22 research outputs found
sj-docx-1-dhj-10.1177_20552076231171475 - Supplemental material for Anonymization of whole slide images in histopathology for research and education
No full textSupplemental material, sj-docx-1-dhj-10.1177_20552076231171475 for Anonymization of whole slide images in histopathology for research and education by Tom Bisson, Michael Franz, Isil Dogan O, Daniel Romberg, Christoph Jansen, Peter Hufnagl and Norman Zerbe in DIGITAL HEALTH</p
Synthesis, characterization and catalytic evaluation of a Ziegler-type model iridium hydrogenation catalyst plus a novel tetrairidium tetrahydride complex
No full text2013 Summer.Includes bibliographical references.Following a critical review of the pertinent literature of Ziegler-type hydrogenation catalysts, the research presented herein is primarily focused on the synthesis, characterization and catalytic properties of a model Ziegler-type hydrogenation catalyst system made from [Ir(1,5-COD)(μ-O2C8H15)]2 plus AlEt3. The studies include: (i) a critical review of the relevant literature, (ii) ranking the activity, lifetime and thermal stability of the resulting Ir(0)n Ziegler nanoparticles; (iii) characterization of the true stabilizer species for Ir(0)n Ziegler nanoparticles as a function of the initial Al/Ir ratio; and (iv) the synthesis and characterization of a novel [Ir(1,5-COD)(μ-H)]4 complex considered as a plausible intermediate en route to Ir(0)n Ziegler nanoparticles. Studies evaluating and ranking the catalytic properties of Ziegler-type catalysts in the test reaction of cyclohexene hydrogenation reveal that the catalyst made with [Ir(1,5-COD)(μ-O2C8H15)]2 plus AlEt3 is a highly catalytically active, long-lived and thermally unusually stable nanoparticle catalyst. The catalytic lifetimes of the Ir(0)n Ziegler nanoparticles are higher than any known Ir(0)n nanoparticles in the extant literature. The nature of the stabilizer species in the Ziegler-type catalyst system made with [Ir(1,5-COD)(μ-O2C8H15)]2 plus AlEt3 at Al/Ir ratios 1-3 is then investigated by comparing 1H, 13C, 27Al NMR and IR data of the catalysts with those of individually-synthesized standards such as AlEt2(O2C8H15), [(n-Bu)4N][AlEt3(O2C8H15)] and [(n-Bu)2Al(µ-OH)]3. The results of the study shows that (i) AlEt2(O2C8H15) (Al/Ir=1, 2 and 3) and (iii) free AlEt3 (Al/Ir=3) are present in the catalyst solution in this model Ziegler-type hydrogenation catalyst system made from [Ir(1,5-COD)(μ-O2C8H15)]2 plus AlEt3. The spectroscopic and catalytic evidence provided in this study helps to rule out the initial hypotheses (iii) that anionic [AlEt3(O2C8H15)]- stabilizer exists and provides DLVO-type, Coulombic-repulsion stabilization. Also ruled out is (iv) that the AlEt3-derived stabilizers are Al-O-Al containing alumoxanes. In a separate study, a novel [Ir(1,5-COD)(μ-H)]4 complex is synthesized and characterized with the goal of (i) obtaining information on formation and stabilization mechanisms of Ziegler-type industrial hydrogenation model catalysts prepared from [Ir(1,5-COD)(μ-O2C8H15)]2 plus AlEt3; and with the goal of (ii) understanding the stabilization efficacies of various Al-based cocatalysts in the absence of any added carboxylate.The synthesis of the previously unavailable [Ir(1,5-COD)(μ-H)]4 complex in 55% recrystallized yield was accomplished starting with commercially available LiBEt3H and [Ir(1,5-COD)(μ-Cl)]2 in the presence of excess 1,5-COD in THF. The resultant [Ir(1,5-COD)(μ-H)]4 was fully characterized by single-crystal XRD, XAFS, ESI-MS, UV-visible, IR, and NMR. In addition to the four main chapters, two appendix chapters (in which Isil K. Hamdemir has significant contributions) are included in the current dissertation due to their relevancy to the research presented herein. The characterization studies showing the presence of Ir~4-15 subnanometer