2,381 results on '"Dirks, P"'
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2. Mental Health and String Education: Identifying Key Concerns within the American String Teachers Association Community
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Rachel L. Dirks, Tawnya D. Smith, Patricia A. González-Moreno, and Allyn Phelps
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At the 2020 American String Teachers Association (ASTA) Conference held in Orlando Florida, an attendee of the Wellness Committee Listening Session recommended that a study be conducted to determine the prevalence and awareness of mental health concerns among students and teachers within the organization. Members agreed that there is more needed to be understood so that ASTA could provide professional development webinars, resources, as well as local, state, and national conference sessions. In response to this request and the clear need for more information, a survey was developed and deployed to the ASTA membership in the fall of 2020. Follow-up interviews with members who volunteered in response to an invitation on the survey were conducted in the spring and early summer of 2021. Teachers reported a high prevalence of student mental health issues prior to and during the pandemic and reported concerning levels of work overload, compassion fatigue/burnout, and mental health issues. Generational differences in mental health perceptions were noted, as were opportunities to provide targeted professional development and community-level services.
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- 2024
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3. Age Impacts Speech-in-Noise Recognition Differently for Nonnative and Native Listeners
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Ian Phillips, Rebecca E. Bieber, Coral Dirks, Ken W. Grant, and Douglas S. Brungart
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Purpose: The purpose of this study was to explore potential differences in suprathreshold auditory function among native and nonnative speakers of English as a function of age. Method: Retrospective analyses were performed on three large data sets containing suprathreshold auditory tests completed by 5,572 participants who were self-identified native and nonnative speakers of English between the ages of 18-65 years, including a binaural tone detection test, a digit identification test, and a sentence recognition test. Results: The analyses show a significant interaction between increasing age and participant group on tests involving speech-based stimuli (digit strings, sentences) but not on the binaural tone detection test. For both speech tests, differences in speech recognition emerged between groups during early adulthood, and increasing age had a more negative impact on word recognition for nonnative compared to native participants. Age-related declines in performance were 2.9 times faster for digit strings and 3.3 times faster for sentences for nonnative participants compared to native participants. Conclusions: This set of analyses extends the existing literature by examining interactions between aging and self-identified native English speaker status in several auditory domains in a cohort of adults spanning young adulthood through middle age. The finding that older nonnative English speakers in this age cohort may have greater-than-expected deficits on speech-in-noise perception may have clinical implications on how these individuals should be diagnosed and treated for hearing difficulties.
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- 2024
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4. The minimal exponent of cones over smooth complete intersection projective varieties
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Chen, Qianyu, Dirks, Bradley, and Mustaţă, Mircea
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Mathematics - Algebraic Geometry ,14F10, 14B05, 32S25 - Abstract
We compute the minimal exponent of the affine cone over a complete intersection of smooth projective hypersurfaces intersecting transversely. The upper bound for the minimal exponent is proved, more generally, in the weighted homogeneous setting, while the lower bound is deduced from a general lower bound in terms of a strong factorizing resolution in the sense of Bravo and Villamayor., Comment: 14 pages
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- 2024
5. An introduction to $V$-filtrations
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Chen, Qianyu, Dirks, Bradley, and Mustaţă, Mircea
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Mathematics - Algebraic Geometry ,14F10, 32S40, 14B05 - Abstract
We give an introduction to the theory of $V$-filtrations of Malgrange and Kashiwara. After discussing the basic properties of this construction (in the case of a smooth hypersurface and, later, in the general case), we describe the connection with the theory of $b$-functions. As an example, we treat the case of weighted homogeneous isolated singularities. We discuss the compatibility of $V$-filtrations with proper push-forward and duality and the connection with nearby and vanishing cycles via the Riemann-Hilbert correspondence. We end by describing some invariants of singularities via the $V$-filtration., Comment: 67 pages, to appear in Volume VI of Handbook of Geometry and Topology of Singularities
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- 2024
6. A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis
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Wijnen, Cris L., Botet, Ramon, van de Belt, José, Deurhof, Laurens, de Jong, Hans, de Snoo, C. Bastiaan, Dirks, Rob, Boer, Martin P., van Eeuwijk, Fred A., Wijnker, Erik, and Keurentjes, Joost J. B.
