in the prosencephalic neural folds and protein localization in the lower urinary tract at critical periods for forebrain division and urogenital development. Based on these clinical and molecular findings, we propose the association of PPP1R12A pathogenic variants with a congenital malformations syndrome affecting the embryogenesis of the brain and genitourinary systems and including disorders of sex development.
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- 2020
15. Cornelia de Lange syndrome in diverse populations
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Dowsett, Leah, Porras, Antonio R, Kruszka, Paul, Davis, Brandon, Hu, Tommy, Honey, Engela, Badoe, Eben, Thong, Meow‐Keong, Leon, Eyby, Girisha, Katta M, Shukla, Anju, Nayak, Shalini S, Shotelersuk, Vorasuk, Megarbane, Andre, Phadke, Shubha, Sirisena, Nirmala D, Dissanayake, Vajira HW, Ferreira, Carlos R, Kisling, Monisha S, Tanpaiboon, Pranoot, Uwineza, Annette, Mutesa, Leon, Tekendo‐Ngongang, Cedrik, Wonkam, Ambroise, Fieggen, Karen, Batista, Leticia Cassimiro, Moretti‐Ferreira, Danilo, Stevenson, Roger E, Prijoles, Eloise J, Everman, David, Clarkson, Kate, Worthington, Jessica, Kimonis, Virginia, Hisama, Fuki, Crowe, Carol, Wong, Paul, Johnson, Kisha, Clark, Robin D, Bird, Lynne, Masser‐Frye, Diane, McDonald, Marie, Willems, Patrick, Roeder, Elizabeth, Saitta, Sulgana, Anyane‐Yeoba, Kwame, Demmer, Laurie, Hamajima, Naoki, Stark, Zornitza, Gillies, Greta, Hudgins, Louanne, Dave, Usha, Shalev, Stavit, Siu, Victoria, Gupta, Neerja, Kabra, Madhulika, Ades, Ann, Dubbs, Holly, Raible, Sarah, Kaur, Maninder, Salzano, Emanuela, Jackson, Laird, Deardorff, Matthew, Kline, Antonie, Summar, Marshall, Muenke, Maximilian, Linguraru, Marius George, and Krantz, Ian D
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Brain Disorders ,Rare Diseases ,Clinical Research ,Intellectual and Developmental Disabilities (IDD) ,Pediatric ,Neurosciences ,Congenital ,Abnormalities ,Multiple ,Adolescent ,Adult ,Cell Cycle Proteins ,Child ,Child ,Preschool ,Chondroitin Sulfate Proteoglycans ,Chromosomal Proteins ,Non-Histone ,De Lange Syndrome ,Face ,Female ,Humans ,Image Processing ,Computer-Assisted ,Infant ,Infant ,Newborn ,Intellectual Disability ,Male ,Mutation ,Phenotype ,Racial Groups ,Young Adult ,CdLS ,Cornelia de Lange syndrome ,diverse populations ,facial analysis technology ,NIPBL ,underrepresented minorities ,Clinical Sciences ,Clinical sciences - Abstract
Cornelia de Lange syndrome (CdLS) is a dominant multisystemic malformation syndrome due to mutations in five genes-NIPBL, SMC1A, HDAC8, SMC3, and RAD21. The characteristic facial dysmorphisms include microcephaly, arched eyebrows, synophrys, short nose with depressed bridge and anteverted nares, long philtrum, thin lips, micrognathia, and hypertrichosis. Most affected individuals have intellectual disability, growth deficiency, and upper limb anomalies. This study looked at individuals from diverse populations with both clinical and molecularly confirmed diagnoses of CdLS by facial analysis technology. Clinical data and images from 246 individuals with CdLS were obtained from 15 countries. This cohort included 49% female patients and ages ranged from infancy to 37 years. Individuals were grouped into ancestry categories of African descent, Asian, Latin American, Middle Eastern, and Caucasian. Across these populations, 14 features showed a statistically significant difference. The most common facial features found in all ancestry groups included synophrys, short nose with anteverted nares, and a long philtrum with thin vermillion of the upper lip. Using facial analysis technology we compared 246 individuals with CdLS to 246 gender/age matched controls and found that sensitivity was equal or greater than 95% for all groups. Specificity was equal or greater than 91%. In conclusion, we present consistent clinical findings from global populations with CdLS while demonstrating how facial analysis technology can be a tool to support accurate diagnoses in the clinical setting. This work, along with prior studies in this arena, will assist in earlier detection, recognition, and treatment of CdLS worldwide.
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- 2019
16. MicroRNA172b-5p/trehalose-6-phosphate synthase module stimulates trehalose synthesis and microRNA172b-3p/AP2-like module accelerates flowering in barley upon drought stress
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Aleksandra Swida-Barteczka, Andrzej Pacak, Katarzyna Kruszka, Przemyslaw Nuc, Wojciech M. Karlowski, Artur Jarmolowski, and Zofia Szweykowska-Kulinska
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barley ,drought ,MicroRNAs ,flowering ,trehalose-6-phosphate synthase ,APETALA2 ,Plant culture ,SB1-1110 - Abstract
MicroRNAs (miRNAs) are major regulators of gene expression during plant development under normal and stress conditions. In this study, we analyzed the expression of 150 conserved miRNAs during drought stress applied to barley ready to flower. The dynamics of miRNAs expression was also observed after rewatering. Target messenger RNA (mRNAs) were experimentally identified for all but two analyzed miRNAs, and 41 of the targets were not reported before. Drought stress applied to barley induced accelerated flowering coordinated by a pair of two differently expressed miRNAs originating from a single precursor: hvu-miR172b-3p and hvu-miR172b-5p. Increased expression of miRNA172b-3p during drought leads to the downregulation of four APETALA2(AP2)-like genes by their mRNA cleavage. In parallel, the downregulation of the miRNA172b-5p level results in an increased level of a newly identified target, trehalose-6-phosphate synthase, a key enzyme in the trehalose biosynthesis pathway. Therefore, drought-treated plants have higher trehalose content, a known osmoprotectant, whose level is rapidly dropping after watering. In addition, trehalose-6-phosphate, an intermediate of the trehalose synthesis pathway, is known to induce flowering. The hvu-miRNA172b-5p/trehalose-6-phosphate synthase and hvu-miRNA172b-3p/AP2-like create a module leading to osmoprotection and accelerated flowering induction during drought.