clusters and Ir~40-150 nanoparticles, before and after catalytic hydrogenation, respectively, in the Ziegler-type catalyst system made from [Ir(1,5-COD)(μ-O2C8H15)]2 plus AlEt3 catalyst solution has been published (William M. Alley, Isil K. Hamdemir, Qi Wang, Anatoly Frenkel, Long Li, Judith C. Yang, Laurent D. Menard, Ralph G. Nuzzo, Saim Özkar, Kimberly Johnson, Richard G. Finke, "Iridium Ziegler-Type Hydrogenation Catalysts Made from [(1,5-COD)(μ-O2C8H15)]2 and AlEt3: Spectroscopic and Kinetic Evidence for the Irn Species Present and for Nanoparticles as the Fastest Catalyst"). Additionally, a broad distribution of metal cluster sizes from subnanometer to nanometer scale particles was observed in industrial Ziegler-type hydrogenation catalysts made with Co(neodecanoate)2 or Ni(2-ethylhexanoate)2 plus AlEt3 (William M. Alley, Isil K. Hamdemir, Qi Wang, Anatoly I. Frenkel, Long Li, Judith C. Yang, Laurent D. Menard, Ralph G. Nuzzo, Saim Özkar, Kimberly Johnson, Richard G. Finke, "Industrial Ziegler-type Hydrogenation Catalysts made from Co(neodecanoate)2 or Ni(2-ethylhexanoate)2, and AlEt3: Evidence for Nanoclusters and Sub-Nanocluster or Larger Ziegler-Nanocluster Based Catalysis"). These two studies were published as two chapters in the dissertation of, graduate student co-worker, William M. Alley, a dissertation which acknowledges Isil Kayiran Hamdemir's (I.K.H.) contributions
Lasagne : a static binary translator for weak memory model architectures
No full textFunding: This work was supported by a UK RISE Grant.The emergence of new architectures create a recurring challenge to ensure that existing programs still work on them. Manually porting legacy code is often impractical. Static binary translation (SBT) is a process where a program’s binary is automatically translated from one architecture to another, while preserving their original semantics. However, these SBT tools have limited support to various advanced architectural features. Importantly, they are currently unable to translate concurrent binaries. The main challenge arises from the mismatches of the memory consistency model specified by the different architectures, especially when porting existing binaries to a weak memory model architecture. In this paper, we propose Lasagne, an end-to-end static binary translator with precise translation rules between x86 and Arm concurrency semantics. First, we propose a concurrency model for Lasagne’s intermediate representation (IR) and formally proved mappings between the IR and the two architectures. The memory ordering is preserved by introducing fences in the translated code. Finally, we propose optimizations focused on raising the level of abstraction of memory address calculations and reducing the number offences. Our evaluation shows that Lasagne reduces the number of fences by up to about 65%, with an average reduction of 45.5%, significantly reducing their runtime overhead.Postprin
Anonymization of whole slide images in histopathology for research and education
No full textObjective: The exchange of health-related data is subject to regional laws and regulations, such as the General Data Protection Regulation (GDPR) in the EU or the Health Insurance Portability and Accountability Act (HIPAA) in the United States, resulting in non-trivial challenges for researchers and educators when working with these data. In pathology, the digitization of diagnostic tissue samples inevitably generates identifying data that can consist of sensitive but also acquisition-related information stored in vendor-specific file formats. Distribution and off-clinical use of these Whole Slide Images (WSIs) are usually done in these formats, as an industry-wide standardization such as DICOM is yet only tentatively adopted and slide scanner vendors currently do not provide anonymization functionality.
