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Book: Daniel Urban Kiley

Berrizbeitia, Anita / Kiley, Daniel Urban / Saunders, William S

the early gardens

(Landscape views ; 2)

1999

Author's details	William S. Saunders, ed.; with essays by Anita Berrizbeitia
Series title	Landscape views ; 2
Keywords	Landscape architects/Biography ; Landscape architecture
Language	English
Size	80 S, Ill, 22 cm
Edition	1. ed
Publisher	Princeton Architectural Press u.a.
Publishing place	New York
Document type	Book
Note	Includes bibliographical references
ISBN	1568981481 ; 9781568981482
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: GlycoDraw: a python implementation for generating high-quality glycan figures.

Lundstrøm, Jon / Urban, James / Thomès, Luc / Bojar, Daniel

Glycobiology

2023 Volume 33, Issue 11, Page(s) 927–934

Abstract: Glycans are essential to all scales of biology, with their intricate structures being crucial for their biological functions. The structural complexity of glycans is communicated through simplified and unified visual representations according to the ... ...

Abstract	Glycans are essential to all scales of biology, with their intricate structures being crucial for their biological functions. The structural complexity of glycans is communicated through simplified and unified visual representations according to the Symbol Nomenclature for Glycans (SNFGs) guidelines adopted by the community. Here, we introduce GlycoDraw, a Python-native implementation for high-throughput generation of high-quality, SNFG-compliant glycan figures with flexible display options. GlycoDraw is released as part of our glycan analysis ecosystem, glycowork, facilitating integration into existing workflows by enabling fully automated annotation of glycan-related figures and thus assisting the analysis of e.g. differential abundance data or glycomics mass spectra.
MeSH term(s)	Ecosystem ; Polysaccharides/chemistry ; Glycomics ; Tandem Mass Spectrometry
Chemical Substances	Polysaccharides
Language	English
Publishing date	2023-07-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
DOI	10.1093/glycob/cwad063
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Zs.A 3150: Show issues

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Article ; Online: Decoding glycomics with a suite of methods for differential expression analysis.

Lundstrøm, Jon / Urban, James / Bojar, Daniel

Cell reports methods

2023 Volume 3, Issue 12, Page(s) 100652

Abstract: Glycomics, the comprehensive profiling of all glycan structures in samples, is rapidly expanding to enable insights into physiology and disease mechanisms. However, glycan structure complexity and glycomics data interpretation present challenges, ... ...

Abstract	Glycomics, the comprehensive profiling of all glycan structures in samples, is rapidly expanding to enable insights into physiology and disease mechanisms. However, glycan structure complexity and glycomics data interpretation present challenges, especially for differential expression analysis. Here, we present a framework for differential glycomics expression analysis. Our methodology encompasses specialized and domain-informed methods for data normalization and imputation, glycan motif extraction and quantification, differential expression analysis, motif enrichment analysis, time series analysis, and meta-analytic capabilities, synthesizing results across multiple studies. All methods are integrated into our open-source glycowork package, facilitating performant workflows and user-friendly access. We demonstrate these methods using dedicated simulations and glycomics datasets of N-, O-, lipid-linked, and free glycans. Differential expression tests here focus on human datasets and cancer vs. healthy tissue comparisons. Our rigorous approach allows for robust, reliable, and comprehensive differential expression analyses in glycomics, contributing to advancing glycomics research and its translation to clinical and diagnostic applications.
MeSH term(s)	Humans ; Glycomics/methods ; Polysaccharides/chemistry
Chemical Substances	Polysaccharides
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Journal Article
ISSN	2667-2375
ISSN (online)	2667-2375
DOI	10.1016/j.crmeth.2023.100652
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Article ; Online: Location and migration of interstitial Li ions in CsPbI3 crystals

Wei, Wei / Urban, Daniel / Gebhardt, Julian / Elsässer, Christian

2024

Abstract: Halide perovskites are highly promising light-harvesting materials with strong ionic character, enabling in principle the combination of a solar cell and a Li-ion battery in one integrated photobattery device. Here, we investigate Li ions inside crystals ...