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- 2023
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17. The human inactive X chromosome modulates expression of the active X chromosome
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Adrianna K. San Roman, Alexander K. Godfrey, Helen Skaletsky, Daniel W. Bellott, Abigail F. Groff, Hannah L. Harris, Laura V. Blanton, Jennifer F. Hughes, Laura Brown, Sidaly Phou, Ashley Buscetta, Paul Kruszka, Nicole Banks, Amalia Dutra, Evgenia Pak, Patricia C. Lasutschinkow, Colleen Keen, Shanlee M. Davis, Nicole R. Tartaglia, Carole Samango-Sprouse, Maximilian Muenke, and David C. Page
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sex chromosomes ,X chromosome inactivation ,gene expression ,sex differences ,aneuploidy ,turner syndrome ,Genetics ,QH426-470 ,Internal medicine ,RC31-1245 - Abstract
Summary: The “inactive” X chromosome (Xi) has been assumed to have little impact, in trans, on the “active” X (Xa). To test this, we quantified Xi and Xa gene expression in individuals with one Xa and zero to three Xis. Our linear modeling revealed modular Xi and Xa transcriptomes and significant Xi-driven expression changes for 38% (162/423) of expressed X chromosome genes. By integrating allele-specific analyses, we found that modulation of Xa transcript levels by Xi contributes to many of these Xi-driven changes (≥121 genes). By incorporating metrics of evolutionary constraint, we identified 10 X chromosome genes most likely to drive sex differences in common disease and sex chromosome aneuploidy syndromes. We conclude that human X chromosomes are regulated both in cis, through Xi-wide transcriptional attenuation, and in trans, through positive or negative modulation of individual Xa genes by Xi. The sum of these cis and trans effects differs widely among genes.
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- 2023
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18. P148: Novel molecular diagnoses in individuals with holoprosencephaly and prior negative sequencing
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Andrea Cohen, Joel Hughes, Clifton Dalgard, Paul Kruszka, Emmanuele Delot, Vincent Fusaro, Eric Vilain, Maximilian Muenke, and Seth Berger
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Genetics ,QH426-470 ,Medicine - Published
- 2023
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19. P208: SeqFirst: Impact of a precise genetic diagnosis on end-of-life decision making in the NICU
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Alexandra Keefe, Tara Wenger, Joon-Ho Yu, Megan Sikes, Luke Kruidenier, Abbey Scott, Kate McDuffie, Olivia Sommers, Heidi Gildersleeve, Chayna Davis, Paul Kruszka, Kati Buckingham, Jessica Chong, David Veenstra, Kyle Retterer, Kirsty McWalter, Amy Snook, Jane Juusola, Deborah Copenheaver, Danny Miller, Katrina Dipple, Kyle Brothers, and Michael Bamshad
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Genetics ,QH426-470 ,Medicine - Published
- 2023
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20. P414: SeqFirst: Parental perspectives on receiving results from neonatal rapid whole genome sequencing
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Tara Wenger, Alexandra Keefe, Megan Sikes, Luke Kruidenier, Joon-Ho Yu, Kate McDuffie, Olivia Sommers, Heidi Gildersleeve, Abbey Scott, Chayna Davis, Paul Kruszka, Kati Buckingham, Jessica Chong, Kyle Retterer, Kirsty McWalter, Amy Snook, Jane Juusola, Deborah Copenheaver, David Veenstra, Danny Miller, Katrina Dipple, and Michael Bamshad
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Genetics ,QH426-470 ,Medicine - Published
- 2023
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21. P453: Diagnostic yield of copy number variants by exome sequencing vs chromosomal microarray
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Ganka Douglas, Jeanne Meck, Lindsay Havens Dyer, Rhonda Brandon, Lisa Dyer, Patricia Fernandez Ferri, Mingjuan Liao, Shuxi Liu, Ludmila Matyakhina, Evica Rajcan-Separovic, Laura Sack, May Sanyoura, Wei Wang, and Paul Kruszka
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Genetics ,QH426-470 ,Medicine - Published
- 2023
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22. Use of the EVM method for analysis of extending the construction project duration as a result of realization disturbances - case study
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Anna Starczyk-Kołbyk and Leopold Kruszka
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evm method ,realization disturbances ,delays in construction works ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
In pursuing numerous construction projects, investors and contractors regularly face construction delay problems, many of which are likely to have been avoidable. There is found that payment delays and project delays are the two most critical effects of risk factors of construction management. The paper presents the practical application of the Earned Value Management method, which was used to estimate the possible extension of the duration of construction works during which realization disturbances occurred on the example of selected construction investment. The realization disturbances are usually an inseparable element in the implementation of construction works. They are the result of, among others: additional works, changes or design defects, as well as a badly adopted logistics strategy regarding the supply of construction materials. Delays or increasing the total cost of investment is a problem often encountered in the implementation of construction investments, despite advanced construction technologies, including system technologies and proven tools supporting the management of the construction process. The EVM method is used to control investments. It allows you to control delays and acceleration of construction works as well as to estimate their cost and completion date. In the analyzed case it was used to determine the scale of delays arising in construction works and related effects with the specification of the participation of individual participants of the investment process for delays. This paper is a continuation and supplementation of the research presented in the article: “The influence of construction works disturbances on the EVM analysis outcomes – case study” [23].
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- 2021
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23. Perforation analysis of S235 steel sheets up to 573 K using experimental and numerical methods
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Maciej Klosak, Michał Grazka, Leopold Kruszka, and Wojciech Mocko
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steel perforation ,ballistic properties ,fem analysis ,cnc measuring ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
This paper reports on efficient experimental and numerical techniques used in the design of critical infrastructure requiring special protection measures regarding security and safety. The presented results, some of which have already been reported in [1], were obtained from perforation experiments carried out on S235 steel sheets subjected to impacts characterized as moderate velocity (approximately 40–120 m/s). The metal was tested using the Hopkinson Bar Technique and pneumatic gun. The originality of perforation testing consist on using a thermal chamber designed to carry out experiments at higher temperatures. 3D scanners and numerically controlled measuring devices were used for the final shape deformation measurements. Finally, the results of FEM analysis obtained using explicit solver are presented. The full-scale CAD model was used in numeric calculations.