Methods: We developed a guideline for the proper handling of histopathological image data particularly for research and education with regard to the GDPR. In this context, we evaluated existing anonymization methods and examined proprietary format specifications to identify all sensitive information for the most common WSI formats. This work results in a software library that enables GDPR-compliant anonymization of WSIs while preserving the native formats.
Results: Based on the analysis of proprietary formats, all occurrences of sensitive information were identified for file formats frequently used in clinical routine, and finally, an open-source programming library with an executable CLI tool and wrappers for different programming languages was developed.
Conclusions: Our analysis showed that there is no straightforward software solution to anonymize WSIs in a GDPR-compliant way while maintaining the data format. We closed this gap with our extensible open-source library that works instantaneously and offline.
Biological traits and prey consumption of Anthocoris minki fed on Agonoscena pistaciae and Brachycaudus (Thuleaphis) amygdalinus
No full textThe predatory insect Anthocoris minki Dohrn (Heteroptera: Anthocoridae) is an indigenous Anthocoris species for the biological control of pests in pistachio orchards. The pistachio psylla Agonoscena pistaciae Burckhardt and Lauterer (Homoptera: Psyllidae) is an important insect pest in pistachio trees in Turkey. Similarly, Brachycaudus (Thuleaphis) amygdalinus (Schouteden) (Hemiptera: Aphididae) is a pest of almond trees that is considered as alternative prey for A. minki when pistachio psylla are not available in early spring on pistachio trees. The development time, survival percentage of immature stages, longevity, fecundity, prey consumption, and life table parameters of A. minki fed on A. pistaciae and B. amygdalinus nymphs were determined at 25 +/- 1A degrees C, 70 A +/- 5% r.h., and a 16 h:8 h (L:D) photoperiod under laboratory conditions. The nymphal survival rate was significantly higher when nymphs were fed on A. pistaciae (an average of 96.7%) than on B. amygdalinus (an average of 71.4%). The development time of A. minki was significantly shorter when nymphs were fed on B. amygdalinus (10.3 days) as opposed to A. pistaciae (11.0 days). No significant differences among prey species were found for longevity and fecundity. The total female longevity and fecundity of A. minki was 38.0 days and 247.2 eggs, respectively, when nymphs were fed on A. pistaciae; and 35.4 days and 233.0 eggs, respectively, when nymphs were fed on B. amygdalinus. On average, 104.4 A. pistaciae and 77.7 B. amygdalinus nymphs were consumed during the nymphal development time for A. minki. Adults of A. minki consumed significantly more psyllids than aphids throughout their life span. The greater difference did not significantly inpact the longevity and fecundity of A. minki. Females of A. minki consumed an average of 631.0 A. pistaciae and an average of 273.3 B. amygdalinus nymphs, while female predators consumed significantly more prey than males. The intrinsic rate of increase (r (m) ) of A. minki fed on A. pistaciae (0.174) was significantly greater than those fed on B. amygdalinus (0.148). The successful development and reproduction of both A. pistaciae and B. amygdalinus indicates that they are suitable prey for A. minki.TUBITAK (The Scientific and Technological Research Council of Turkey)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TOVAG-107 O 734]We thank TUBITAK (The Scientific and Technological Research Council of Turkey, Project number: TOVAG-107 O 734) for funding. We also thank Dr. Isil Ozdemir from Ankara Plant Protection Central Research Institute, for the identification of aphid species. We extend our appreciation to Dr. Bekir Bukun and Dr. Ergun Dogan (Harran University, Faculty of Agriculture) for contributions during the editing stage
Early Parental Multimodal Input Is Differentially Associated with Later Vocabulary Knowledge for Preterm and Full-Term Infants