Abstract	Halide perovskites are highly promising light-harvesting materials with strong ionic character, enabling in principle the combination of a solar cell and a Li-ion battery in one integrated photobattery device. Here, we investigate Li ions inside crystals of CsPbI3 as a prototype compound by means of density-functional-theory calculations. Our findings demonstrate that the interstitial location and migration of Li ions depend strongly on the dynamic nature of the crystal structure of the perovskite compound. We consider two limiting cases for Li in CsPbI3,(i) the cubic-symmetry structure as a model for the limit of fast-ion motion and (ii) a distorted cubic structure as a model for the limit of slow-ion motion. For both limiting cases we obtain moderate energy barriers for migrating Li ions, which highlight the potential of halide perovskites like CsPbI3 for applications in photobattery devices. 109 14
Keywords	Cesium compounds ; Crystal structure ; Crystals ; Density functional theory ; Ions ; Lithium-ion batteries ; Perovskite ; DDC::600 Technik ; Medizin ; angewandte Wissenschaften::620 Ingenieurwissenschaften
Subject code	540
Language	English
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Editorial: Oncoplastic surgery for breast cancer.

da Costa Vieira, René Aloisio / Facina, Gil / Tiezzi, Daniel Guimarães / Urban, Cicero de Andrade / de Freitas Junior, Ruffo

Frontiers in oncology

2024 Volume 13, Page(s) 1348964

Language	English
Publishing date	2024-03-27
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1348964
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A Deep Learning Algorithm for High-Dimensional Exploratory Item Factor Analysis.

Urban, Christopher J / Bauer, Daniel J

Psychometrika

2021 Volume 86, Issue 1, Page(s) 1–29

Abstract: Marginal maximum likelihood (MML) estimation is the preferred approach to fitting item response theory models in psychometrics due to the MML estimator's consistency, normality, and efficiency as the sample size tends to infinity. However, state-of-the- ... ...

Abstract	Marginal maximum likelihood (MML) estimation is the preferred approach to fitting item response theory models in psychometrics due to the MML estimator's consistency, normality, and efficiency as the sample size tends to infinity. However, state-of-the-art MML estimation procedures such as the Metropolis-Hastings Robbins-Monro (MH-RM) algorithm as well as approximate MML estimation procedures such as variational inference (VI) are computationally time-consuming when the sample size and the number of latent factors are very large. In this work, we investigate a deep learning-based VI algorithm for exploratory item factor analysis (IFA) that is computationally fast even in large data sets with many latent factors. The proposed approach applies a deep artificial neural network model called an importance-weighted autoencoder (IWAE) for exploratory IFA. The IWAE approximates the MML estimator using an importance sampling technique wherein increasing the number of importance-weighted (IW) samples drawn during fitting improves the approximation, typically at the cost of decreased computational efficiency. We provide a real data application that recovers results aligning with psychological theory across random starts. Via simulation studies, we show that the IWAE yields more accurate estimates as either the sample size or the number of IW samples increases (although factor correlation and intercepts estimates exhibit some bias) and obtains similar results to MH-RM in less time. Our simulations also suggest that the proposed approach performs similarly to and is potentially faster than constrained joint maximum likelihood estimation, a fast procedure that is consistent when the sample size and the number of items simultaneously tend to infinity.
MeSH term(s)	Algorithms ; Deep Learning ; Factor Analysis, Statistical ; Likelihood Functions ; Psychometrics
Language	English
Publishing date	2021-02-02
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209479-4
ISSN	1860-0980 ; 0033-3123
ISSN (online)	1860-0980
ISSN	0033-3123
DOI	10.1007/s11336-021-09748-3
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Article ; Online: Guided bone regeneration in implant dentistry: Basic principle, progress over 35 years, and recent research activities.

Buser, Daniel / Urban, Istvan / Monje, Alberto / Kunrath, Marcel F / Dahlin, Christer

Periodontology 2000

2024 Volume 93, Issue 1, Page(s) 9–25

Abstract: Bone augmentation procedures are frequent today in implant patients, since an implant should be circumferentially anchored in bone at completion of bone healing to have a good long-term stability. The best documented surgical technique to achieve this ... ...