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- 2024
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7. Single-cell atlas of the human brain vasculature across development, adulthood and disease
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Wälchli, Thomas, Ghobrial, Moheb, Schwab, Marc, Takada, Shigeki, Zhong, Hang, Suntharalingham, Samuel, Vetiska, Sandra, Gonzalez, Daymé Rodrigues, Wu, Ruilin, Rehrauer, Hubert, Dinesh, Anuroopa, Yu, Kai, Chen, Edward L. Y., Bisschop, Jeroen, Farnhammer, Fiona, Mansur, Ann, Kalucka, Joanna, Tirosh, Itay, Regli, Luca, Schaller, Karl, Frei, Karl, Ketela, Troy, Bernstein, Mark, Kongkham, Paul, Carmeliet, Peter, Valiante, Taufik, Dirks, Peter B., Suva, Mario L., Zadeh, Gelareh, Tabar, Viviane, Schlapbach, Ralph, Jackson, Hartland W., De Bock, Katrien, Fish, Jason E., Monnier, Philippe P., Bader, Gary D., and Radovanovic, Ivan
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- 2024
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8. Pediatric Moyamoya Revascularization Perioperative Care: A Modified Delphi Study.
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Sun, Lisa, Jordan, Lori, Smith, Edward, Aldana, Philipp, Kirschen, Matthew, Guilliams, Kristin, Gupta, Nalin, Steinberg, Gary, Fox, Christine, Harrar, Dana, Lee, Sarah, Chung, Melissa, Dirks, Peter, Dlamini, Nomazulu, Maher, Cormac, Lehman, Laura, Hong, Sue, Strahle, Jennifer, Pineda, Jose, Beslow, Lauren, Rasmussen, Lindsey, Mailo, Janette, Piatt, Joseph, Lang, Shih-Shan, Adelson, P, Dewan, Michael, Mineyko, Aleksandra, McClugage, Samuel, Vadivelu, Sudhakar, Dowling, Michael, and Hersh, David
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Cerebral revascularization ,Children ,Delphi technique ,Ischemic stroke ,Moyamoya disease ,Pediatric stroke ,Perioperative care ,Child ,Humans ,Delphi Technique ,Moyamoya Disease ,Stroke ,Perioperative Care ,Postoperative Care ,Cerebral Revascularization ,Treatment Outcome ,Retrospective Studies - Abstract
BACKGROUND: Surgical revascularization decreases the long-term risk of stroke in children with moyamoya arteriopathy but can be associated with an increased risk of stroke during the perioperative period. Evidence-based approaches to optimize perioperative management are limited and practice varies widely. Using a modified Delphi process, we sought to establish expert consensus on key components of the perioperative care of children with moyamoya undergoing indirect revascularization surgery and identify areas of equipoise to define future research priorities. METHODS: Thirty neurologists, neurosurgeons, and intensivists practicing in North America with expertise in the management of pediatric moyamoya were invited to participate in a three-round, modified Delphi process consisting of a 138-item practice patterns survey, anonymous electronic evaluation of 88 consensus statements on a 5-point Likert scale, and a virtual group meeting during which statements were discussed, revised, and reassessed. Consensus was defined as ≥ 80% agreement or disagreement. RESULTS: Thirty-nine statements regarding perioperative pediatric moyamoya care for indirect revascularization surgery reached consensus. Salient areas of consensus included the following: (1) children at a high risk for stroke and those with sickle cell disease should be preadmitted prior to indirect revascularization; (2) intravenous isotonic fluids should be administered in all patients for at least 4 h before and 24 h after surgery; (3) aspirin should not be discontinued in the immediate preoperative and postoperative periods; (4) arterial lines for blood pressure monitoring should be continued for at least 24 h after surgery and until active interventions to achieve blood pressure goals are not needed; (5) postoperative care should include hourly vital signs for at least 24 h, hourly neurologic assessments for at least 12 h, adequate pain control, maintaining normoxia and normothermia, and avoiding hypotension; and (6) intravenous fluid bolus administration should be considered the first-line intervention for new focal neurologic deficits following indirect revascularization surgery. CONCLUSIONS: In the absence of data supporting specific care practices before and after indirect revascularization surgery in children with moyamoya, this Delphi process defined areas of consensus among neurosurgeons, neurologists, and intensivists with moyamoya expertise. Research priorities identified include determining the role of continuous electroencephalography in postoperative moyamoya care, optimal perioperative blood pressure and hemoglobin targets, and the role of supplemental oxygen for treatment of suspected postoperative ischemia.