No full textGoksun, Tilbe/0000-0002-0190-7988This study examined whether (1) parents' language input and its modality differed in Turkish-learning preterm (PT) (<37 weeks of gestation) and full-term infants (FT), and (2) the type of language input (i.e. verbal and multimodal) had differential concurrent and longitudinal effects on PT and FT infants' vocabulary development. At Time 1 (Mage = 14 months, N = 73, 36 PT) and Time 2 (Mage = 20.1 months, N = 61, 27 PT), PT infants' parents produced fewer frequent multimodal input (i.e., co-speech deictic gestures) than FT infants' parents. The frequency of verbal input (i.e., word count) between groups differed only at Time 1. Parents' verbal input was concurrently associated with infants' receptive vocabulary at 14 months, yet parents' multimodal input was only linked to PT infants' receptive vocabulary. At 20 months, parents' verbal input was not related to expressive vocabulary in either group; however, parents' multimodal input was again associated with PT infants' expressive vocabulary scores. Parents' multimodal input at 14 months predicted infants' expressive vocabulary scores at 20 months, only for the PT group. These findings suggest that the variability of multimodal input infants receives from their parents and the contribution of such input to vocabulary development change as a function of infants' neonatal status.James S. McDonnell Foundation [220020510]This work was supported by the James S. McDonnell Foundation Scholar Award Grant no: [220020510] to Tilbe Goksun.Social Science Citation Index - Arts & Humanities Citation Inde
Narratives of Preterm and Full-Term Preschool-Aged Children: Analyses of Different Narrative Dimensions
No full textAkkan, Ibrahim/0000-0002-9404-6741Preterm birth increases the likelihood of early language and cognitive delays, but less is known about later aspects of language development, such as narrative generation. Narrative skills involve dimensions, such as linguistic and narrative complexity, and preterm (PT) and full-term (FT) children's narrative performances may vary across these dimensions. We investigated the role of neonatal status on the total number of words produced, linguistic complexity, and narrative complexity across two presentation modes: narrative generation while seeing pictures and narrative generation after watching an animated video. Seventy-one Turkish-reared preschool-aged children (31 PT [Mage = 48.70, SD = 1.53] and 40 FT [Mage = 48.83, SD = 1.63]) participated in the study. Despite having lower expressive vocabulary skills (assessed by a standardized task) than full-term children, preterm children performed comparably in both picture and animated video-stories, except PT children tended to produce longer narratives in the picture story, possibly due to the different demand characteristics of the tasks. Overall, our findings support the possibility of interacting factors that may help PT children overcome challenges in narrative development.James S. McDonnell FoundationJames S. McDonnell FoundationSocial Science Citation Inde
Influence of Menstrual Cycle on P Wave Dispersion
No full textFemale gender is an independent risk factor for some types of arrhythmias. We sought to determine whether the menstrual cycle affects P wave dispersion, which is a predictor of atrial fibrillation. The study population consisted of 59 women in follicular phase (mean age, 29.3 +/- 7.7 years) (group F) and 53 women in luteal phase (mean age, 28.1 +/- 6.8 years) (group L). The ECGs of 35 patients (mean age, 26.4 +/- 4.5) were obtained in both follicular and luteal phase. Both groups underwent a standard 12-lead surface electrocardiogram recorded at 50 mm/s. Maximal (Pmax) and minimal P wave durations (Pmin) were measured. P wave dispersion (PD) was defined as the difference between Pmax and Pmin. PD was significantly higher in group L than group F (46.6 +/- 18.5 versus 40.1 +/- 12.7; P < 0.05). Pmin was significantly lower in group L than group F (51.6 +/- 12.1 versus 59.1 +/- 12.1; P = 0.002). When we compared ECGs in different phases of the 35 patients, PD was significantly higher in luteal phase than follicular phase (53.2 +/- 12.3 versus 42.8 +/- 10.2; P < 0.05). Pmin was significantly lower in luteal phase than follicular phase (47.6 +/- 6.6 versus 56 +/- 10.1; P = 0.05). We detected a significant correlation between the day of the menses and PD (r = 0.27; P < 0.05). PD was increased in luteal phase compared to follicular phase, and this difference was more prominent as the days of the cycle progressed. (Int Heart J 2011; 52: 23-26
Volumetric Reconstruction of Prostatectomy Specimens from Histology