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- 2021
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24. Stretching magnetism with an electric field in a nitride semiconductor
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Sztenkiel, D., Foltyn, M., Mazur, G. P., Adhikari, R., Kosiel, K., Gas, K., Zgirski, M., Kruszka, R., Jakiela, R., Li, Tian, Piotrowska, A., Bonanni, A., Sawicki, M., and Dietl, T.
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Condensed Matter - Materials Science - Abstract
By direct magnetization measurements, performed employing a new detection scheme, we demonstrate an electrical control of magnetization in wurtzite (Ga,Mn)N. In this dilute magnetic insulator the Fermi energy is pinned by Mn ions in the mid-gap region, and the Mn3+ ions show strong single-ion anisotropy. We establish that (Ga,Mn)N sustains an electric field up to at least 5 MV/cm, indicating that Mn doping turns GaN into a worthwhile semi-insulating material. Under these conditions, the magnetoelectric coupling may be driven by the inverse piezoelectric effect that stretches the elementary cell along the c axis and, thus, affects the magnitude of magnetic anisotropy. We develop a corresponding theory and show that it describes the experimentally determined dependence of magnetization on the electric field quantitatively with no adjustable parameters as a function of the magnetic field and temperature. In this way, our work bridges two research domains developed so far independently: piezoelectricity of wurtzite semiconductors and electrical control of magnetization in hybrid and composite magnetic structures containing piezoelectric components., Comment: 11 pages, 10 figures, version after revision
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- 2016
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25. Performance characteristics of Hopkinson’s set-up pneumatic launcher
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Kamil Sobczyk, Leopold Kruszka, Ryszard Chmielewski, and Ryszard Rekucki
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pneumatic launcher ,hopkinson measuring bar ,direct impact tests ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
The paper presents a performance characteristics of a pneumatic launcher, which is an important element of the split Hopkinson bar set-up (SHPB) at the Department of Military Engineering and Infrastructure (the Military University of Technology in Warsaw) for the purpose of dynamic strength tests of construction materials. The process of experimental calibration of the launcher for selected loading bar-projectiles is shown. Two types of compression during direct impact tests were also used simultaneously to investigate the behaviour of metallic samples with the use of this launcher as well as the Hopkinson measuring bar: the first — a short cylindrical sample, including a miniature (small diameter) sample, and the second — a long cylindrical sample (Taylor test). The relationships describing the stress and strain state as a function of strain rate for the first type of the experiment and engineering empirical formulas for the second type of the research were given.
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- 2021
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26. Lessons Learned From the Implementation of Seek, Test, Treat, Retain Interventions Using Mobile Phones and Text Messaging to Improve Engagement in HIV Care for Vulnerable Populations in the United States
- Author
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Christopoulos, Katerina A, Cunningham, William E, Beckwith, Curt G, Kuo, Irene, Golin, Carol E, Knight, Kevin, Flynn, Patrick M, Spaulding, Anne C, Coffin, Lara S, Kruszka, Bridget, Kurth, Ann, Young, Jeremy D, Mannheimer, Sharon, Crane, Heidi M, and Kahana, Shoshana Y
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Health Services and Systems ,Health Sciences ,Clinical Research ,Clinical Trials and Supportive Activities ,HIV/AIDS ,Infectious Diseases ,Behavioral and Social Science ,7.1 Individual care needs ,Management of diseases and conditions ,Good Health and Well Being ,Adult ,Aged ,Anti-HIV Agents ,Cell Phone ,Continuity of Patient Care ,Female ,HIV Infections ,Humans ,Male ,Middle Aged ,Program Evaluation ,Reminder Systems ,Telemedicine ,Text Messaging ,United States ,Vulnerable Populations ,mHealth ,SMS ,Text messaging ,Retention in HIV care ,Engagement in HIV care ,Public Health and Health Services ,Social Work ,Public Health ,Public health - Abstract
In the United States, little is known about interventions that rely on mobile phones and/or text messaging to improve engagement in HIV care for vulnerable populations. Domestic studies using these technologies as part of the National Institute on Drug Abuse "Seek, Test, Treat, Retain" research initiative were queried regarding intervention components, implementation issues, participant characteristics, and descriptive statistics of mobile phone service delivery. Across five studies with 1,135 predominantly male, minority participants, implementation challenges occurred in three categories: (1) service interruptions; (2) billing/overage issues, and; (3) the participant user experience. Response rules for automated text messages frequently frustrated participants. The inability to reload minutes/texting capacity remotely was a significant barrier to intervention delivery. No study encountered confidentiality breaches. Service interruption was common, even if studies provided mobile phones and plans. Future studies should attend to the type of mobile phone and service, the participant user experience, and human subjects concerns.
- Published
- 2017
27. Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay
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Weiss, Karin, Wigby, Kristen, Fannemel, Madeleine, Henderson, Lindsay B, Beck, Natalie, Ghali, Neeti, Study, DDD, Anderlid, Britt-Marie, Lundin, Johanna, Hamosh, Ada, Jones, Marilyn C, Ghedia, Sondhya, Muenke, Maximilian, and Kruszka, Paul
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Pediatric ,Congenital Structural Anomalies ,Clinical Research ,Human Genome ,Genetics ,Rare Diseases ,Dental/Oral and Craniofacial Disease ,Aetiology ,2.1 Biological and endogenous factors ,Adult ,Agenesis of Corpus Callosum ,Blepharoptosis ,Child ,Child ,Preschool ,Craniofacial Abnormalities ,DNA-Binding Proteins ,Developmental Disabilities ,Female ,Haploinsufficiency ,Humans ,Infant ,Male ,Nerve Tissue Proteins ,Syndrome ,Transcription Factors ,Clinical Sciences ,Genetics & Heredity - Abstract
The introduction of whole-exome sequencing into the Pediatric Genetics clinic has increased the identification of novel genes associated with neurodevelopmental disorders and congenital anomalies. This agnostic approach has shed light on multiple proteins and pathways not previously known to be associated with disease. Here we report eight subjects from six families with predicted loss of function variants in ZNF462, a zinc-finger protein of unknown function. These individuals have overlapping phenotypes that include ptosis, metopic ridging, craniosynostosis, dysgenesis of the corpus callosum, and developmental delay. We propose that ZNF462 plays an important role in embryonic development, and is associated with craniofacial and neurodevelopmental abnormalities.