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- 2024
9. The Influence of Two Stage Collaborative Testing on Peer Relationships: A Study of First Year University Student Perceptions
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Brian Rempel, Elizabeth McGinitie, and Maria Dirks
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Two-stage testing is a form of collaborative assessment that creates an active learning environment during test taking. In two-stage testing, students first complete an exam individually, and then complete a subset of the same questions as part of a learning team with the ultimate exam score being a weighted average of the individual and team portions. In the second (team-based) part of the exam, students are encouraged to discuss solutions until a consensus among team members is achieved, thus actively engaging students with course material and each other during the exam. A short open-ended survey was administered to students at the end of the semester, and the responses coded by thematic analysis, with themes generated using inductive coding based on the principles of grounded theory. The most important conclusion was that students overwhelmingly preferred two-stage tests for the development of positive peer relationships in class. The most common themes that emerged from student responses involved positive feelings from forced interaction with their peers, the benefits of meeting and socializing with other students, sharing of knowledge with others, and solidarity or positive affect towards the process of working as part of a team. Finally, students also expressed an overall preference for two-stage exams when compared to solely individual, one-stage exams.
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- 2023
10. Assessment of MR blood-oxygen-level-dependent (BOLD) cerebrovascular reactivity under general anesthesia in children with moyamoya
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Choi, Eun Jung, Levin, David, Robertson, Amanda, Kirkham, Fenella J., Muthusami, Prakash, Krishnan, Pradeep, Shroff, Manohar, Moharir, Mahendranath, Dirks, Peter, MacGregor, Daune, Pulcine, Elizabeth, Bhathal, Ishvinder, Kassner, Andrea, Walker, Kirstin, Allan, Warwick, deVeber, Gabrielle, Logan, William J., and Dlamini, Nomazulu
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- 2024
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11. Benchmarking Site Activation and Patient Enrollment
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Lamberti, Mary Jo, Dirks, Abigail, Kikuchi, Nicholas, Patel Cervantes, Neha, and Getz, Kenneth
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- 2024
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12. Transition to Motherhood: Adverse Childhood Experiences, and Support from Partner, Family and Friends
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Mathijssen, J. J. P., Dirks, E., and van Bakel, H. J. A.
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- 2024
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13. Comprehensive Assessment of Risk-Based Quality Management Adoption in Clinical Trials
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Dirks, Abigail, Florez, Maria, Torche, Francois, Young, Steve, Slizgi, Brian, and Getz, Kenneth
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- 2024
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14. Some applications of microlocalization for local complete intersection subvarieties
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Dirks, Bradley
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Mathematics - Algebraic Geometry ,14B05, 14J17, 32S35 - Abstract
Saito's microlocalization construction has been used to great effect in understanding hypersurface singularities. In this paper, we introduce what we believe to be a suitable analogue of the microlocalization construction for local complete intersection subvarieties. As evidence, we relate our construction to Saito's in the codimension one case. Moreover, we use this construction to study various natural questions concerning the minimal exponent of LCI subvarieties. We show that the minimal exponent agrees with the smallest Bernstein-Sato root, which was expected to be true. We also show that, in the isolated complete intersection singularities case, the minimal exponent agrees with the smallest non-zero spectral number, as defined by Dimca, Maisonobe and Saito. As applications of these results, we prove constructibility of the minimal exponent along certain Whitney stratifications and we prove that the spectrum (hence, the minimal exponent) is constant in equisingular families of ICIS varieties, in the sense of Gaffney., Comment: 24 pages, comments are welcome. v2: filled a gap in the proof of Theorem 1.1, edited the statement and made expository changes (by adding Lemmas 2.6 and 2.7) to make the proof more readable. Fixed typos
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- 2023
15. Data reduction for directed feedback vertex set on graphs without long induced cycles
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Dirks, Jona, Gerhard, Enna, Grobler, Mario, Mouawad, Amer E., and Siebertz, Sebastian
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Computer Science - Data Structures and Algorithms - Abstract
We study reduction rules for Directed Feedback Vertex Set (DFVS) on instances without long cycles. A DFVS instance without cycles longer than $d$ naturally corresponds to an instance of $d$-Hitting Set, however, enumerating all cycles in an $n$-vertex graph and then kernelizing the resulting $d$-Hitting Set instance can be too costly, as already enumerating all cycles can take time $\Omega(n^d)$. We show how to compute a kernel with at most $2^dk^d$ vertices and at most $d^{3d}k^d$ induced cycles of length at most $d$ (which however, cannot be enumerated efficiently), where $k$ is the size of a minimum directed feedback vertex set. We then study classes of graphs whose underlying undirected graphs have bounded expansion or are nowhere dense; these are very general classes of sparse graphs, containing e.g. classes excluding a minor or a topological minor. We prove that for such classes without induced cycles of length greater than $d$ we can compute a kernel with $O_d(k)$ and $O_{d,\epsilon}(k^{1+\epsilon})$ vertices for any $\epsilon>0$, respectively, in time $O_d(n^{O(1)})$ and $O_{d,\epsilon}(n^{O(1)})$, respectively. The most restricted classes we consider are strongly connected planar graphs without any (induced or non-induced) long cycles. We show that these have bounded treewidth and hence DFVS on planar graphs without cycles of length greater than $d$ can be solved in time $2^{O(d)}\cdot n^{O(1)}$. We finally present a new data reduction rule for general DFVS and prove that the rule together with a few standard rules subsumes all the rules applied by Bergougnoux et al. to obtain a polynomial kernel for DFVS[FVS], i.e., DFVS parameterized by the feedback vertex set number of the underlying (undirected) graph. We conclude by studying the LP-based approximation of DFVS.