Abstract	Bone augmentation procedures are frequent today in implant patients, since an implant should be circumferentially anchored in bone at completion of bone healing to have a good long-term stability. The best documented surgical technique to achieve this goal is guided bone regeneration (GBR) utilizing barrier membranes in combination with bone fillers. This clinical review paper reflects 35 years of development and progress with GBR. In the 1990s, GBR was developed by defining the indications for GBR, examining various barrier membranes, bone grafts, and bone substitutes. Complications were identified and reduced by modifications of the surgical technique. Today, the selection criteria for various surgical approaches are much better understood, in particular, in post-extraction implant placement. In the majority of patients, biodegradable collagen membranes are used, mainly for horizontal bone augmentation, whereas bioinert PTFE membranes are preferred for vertical ridge augmentation. The leading surgeons are using a composite graft with autogenous bone chips to accelerate bone formation, in combination with a low-substitution bone filer to better maintain the augmented bone volume over time. In addition, major efforts have been made since the millenium change to reduce surgical trauma and patient morbidity as much as possible. At the end, some open questions related to GBR are discussed.
MeSH term(s)	Humans ; Bone Regeneration ; Bone Substitutes/therapeutic use ; Bone Transplantation ; Dental Care ; Research
Chemical Substances	Bone Substitutes
Language	English
Publishing date	2024-01-08
Publishing country	Denmark
Document type	Journal Article ; Review
ZDB-ID	1200504-6
ISSN	1600-0757 ; 0906-6713
ISSN (online)	1600-0757
ISSN	0906-6713
DOI	10.1111/prd.12539
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Article ; Online: A rövidbél-szindróma korszerű sebészi kezelése: autológ rekonstrukció és intestinalis rehabilitáció.

Urbán, Dániel / Kőnig, Róbert / Cserni, Tamás

Orvosi hetilap

2020 Volume 161, Issue 7, Page(s) 243–251

Abstract: Based on the latest definition, short bowel syndrome is defined as intestinal failure due to the loss of significant small bowel length or function, when the homeostasis and growth can only be maintained with intravenous supplementation of fluid, ... ...

Title translation	Autologous reconstructive surgery and intestinal rehabilitation in the management of short bowel syndrome.
Abstract	Based on the latest definition, short bowel syndrome is defined as intestinal failure due to the loss of significant small bowel length or function, when the homeostasis and growth can only be maintained with intravenous supplementation of fluid, electrolytes and macronutrients. The natural adaptation of the short bowel can only compensate for the loss up to a certain level. According to this, we differentiate (1) acute, (2) prolonged and (3) chronic types of intestinal failure/short bowel syndrome. The most common causes are necrotising enterocolits, intestinal malrotation and volvulus, gastroschisis and ileal atresia. The management of type 3 short bowel syndrome has evolved significantly during the last decades, due to the multidisciplinary approach, hence the survival and quality of life of the patients have improved and transplantation is rarely necessary. Our aim was to review the most important considerations of intestinal rehabilitation, like management of increased gastrin secretion, high output stoma, decreased transit time, central venous lines, enteral and parenteral nutrition and the enhancement of the natural adaptation. We reviewed the former and the latest options of the autologous intestinal reconstructive surgery (AIRS) like the reversed segment, small bowel interposition, ileocaecal valve replacement, bowel lengthening and tailoring (LILT, STEP and SILT), controlled bowel expansion and the latest results with distraction enterogenesis and tissue engineering. Orv Hetil. 2020; 161(7): 243-251.
MeSH term(s)	Humans ; Intestines/transplantation ; Reconstructive Surgical Procedures/methods ; Short Bowel Syndrome/surgery ; Transplantation, Autologous
Language	Hungarian
Publishing date	2020-02-05
Publishing country	Hungary
Document type	Journal Article ; Review
ZDB-ID	123879-6
ISSN	1788-6120 ; 0030-6002
ISSN (online)	1788-6120
ISSN	0030-6002
DOI	10.1556/650.2020.31655
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Bladder augmentation from an insider's perspective: a review of the literature on microcirculatory studies.