- Published
- 2017
28. In-situ thin film copper–copper thermocompression bonding for quantum cascade lasers
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Rouhi, Sina, Ozdemir, Mehtap, Ekmekcioglu, Merve, Yigen, Serap, Demirhan, Yasemin, Szerling, Anna, Kosiel, Kamil, Kozubal, Maciej, Kruszka, Renata, Prokaryn, Piotr, Ertugrul, Mehmet, Reno, John L., Aygun, Gulnur, and Ozyuzer, Lutfi
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- 2021
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29. Experimental Investigation of Dynamic Behavior of Silty Sand
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Ryszard Chmielewski, Leopold Kruszka, Ryszard Rekucki, and Kamil Sobczyk
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soil mechanics ,experimental dynamic testing ,split hopkinson pressure bar ,oedometric test ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
The paper includes experimental research using the Split Hopkinson Pressure Bar to determine dynamic compression curves and strength dynamic parameters to depend on the strain rate and moisture for silty sand soil samples. Those experiments are oedometric type based in a rigid confining cylinder. Samples of silty sand with fine a fraction content were taken for the study. To ensure sufficiently uniaxial strain of the tested material, the soil samples were placed in properly prepared casings made of duralumin for the needs of the tests. Thanks to the use of measuring strain gauges on the initiating and transmitting bars, as well as the casing, the nature of the loading pulse was obtained, which was then subjected to the process of filtration and data processing to obtain the nature of the incident, reflected and transmitted wave. During the above dynamic experiments with the representative of silty sand soils, it was observed that its dynamic compaction at a high strain rate is different than in the case of the Proctor test. This is due to higher compaction energy, which additionally changes the grain size by destroying the grains in the structure. The paper presents the results of particle size distribution analysis for two different types of soil samples - this type of analysis is unique. Hence experiments should be further continued for such soils with different granulations and various moisture using, for example, Hopkinson measuring bar technique to confirm for other silty sand soils that are often subgrade of various engineering objects.
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- 2021
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30. Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses
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Pawel Sega, Katarzyna Kruszka, Dawid Bielewicz, Wojciech Karlowski, Przemyslaw Nuc, Zofia Szweykowska-Kulinska, and Andrzej Pacak
- Subjects
Phosphate regulatory network ,Barley ,Small RNAs ,Degradome ,RNA-Seq ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, Bonferroni adjusted p-value
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- 2021
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31. Analysis of the Influence of Silty Sands Moisture Content and Impact Velocity in SHPB Testing on Their Compactability and Change in Granulometric Composition
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Kamil Sobczyk, Ryszard Chmielewski, Leopold Kruszka, and Ryszard Rekucki
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granulometric composition ,grain crushing ,laser particle size analyzer ,silty sand ,soil ,high strain rate ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
This paper presents the results of a test cycle of two types of silty sand (siSa) with different contents of fine fractions. Fine fractions are understood as soil grains with a grain diameter of less than 63 µm (as the sum of silt and clay fractions). The soils tested had a content of fine fractions of fSi+Cl,1 = 15.14% and fSi+Cl,2 = 20.48%, respectively, before the study. Changes in the content of these fractions after the experiments were analyzed. These experiments consisted of dynamic bar projectile impact loading, and a split Hopkinson pressure bar (SHPB) test stand was used in the study. Changes in the granulometric composition of the silty sands studied were carried out in a laser particle size analyzer, allowing measurement of fractional content in the grain size range from 0.01 µm to 3500 µm. As a result, a summary of changes in soil grain size curves in the range of fine fractions was compiled. Repeated trends were observed in the changes in the granulometric composition of the soil samples as a function of the moisture content of the soil sample (w1 = 0%, w2 = 5%, w3 = 10%, and w4 = 15%) and the impact velocity of the loading bar projectile for SHPB pneumatic launcher pressures (p1 = 1.2 bar → v1 = 12.76 m/s, p2 = 1.8 bar → v2 = 17.69 m/s and p3 = 2.4 bar → v3 = 21.32 m/s). The influence of the initial moisture content of the investigated soil on the value of the optimum moisture content obtained during its dynamic compaction was discussed. The trend in the behavior of the change in the granulometric composition of the tested samples was determined, taking the value of the initial moisture content of the soil in relation to the optimum moisture content of the reference sample as a reference. The largest percentage change in granulometric composition through an increase in the value of the silt and clay fraction relative to the reference sample fSi+Cl for both types of silty sand tested occurs for the same moisture content variant w2 = 5%–for soil fSi+Cl,1 = 15.14% there is an increase in the fine fraction of 11.08% and for soil fSi+Cl,2 = 20.48% there is an increase in the fine fraction of 15.17%. In general, it can be seen that more silty soil is more strongly susceptible to the phenomenon of grain crushing for moisture content w1 = 0% and w2 = 5% less than its optimum moisture content wopt,1 = 8.70%. In contrast, less silty soil is more susceptible to the phenomenon of grain crushing for moisture contents w3 = 10% and w4 = 15% greater than its optimum moisture content wopt,2 = 9.20%. The presented dynamic physical phenomenon of soil behavior is crucial during explosive and impact impacts on structures made of soil, e.g., as ground protection layers.