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- 2023
16. Evidence for a large off-centered galactic outflow and its connection to the extraplanar diffuse ionized gas in IC 1553
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Dirks, Lukas, Dettmar, Ralf-Jürgen, Bomans, Dominik J., Kamphuis, Peter, and Schilling, Ulrich
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Astrophysics - Astrophysics of Galaxies - Abstract
Aims. We analyze a MUSE optical integral field spectrum of the star-forming edge-on galaxy IC 1553 in order to study its extraplanar diffuse ionized gas (eDIG) and the processes shaping its disk-halo interface. Methods. We extracted the optical emission line properties from the integral field spectrum and generated the commonly used emission line diagnostic diagrams in order to analyze the ionization conditions and the distribution of the eDIG. Furthermore, we performed gravitational potential fitting to investigate the kinematics of a suspected galactic outflow. Results. We find that the eDIG scale height has a maximum value of approximately 1.0 kpc and decreases roughly linearly with the radial distance from the galactic center in projection. The ionization state of the eDIG is not consistent with a pure photoionization scenario and instead requires a significant contribution from shock ionization. This, in addition to the gas kinematics, strongly suggests the presence of a galactic scale outflow, the origin of which lies at least 1.4 kpc away from the galactic center. The inferred shock velocity in the eDIG of approximately 225 km s-1 is comparable to the escape velocity estimated from our potential modelling. The asymmetric distribution of currently star-forming clusters produces a range of different ionization conditions in the eDIG. As a result, the vertical emission line profiles vary quantitatively and qualitatively along the major axis of the galaxy. This analysis illustrates that it is crucial in studies of the eDIG to use observations that take the spatial and kinematical distributions into account, such as those done with integral field units, to form an accurate picture of the relevant physical properties., Comment: Accepted for publication by Astronomy & Astrophysics on August 1, 2023
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- 2023
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17. The Living Library: a process-based tool for open literature review, probing the boundaries of open science
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Angerer, Elisabeth, Burke, Maura Cassidy, Dirks, Simon, Bakker, Arthur, Bilinski Torres, Aitana, and Pieters, Toine
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- 2024
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18. Mitochondrial bioenergetics are not associated with myofibrillar protein synthesis rates
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Andrew M. Holwerda, Marlou L. Dirks, Pierre‐Andre Barbeau, Joy Goessens, Annemie Gijsen, Luc J.C. vanLoon, and Graham P. Holloway
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Aging ,Muscle protein synthesis ,Physical inactivity ,Reactive oxygen species ,Skeletal muscle ,Diseases of the musculoskeletal system ,RC925-935 ,Human anatomy ,QM1-695 - Abstract
Abstract Background Mitochondria represent key organelles influencing cellular homeostasis and have been implicated in the signalling events regulating protein synthesis. Methods We examined whether mitochondrial bioenergetics (oxidative phosphorylation and reactive oxygen species (H2O2) emission, ROS) measured in vitro in permeabilized muscle fibres represent regulatory factors for integrated daily muscle protein synthesis rates and skeletal muscle mass changes across the spectrum of physical activity, including free‐living and bed‐rest conditions: n = 19 healthy, young men (26 ± 4 years, 23.4 ± 3.3 kg/m2) and following 12 weeks of resistance‐type exercise training: n = 10 healthy older men (70 ± 3 years, 25.2 ± 2.1 kg/m2). Additionally, we evaluated the direct relationship between attenuated mitochondrial ROS emission and integrated daily myofibrillar and sarcoplasmic protein synthesis rates in genetically modified mice (mitochondrial‐targeted catalase, MCAT). Results Neither oxidative phosphorylation nor H2O2 emission were associated with muscle protein synthesis rates in healthy young men under free‐living conditions or following 1 week of bed rest (both P > 0.05). Greater increases in GSSG concentration were associated with greater skeletal muscle mass loss following bed rest (r = −0.49, P 0.05). Additionally, MCAT mice displayed no differences in myofibrillar (2.62 ± 0.22 vs. 2.75 ± 0.15%/day) and sarcoplasmic (3.68 ± 0.35 vs. 3.54 ± 0.35%/day) protein synthesis rates when compared with wild‐type mice (both P > 0.05). Conclusions Mitochondrial oxidative phosphorylation and reactive oxygen emission do not seem to represent key factors regulating muscle protein synthesis or muscle mass regulation across the spectrum of physical activity.