No full textSurgical treatment for prostate cancer often involves organ removal, i.e., prostatectomy. Pathology reports on these specimens convey treatment-relevant information. Beyond these reports, the diagnostic process generates extensive and complex information that is difficult to represent in reports, although it is of significant interest to the other medical specialties involved. 3D tissue reconstruction would allow for better spatial visualization, as well as combinations with other imaging modalities. Existing approaches in this area have proven labor-intensive and challenging to integrate into clinical workflows. 3D-SLIVER provides a simplified solution, implemented as an open-source 3DSlicer extension. We outline three specific real-world scenarios to illustrate its potential to improve transparency in diagnostic workflows and contribute to multi-modal research endeavors. Implementing the 3D reconstruction process involved four sub-modules of 3D-SLIVER: digitization of slicing protocol, virtual slicing of arbitrary 3D models based on that protocol, registration of slides with virtual slices using the Coherent Point Drift algorithm, and 3D reconstruction of registered information using convex hulls, Gaussian splatter and linear extrusion. Three use cases to employ 3D-SLIVER are presented: a low-effort approach to pathology workflow integration and two research-related use cases illustrating how to perform retrospective evaluations of PI-RADS predictions and statistically model 3D distributions of morphological patterns. 3D-SLIVER allows for improved interdisciplinary communication among specialties. It is designed for simplicity in application, allowing for flexible integration into various workflows and use cases. Here we focused on the clinical care of prostate cancer patients, but future possibilities are extensive with other neoplasms and in education and research
Motor skills, language development, and visual processing in preterm and full-term infants
No full textLanguage development is intertwined with motor development. This study examined how visual processing might mediate the relation between language development and motor skills in preterm (PT, n = 34, Mean gestational age = 30 weeks) and full-term infants (FT, n = 35, Mean gestational age = 38.9 weeks) at 13 months of age. Infants' visual processing, fine and gross motor skills were tested using the Mullen Scales of Early Learning. Parents reported on infants' language skills (word comprehension and early communicative behavior), using the Turkish version of CDI (TCDI). Results showed that PT infants performed worse than their FT peers on gross motor skills and visual processing, but not on language. When controlling for age and neonatal condition (being preterm or not), visual processing mediated the relation between gross motor skills and word comprehension as well as early communicative behavior. However, for fine motor skills, visual processing mediated the relation between fine motor skills and early communicative behavior but not word comprehension. The relations between motor skills and visual processing were more robust for the PT group than the FT group. Following developmental cascades, these findings suggest that motor skills contribute to language development through visual processing. These relations are prominent for preterm infants who have delays in motor skills. PT children's limited interactions with their environment due to problems in motor skills can be connected to delays in visual processing.James S. McDonnell Foundation Scholar Award [220020510]This work was supported by the James S. McDonnell Foundation Scholar Award (Grant no: 220020510) to Tilbe Goksun. We thank everyone at the Language and Cognition Lab at Koc University for their invaluable contributions to this project. Special thanks to Cerebral Palsy Turkey Metin Sabanc Center for Family Counseling for the institutional support, Dr. Nihan Hande Akcakaya, Banu Bingol, and Rahime Gokboa from Cerebral Palsy Turkey to their support for the project, El Bebek Gul Bebek Foundation for Premature Birth and Gymboree Classes for helping us reach out the families Special thanks to Feyza Nur Dik, pek Bahar Ungan, Merve Duran, ozge Eser, Rengim Lal Klavuz, layda Deringor, and lke Uysal who assisted with data transcription coding, and reliability. We are grateful to the children and parents who participated in the study. The data that support the findings of this study are available from the corresponding author upon reasonable request