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- 2023
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32. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer
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Hampras, Shalaka S, Sucheston-Campbell, Lara E, Cannioto, Rikki, Chang-Claude, Jenny, Modugno, Francesmary, Dörk, Thilo, Hillemanns, Peter, Preus, Leah, Knutson, Keith L, Wallace, Paul K, Hong, Chi-Chen, Friel, Grace, Davis, Warren, Nesline, Mary, Pearce, Celeste L, Kelemen, Linda E, Goodman, Marc T, Bandera, Elisa V, Terry, Kathryn L, Schoof, Nils, Eng, Kevin H, Clay, Alyssa, Singh, Prashant K, Joseph, Janine M, Aben, Katja KH, Anton-Culver, Hoda, Antonenkova, Natalia, Baker, Helen, Bean, Yukie, Beckmann, Matthias W, Bisogna, Maria, Bjorge, Line, Bogdanova, Natalia, Brinton, Louise A, Brooks-Wilson, Angela, Bruinsma, Fiona, Butzow, Ralf, Campbell, Ian G, Carty, Karen, Cook, Linda S, Cramer, Daniel W, Cybulski, Cezary, Dansonka-Mieszkowska, Agnieszka, Dennis, Joe, Despierre, Evelyn, Dicks, Ed, Doherty, Jennifer A, du Bois, Andreas, Dürst, Matthias, Easton, Doug, Eccles, Diana, Edwards, Robert P, Ekici, Arif B, Fasching, Peter A, Fridley, Brooke L, Gao, Yu-Tang, Gentry-Maharaj, Aleksandra, Giles, Graham G, Glasspool, Rosalind, Gronwald, Jacek, Harrington, Patricia, Harter, Philipp, Hasmad, Hanis Nazihah, Hein, Alexander, Heitz, Florian, Hildebrandt, Michelle AT, Hogdall, Claus, Hogdall, Estrid, Hosono, Satoyo, Iversen, Edwin S, Jakubowska, Anna, Jensen, Allan, Ji, Bu-Tian, Karlan, Beth Y, Kellar, Melissa, Kelley, Joseph L, Kiemeney, Lambertus A, Klapdor, Rüdiger, Kolomeyevskaya, Nonna, Krakstad, Camilla, Kjaer, Susanne K, Kruszka, Bridget, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Le, Nhu D, Lee, Alice W, Lele, Shashikant, Leminen, Arto, Lester, Jenny, Levine, Douglas A, Liang, Dong, Lissowska, Jolanta, Liu, Song, Lu, Karen, Lubinski, Jan, Lundvall, Lene, Massuger, Leon FAG, Matsuo, Keitaro, and McGuire, Valeria
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Ovarian Cancer ,Rare Diseases ,Cancer ,Genetics ,2.1 Biological and endogenous factors ,Aetiology ,Adenocarcinoma ,Clear Cell ,Adult ,Aged ,Carcinoma ,Ovarian Epithelial ,Female ,Gene Expression Regulation ,Neoplastic ,Gene Frequency ,Genetic Predisposition to Disease ,Genotype ,Humans ,Middle Aged ,Neoplasms ,Glandular and Epithelial ,Ovarian Neoplasms ,Polymorphism ,Single Nucleotide ,Protein Serine-Threonine Kinases ,Receptor ,Transforming Growth Factor-beta Type II ,Receptors ,Transforming Growth Factor beta ,Risk Factors ,T-Lymphocytes ,Regulatory ,ovarian cancer ,immunosuppression ,biomarkers ,genetic variation ,TGFBR2 ,TGFBR2 ,Oncology and carcinogenesis - Abstract
BackgroundRegulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer.MethodsIn a population of 15,596 epithelial ovarian cancer (EOC) cases and 23,236 controls, we measured genetic associations of 1,351 SNPs in Treg cell pathway genes with odds of ovarian cancer and tested pathway and gene-level associations, overall and by histotype, for the 25 genes, using the admixture likelihood (AML) method. The most significant single SNP associations were tested for correlation with expression levels in 44 ovarian cancer patients.ResultsThe most significant global associations for all genes in the pathway were seen in endometrioid ( p = 0.082) and clear cell ( p = 0.083), with the most significant gene level association seen with TGFBR2 ( p = 0.001) and clear cell EOC. Gene associations with histotypes at p < 0.05 included: IL12 ( p = 0.005 and p = 0.008, serous and high-grade serous, respectively), IL8RA ( p = 0.035, endometrioid and mucinous), LGALS1 ( p = 0.03, mucinous), STAT5B ( p = 0.022, clear cell), TGFBR1 ( p = 0.021 endometrioid) and TGFBR2 ( p = 0.017 and p = 0.025, endometrioid and mucinous, respectively).ConclusionsCommon inherited gene variation in Treg cell pathways shows some evidence of germline genetic contribution to odds of EOC that varies by histologic subtype and may be associated with mRNA expression of immune-complex receptor in EOC patients.
- Published
- 2016
33. Calcium Intake From Diet and Supplements and the Risk of Coronary Artery Calcification and its Progression Among Older Adults: 10-Year Follow-up of the Multi-Ethnic Study of Atherosclerosis (MESA).
- Author
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Anderson, John JB, Kruszka, Bridget, Delaney, Joseph AC, He, Ka, Burke, Gregory L, Alonso, Alvaro, Bild, Diane E, Budoff, Matthew, and Michos, Erin D
- Subjects
Humans ,Disease Progression ,Calcium ,Dietary ,Tomography ,X-Ray Computed ,Diet ,Incidence ,Cohort Studies ,Longitudinal Studies ,Follow-Up Studies ,Dietary Supplements ,Aged ,Aged ,80 and over ,Middle Aged ,United States ,Female ,Male ,Atherosclerosis ,Coronary Artery Disease ,Vascular Calcification ,calcium ,cardiovascular imaging ,coronary artery calcium ,diet ,epidemiology ,Clinical Trials and Supportive Activities ,Cardiovascular ,Clinical Research ,Heart Disease - Coronary Heart Disease ,Aging ,Heart Disease ,Nutrition ,Prevention ,6.1 Pharmaceuticals ,3.3 Nutrition and chemoprevention ,Cardiorespiratory Medicine and Haematology - Abstract
BackgroundRecent randomized data suggest that calcium supplements may be associated with increased risk of cardiovascular disease (CVD) events. Using a longitudinal cohort study, we assessed the association between calcium intake, from both foods and supplements, and atherosclerosis, as measured by coronary artery calcification (CAC).Methods and resultsWe studied 5448 adults free of clinically diagnosed CVD (52% female; aged 45-84 years) from the Multi-Ethnic Study of Atherosclerosis. Baseline total calcium intake was assessed from diet (using a food frequency questionnaire) and calcium supplements (by a medication inventory) and categorized into quintiles. Baseline CAC was measured by computed tomography, and CAC measurements were repeated in 2742 participants ≈10 years later. At baseline, mean calcium intakes across quintiles were 313.3, 540.3, 783.0, 1168.9, and 2157.4 mg/day. Women had higher calcium intakes than men. After adjustment for potential confounders, among 1567 participants without baseline CAC, the relative risk (RR) of developing incident CAC over 10 years, by quintile 1 to 5 of calcium intake, were 1 (reference), 0.95 (0.79-1.14), 1.02 (0.85-1.23), 0.86 (0.69-1.05), and 0.73 (0.57-0.93). After accounting for total calcium intake, calcium supplement use was associated with increased risk for incident CAC (RR=1.22 [1.07-1.39]). No relation was found between baseline calcium intake and 10-year changes in log-transformed CAC among those participants with baseline CAC >0.ConclusionsHigh total calcium intake was associated with a decreased risk of incident atherosclerosis over long-term follow-up, particularly if achieved without supplement use. However, calcium supplement use may increase the risk for incident CAC.