Urbán, Dániel / Cserni, Tamás / Boros, Mihály / Juhász, Árpád / Érces, Dániel / Varga, Gabriella

International urology and nephrology

2021 Volume 53, Issue 11, Page(s) 2221–2230

Abstract: Augmentation cystoplasty is an exemplary multiorgan intervention in urology which is particularly associated with microvascular damage. Our aim was to review the available intravital imaging techniques and data obtained from clinical and experimental ... ...

Abstract	Augmentation cystoplasty is an exemplary multiorgan intervention in urology which is particularly associated with microvascular damage. Our aim was to review the available intravital imaging techniques and data obtained from clinical and experimental microcirculatory studies involving the most important donor organs applied in bladder augmentation. Although numerous direct or indirect methods are available to assess the condition of microvessels the implementation of microcirculatory diagnostic methods in humans is still challenging and the assessment of organ microcirculation in the operating theatre has limitations. Nevertheless, preclinical studies generally report good internal validity and although prospective human protocols with reduced variability are needed, a possible positive impact of microcirculatory diagnostics on the clinical outcomes of urologic surgery can be anticipated.
MeSH term(s)	Humans ; Microcirculation ; Urinary Bladder/blood supply ; Urinary Bladder/surgery ; Urologic Surgical Procedures/methods
Language	English
Publishing date	2021-08-25
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	204048-7
ISSN	1573-2584 ; 0301-1623 ; 0042-1162
ISSN (online)	1573-2584
ISSN	0301-1623 ; 0042-1162
DOI	10.1007/s11255-021-02971-y
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Article ; Online: A Non-invasive Method to Estimate the Stress-Strain Curve of Soft Tissue Using Ultrasound Elastography.

Wang, Yuqi / Jacobson, Daniel S / Urban, Matthew W

Ultrasound in medicine & biology

2022 Volume 48, Issue 5, Page(s) 786–807

Abstract: Ultrasound elastography performed under small strain conditions has been intensively studied. However, small deformations may be not sufficiently large to differentiate some abnormal tissues. By combining quasi-static and shear wave elastography, we ... ...

Abstract	Ultrasound elastography performed under small strain conditions has been intensively studied. However, small deformations may be not sufficiently large to differentiate some abnormal tissues. By combining quasi-static and shear wave elastography, we developed a non-invasive method to estimate the localized stress- strain curve of materials. This method exerts progressive multistep uniaxial compression on the materials, and shear wave measurements were performed at every compression step. This method estimates the 2-D displacements between steps via a 2-D region growing motion tracking method and accumulates these displacements to obtain the large material displacements with respect to the initial configuration. At each step, the shear modulus and stress were calculated according to linear elastic theory. The proposed method was tested on custom-made tissue-mimicking phantoms. Mechanical compression testing was conducted on the samples made of the same material as the phantoms and taken as the reference. The stress-strain curves for the same material from the proposed method and from mechanical testing are in good agreement. The root mean square error (RMSE) and area percentage error (APE) of the stress-strain curve between ultrasound measurement and mechanical testing for soft materials ranged from 0.18 to 0.26 kPa and from 5.6% to 7.8%, respectively. The RMSE and APE for stiff materials ranged from 0.56 to 1.17 kPa and 8.0% to 17.9%. Therefore, our method was able to provide good estimates of the stress-strain curve for tissue-mimicking materials.
MeSH term(s)	Elastic Modulus ; Elasticity Imaging Techniques/methods ; Motion ; Phantoms, Imaging ; Stress, Mechanical ; Ultrasonography
Language	English
Publishing date	2022-02-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186150-5
ISSN	1879-291X ; 0301-5629
ISSN (online)	1879-291X
ISSN	0301-5629
DOI	10.1016/j.ultrasmedbio.2021.12.016
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