- Published
- 2016
34. MT38 Identifying High Cost and High Mortality Genetic Disease in the NICU
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Liu, Z., primary, Higashi, M., additional, Wu, H., additional, Wain, K., additional, Napier, M., additional, and Kruszka, P., additional
- Published
- 2023
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35. HYBRID METHODOLOGY AND MATERIAL CHANGE OF INTEREST RATE BENCHMARKS
- Author
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Michał KRUSZKA
- Subjects
interest rate benchmark ,euribor ,libor ,Law ,Law in general. Comparative and uniform law. Jurisprudence ,K1-7720 ,Social Sciences ,Finance ,HG1-9999 - Abstract
The development of financial markets over the past several decades pointed out a very important role of financial benchmarks, which are used as a reference price for financial instruments or to determine interest payments. However, after the global financial crisis, allegations emerged that interbank interest rate benchmarks had been manipulated. A significant decrease in the size of interbank transactions was observed as well. Both elements lower the credibility of the interest rate benchmarks used so far. Taking into account the responsibility for financial stability, the EU bodies adopted a regulation on benchmarks (BMR) in 2016. The main purpose of this paper is to provide an analysis of this piece of legislation from the perspective of legal continued viability of interest rate benchmarks. The main subject of the analysis was the development of the EURIBOR and LIBOR methodology. The results of the analysis showed that the new hybrid methodology, which utilises eligible transaction data, transaction-derived data, and databased expert judgement, is a robust evolution of the quote-based methodology. It means that administrators did not change benchmark’s underlying interest, and no one should diagnose the risk to the continued viability of EURIBOR and LIBOR rates.
- Published
- 2020
36. Prenatal exposure to pesticides and risk for holoprosencephaly: a case-control study
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Yonit A. Addissie, Paul Kruszka, Angela Troia, Zoë C. Wong, Joshua L. Everson, Beth A. Kozel, Robert J. Lipinski, Kristen M. C. Malecki, and Maximilian Muenke
- Subjects
Pesticides ,Holoprosencephaly ,Forebrain defect ,Environmental exposure ,Prenatal exposure ,Industrial medicine. Industrial hygiene ,RC963-969 ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background Pesticide exposure during susceptible windows and at certain doses are linked to numerous birth defects. Early experimental evidence suggests an association between active ingredients in pesticides and holoprosencephaly (HPE), the most common malformation of the forebrain in humans (1 in 250 embryos). No human studies to date have examined the association. This study investigated pesticides during multiple windows of exposure and fetal risk for HPE. It is hypothesized that pre-conception and early pregnancy, the time of brain development in utero, are the most critical windows of exposure. Methods A questionnaire was developed for this retrospective case-control study to estimate household, occupational, and environmental pesticide exposures. Four windows of exposure were considered: preconception, early, mid and late pregnancy. Cases were identified through the National Human Genome Research Institute’s ongoing clinical studies of HPE. Similarly, controls were identified as children with Williams-Beuren syndrome, a genetic syndrome also characterized by congenital malformations, but etiologically unrelated to HPE. We assessed for differences in odds of exposures to pesticides between cases and controls. Results Findings from 91 cases and 56 controls showed an increased risk for HPE with reports of maternal exposure during pregnancy to select pesticides including personal insect repellants (adjusted odds ratio (aOR) 2.89, confidence interval (CI): 0.96–9.50) and insecticides and acaricides for pets (aOR 3.84, CI:1.04–16.32). Exposure to household pest control products during the preconception period or during pregnancy was associated with increased risk for HPE (aOR 2.60, OR: 0.84–8.68). No associations were found for occupational exposures to pesticides during pregnancy (aOR: 1.15, CI: 0.11–11.42), although exposure rates were low. Higher likelihood for HPE was also observed with residency next to an agricultural field (aOR 3.24, CI: 0.94–12.31). Conclusions Observational findings are consistent with experimental evidence and suggest that exposure to personal, household, and agricultural pesticides during pregnancy may increase risk for HPE. Further investigations of gene by environment interactions are warranted.
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- 2020
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37. The Influence of Construction Works Disturbances on the EVM Analysis Outcomes – Case Study
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A. Starczyk-Kołbyk and L. Kruszka
- Subjects
building disturbances ,delays in construction works ,schedule changes ,contractual penalties ,evm method ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
The paper presents the problem of building disturbances, which are usually an inseparable element during the implementation of construction projects. They were classified, their causes and sides of the construction process responsible for their creation were identified on the basis of the analyzed construction investment. In addition, using the Earned Value Management method, the scale of delays arising in construction works and the related effects were determined. The important role of close cooperation and good communication between all participants of the construction process was emphasized, which would reduce the phenomenon of building disturbances, but also mitigate the negative effects of delays that have already occurred.
- Published
- 2020
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38. Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses
- Author
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Sega, Pawel, Kruszka, Katarzyna, Bielewicz, Dawid, Karlowski, Wojciech, Nuc, Przemyslaw, Szweykowska-Kulinska, Zofia, and Pacak, Andrzej
- Published
- 2021
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39. Identification of transcription factors that bind to the 5′-UTR of the barley PHO2 gene
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Sega, Paweł, Kruszka, Katarzyna, Szewc, Łukasz, Szweykowska-Kulińska, Zofia, and Pacak, Andrzej
- Published
- 2020
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40. Proceedings from the Turner Resource Network symposium: The crossroads of health care research and health care delivery
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Backeljauw, Philippe F, Bondy, Carolyn, Chernausek, Steven D, Cernich, Joseph T, Cole, David A, Fasciano, Laura P, Foodim, Joan, Hawley, Scott, Hong, David S, Knickmeyer, Rebecca C, Kruszka, Paul, Lin, Angela E, Lippe, Barbara M, Lorigan, Gary A, Maslen, Cheryl L, Mauras, Nelly, Page, David C, Pemberton, Victoria L, Prakash, Siddharth K, Quigley, Charmian A, Ranallo, Kelly C, Reiss, Allan L, Sandberg, David E, Scurlock, Cindy, and Silberbach, Michael
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Rare Diseases ,Pediatric ,7.1 Individual care needs ,Management of diseases and conditions ,Congenital ,Good Health and Well Being ,Delivery of Health Care ,Female ,Genetic Research ,Health Services Research ,Humans ,Registries ,Sex Chromosomes ,Turner Syndrome ,monosomy X ,Turner syndrome ,women ,congenital heart disease ,genetics ,neurodevelopment ,chromosome ,sex chromosomes ,women's health ,quality of life ,Clinical Sciences ,Clinical sciences - Abstract
Turner syndrome, a congenital condition that affects ∼1/2,500 births, results from absence or structural alteration of the second sex chromosome. There has been substantial effort by numerous clinical and genetic research groups to delineate the clinical, pathophysiological, cytogenetic, and molecular features of this multisystem condition. Questions about the molecular-genetic and biological basis of many of the clinical features remain unanswered, and health care providers and families seek improved care for affected individuals. The inaugural "Turner Resource Network (TRN) Symposium" brought together individuals with Turner syndrome and their families, advocacy group leaders, clinicians, basic scientists, physician-scientists, trainees and other stakeholders with interest in the well-being of individuals and families living with the condition. The goal of this symposium was to establish a structure for a TRN that will be a patient-powered organization involving those living with Turner syndrome, their families, clinicians, and scientists. The TRN will identify basic and clinical questions that might be answered with registries, clinical trials, or through bench research to promote and advocate for best practices and improved care for individuals with Turner syndrome. The symposium concluded with the consensus that two rationales justify the creation of a TRN: inadequate attention has been paid to the health and psychosocial issues facing girls and women who live with Turner syndrome; investigations into the susceptibility to common disorders such as cardiovascular or autoimmune diseases caused by sex chromosome deficiencies will increase understanding of disease susceptibilities in the general population.
- Published
- 2015
41. Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks.
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El-Samad, Hana, Lipinski-Kruszka, J, Stewart-Ornstein, J, and Chevalier, MW
- Abstract
Cellular decision making is accomplished by complex networks, the structure of which has traditionally been inferred from mean gene expression data. In addition to mean data, quantitative measures of distributions across a population can be obtained using
- Published
- 2015
42. Magnetically active vacancy related defects in irradiated GaN layers
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Kilanski, L., Tuomisto, F., Szymczak, R., and Kruszka, R.
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Condensed Matter - Materials Science - Abstract
We present the studies of magnetic properties of 2 MeV 4He+-irradiated GaN grown by metal-organic chemical-vapor deposition. Particle irradiation allowed controllable introduction of Ga-vacancy in the samples. The magnetic moments with concentrations changing between 4.3...8.3x10^17 cm^-3 showing superparamagnetic blocking at room temperature are observed. The appearance of clear hysteresis curve at T = 5 K with coercive field of about H_C = 270 Oe suggests that the formation of more complex Ga vacancy related defects is promoted with increasing Ga vacancy content. The small concentration of the observed magnetically-active defects with respect to the total Ga- vacancy concentration suggests that the presence of the oxygen/hydrogen-related vacancy complexes is the source of the observed magnetic moments., Comment: 3 pages, 3 figures
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- 2012
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43. Ciągłość prawna wskaźników referencyjnych stopy procentowej
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Michał Kruszka
- Subjects
wskaźnik referencyjny stopy procentowej ,BMR ,EURIBOR ,LIBOR ,Law ,Social Sciences - Abstract
Rozwój rynków finansowych w ciągu ostatnich kilkudziesięciu lat wskazał na bardzo ważną rolę finansowych wskaźników referencyjnych, które są wykorzystywane jako bazowa wycena instrumentów finansowych lub do określenia płatności odsetkowych. Po światowym kryzysie finansowym pojawiły się jednak zarzuty, że wskaźniki referencyjne stóp procentowych podlegały manipulacjom. Zaobserwowano również znaczny spadek wartości i znaczenia niezabezpieczonych transakcji międzybankowych. Oba czynniki obniżyły wiarygodność stosowanych dotychczas wskaźników referencyjnych stóp procentowych. Ze względu na odpowiedzialność za stabilność finansową, Parlament Europejski i Rada Unii Europejskiej przyjęły w 2016 r. rozporządzenie w sprawie wskaźników referencyjnych (BMR). Głównym celem niniejszego artykułu jest weryfikacja hipotezy przeprowadzenia istotnej zmiany, której wystąpienie może zagrażać prawnej ciągłości wskaźników referencyjnych stóp procentowych. Głównym przedmiotem analizy były modyfikacje metody opracowywania EURIBOR i LIBOR. Wyniki analizy wykazały, że nowa metoda kaskadowa, która wykorzystuje odpowiednio wyspecyfikowane dane o transakcjach międzybankowych, informacje opisujące dane pochodzące z transakcji na rynkach powiązanych oraz weryfikowalną ocenę ekspercką, stanowi wyłącznie ewolucję metody opartej na kwotowaniach. Oznacza to, że administratorzy nie zmienili rynku, którego pomiar jest celem wskaźników referencyjnych stóp procentowych i nie ma podstaw do diagnozowania ryzyka dla prawnej ciągłości EURIBOR i LIBOR.
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- 2020
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44. Various in vitro systems of Ragged Robin (Lychnis flos-cuculi L.): a new potential source of phytoecdysteroids?
- Author
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Maliński, Michał P., Kikowska, Małgorzata, Kruszka, Dariusz, Napierała, Marta, Florek, Ewa, Sliwinska, Elwira, and Thiem, Barbara
- Published
- 2019
- Full Text
- View/download PDF
45. Low-level parental mosaicism affects the recurrence risk of holoprosencephaly
- Author
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Hu, Ping, Martinez, Ariel F., Kruszka, Paul, Berger, Seth, Roessler, Erich, and Muenke, Maximilian
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- 2019
- Full Text
- View/download PDF
46. Generation of human induced pluripotent stem cell line (NIDCRi001-A) from a Muenke syndrome patient with an FGFR3 p.Pro250Arg mutation
- Author
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Byron W.H. Mui, Deepika Arora, Barbara S. Mallon, Ariel F. Martinez, Janice S. Lee, Maximilian Muenke, Paul Kruszka, Fahad K. Kidwai, and Pamela G. Robey
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Muenke syndrome is the leading genetic cause of craniosynostosis and results in a variety of disabling clinical phenotypes. To model the disease and study the pathogenic mechanisms, a human induced pluripotent stem cell (hiPSC) line was generated from a patient diagnosed with Muenke syndrome. Successful reprogramming was validated by morphological features, karyotyping, loss of reprogramming factors, expression of pluripotency markers, mutation analysis and teratoma formation.
- Published
- 2020
- Full Text
- View/download PDF
47. The selection of methods for strengthening of the reinforced-concrete structure of the open tank
- Author
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R. Chmielewski, L. Kruszka, and P. Muzolf
- Subjects
Strengthening the construction ,Reinforced concrete wall ,Open tank chamber ,Technical condition ,Pile foundation ,Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
The paper presents the solution to the selection of methods for strengthening a reinforced concrete wall of an open tank structure, located in a sewage treatment plant. Originally, this construction was reinforced with three massive retaining blocks topped with a beam. The reason for designing additional reinforcement of the wall structure was the damage in the form of cracks parallel to external walls observed during the implementation of the tank tightness testing in 2002. The measured cracks had a variable width up to 4.1 mm. The cause of the resulting damage was insufficient cross-section of the bottom plate reinforcement in the areas of connection with the walls. During the expansion of the sewage-treatment plant in 2014, additional bioreactor tanks were designed in the vicinity of existing retaining blocks. This implied the necessity to remove the supporting, retaining blocks and to make a new reinforcing structure. Several strengthening solutions have been analysed taking into account the continuous operation of the sewage treatment plant as well as the design variants that do not interfere with the interior of the existing tank chamber. A solution in the form of a support structure anchored on a palisade of bored piles was adopted.
- Published
- 2020
- Full Text
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48. Normy ostrożnościowe oceny ryzyka kredytobiorcy hipotecznego
- Author
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Michał Kruszka and Marcin Wroński
- Subjects
nadzór bankowy ,nadzór makroostrożnościowy ,rynek nieruchomości ,ryzyko systemowe ,LTV ,DSTI, DTI ,JEL: G21, G28, K23 ,Law ,Social Sciences - Abstract
Ostatni kryzys finansowy ujawnił istotne powiązanie stabilności systemu bankowego z kredytowaniem nieruchomości. Celem artykułu jest przedstawienie narzędzi z zakresu nadzoru bankowego (sensu stricto, jak też largo) jako czynników, które mogą ograniczyć popyt na ten rodzaj kredytów. Badaniu poddano głównie środki nadzorcze zastosowane w państwach Europejskiego Obszaru Gospodarczego. Omówiono zakres stosowania środków nadzorczych ograniczających możliwość wykorzystania nieruchomości jako zabezpieczenia kredytu oraz środków nadzorczych ograniczających możliwość wykorzystania całego dochodu kredytobiorcy do spłaty kredytu. Szczególną uwagę poświecono międzynarodowemu zróżnicowaniu stosowanych środków nadzorczych, wskazując, jak odpowiadają one na priorytety regulatorów rynku finansowego w danym kraju.
- Published
- 2019
- Full Text
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49. A child with multiple congenital anomalies due to partial trisomy 7q22.1 → qter resulting from a maternally inherited balanced translocation: a case report and review of literature
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C. S. Paththinige, N. D. Sirisena, U. G. I. U. Kariyawasam, R. C. Ediriweera, P. Kruszka, M. Muenke, and V. H. W. Dissanayake
- Subjects
Congenital malformations ,Translocation (7 ,14) ,Trisomy 7q ,Fluorescence in-situ hybridization ,SNP array ,Internal medicine ,RC31-1245 ,Genetics ,QH426-470 - Abstract
Abstract Background Parental balanced reciprocal translocations can result in partial aneuploidies in the offspring due to unbalanced meiotic segregation during gametogenesis. Herein, we report the phenotypic and molecular cytogenetic characterization of a 2 years and 4 months old female child with partial trisomy 7q22 → qter. This is the first such reported case resulting from a parental balanced translocation involving the long arms of chromosomes 7 and 14. The phenotype of the proband was compared with that of previously reported cases of trisomy 7q21 → qter or 7q22 → qter resulting from parental balanced translocations. Case presentation The proband was born pre-term to a 34-year-old mother with a history of two first trimester miscarriages and an early infant death. She was referred at the age of 8 months for genetic evaluation due to prenatal and postnatal growth retardation, developmental delay and multiple congenital anomalies. On clinical evaluation, she had craniofacial dysmorphic features such as scaphocephaly, large anterior fontanelle with open posterior fontanelle, prominent occiput, triangular face, high forehead, hypertelorism, down slanting eyes, flat nasal bridge, small nose, low set ears, micro-retrognathia, high arched palate and short neck. Cranial computerized tomography scan showed lateral ventriculomegaly with features of early cerebral atrophy. Conventional cytogenetic analysis showed the karyotype 46,XX,der(14)t(7;14)(q22;q32)mat in the proband due to an unbalanced segregation of a maternal balanced translocation t(7;14)(q22;q32). Fluorescence in-situ hybridization analysis confirmed the partial trisomy 7q22 → qter in the proband with a minimal loss of genetic material on chromosome 14. Single nucleotide polymorphism array further confirmed the duplication on chromosome 7q22.1 → qter and a small terminal deletion on chromosome 14q32.3 → qter. Conclusion We report the longest-surviving child with trisomy 7q22 → qter due to a parental balanced translocation between chromosomes 7 and 14. Clinical features observed in the proband were consistent with the consensus phenotype of partial trisomy 7q22 → qter reported in the scientific literature. Early diagnosis of these patients using molecular cytogenetic techniques is important for establishing the precise diagnosis and for making decisions pertaining to the prognostication and management of affected individuals.
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- 2018
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50. Clinical Spectrum of congenital heart defects (CHD) detected at the child health Clinic in a Tertiary Health Facility in Ghana: a retrospective analysis
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Thomford, Nicholas Ekow, Biney, Robert Peter, Okai, Emmanuel, Anyanful, Akwasi, Nsiah, Paul, Frimpong, Prosperity G., Boakye, Dominic O., Adongo, Charles A., Kruszka, Paul, and Wonkam, Ambroise
- Published
- 2020
- Full Text
- View/download PDF
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