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- 2024
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19. Evaluation of Dietary Supplementation of a Multi-Carbohydrase Enzyme Complex on Growth Performance and Carcass Traits of Pekin Ducks Fed Corn–Soy Based Diets
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Hector Leyva-Jimenez, Emily Jiral, Melinda Grimes, Jessica J. Rocha, Carlos Soto, Yemi Burden, Brian P. Dirks, and Gregory S. Archer
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carbohydrase enzyme complex ,Pekin duck ,performance ,carcass ,yield ,Animal culture ,SF1-1100 - Abstract
The present study investigated the effect of supplementing a multi-carbohydrase enzyme complex (MCE) in corn–soy-based diets of Pekin ducks. The treatments were as follows: positive control (PC, 2980 and 3120 kcal/kg for starter and grower, respectively); negative control (NC, −132 kcal/kg energy reduction to PC achieved by reduction of fat and wheat middlings as filler); NC + MCE at 75 ppm (E75); 100 ppm (E100); and 125 ppm (E125) randomly distributed in 10 replicate pens with 25 birds each. Performance was evaluated after 14 and 35 d. On day 36 of the trial, five ducks/pen were processed to evaluate carcass traits. During days 1–14, the PC had a lower (p < 0.01) feed intake compared to all other treatments. At 14 and 35 d of age the NC decreased (p < 0.001) the body weight (BW) of the ducks compared to the PC by −8.3% and −5.3%, respectively. The NC BW was lower (p < 0.001) compared to all MCE-supplemented treatments at 14 and 35 d. The BW of E75, E100, and E125 treatments was not different (p > 0.05) from the PC at both evaluation periods. Cumulatively (1–35 d), the NC resulted in a weight-adjusted FCR increase (p = 0.001) of 9.9% compared to the PC, and the FCR of E75, E100, and E125 were able to recover 72.3%, 66.4%, and 63.5%, respectively, compared to the PC. The carcass and breast weights were lower (p < 0.001) in the NC compared to all other treatments, and no differences (p > 0.05) were observed between the MCE-supplemented treatments and the PC. In conclusion, these results suggest that the MCE supplementation can maintain duck growth performance with no negative effects on carcass traits in energy-reduced corn–soybean meal-based diets. From the results of the trial, 75 ppm MCE delivered the best performance recovery and 125 ppm MCE supplementation had the best % breast yield.
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- 2024
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20. A starfish-inspired 4D self-healing morphing structure
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Raman, Susanna Labisch, and Jan-Henning Dirks
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Medicine ,Science - Abstract
Abstract Inspired by the starfish's unique ability to achieve flexibility and posture-holding with minimal energy expenditure, we present a novel bioinspired morphing structure. Our two-component design, consisting of a thermoplastic mesh and elastomeric jacket, effectively mimics the functions of the starfish's ossicles, mutable collagenous tissues, and derma. This structure exhibits a remarkable combination of self-healing, time-dependent shape memory, and self-posture-holding properties. Systematic variations in mesh geometry demonstrate precise control over structural stiffness and thermal response, enabling customization for specific applications. The structure's scalability and ease of fabrication further enhance its adaptability. We experimentally demonstrate the potential of our biomimetic morphing structure using several prototypes. This work lays the foundation for developing a new type of versatile morphing structures with applications in diverse fields, including robotics, biomedical devices, and adaptive structures.
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- 2024
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21. The implementation of EMI-Heart, a family-tailored early motor intervention in infants with complex congenital heart disease, in practice: a feasibility RCT
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Elena Mitteregger, Tineke Dirks, Manuela Theiler, Oliver Kretschmar, and Beatrice Latal
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Congenital heart disease ,Open-heart surgery ,Early intervention ,Paediatric physiotherapy ,Partnering with parents ,Video feedback ,Medicine (General) ,R5-920 - Abstract
Abstract Background Children with congenital heart disease (CHD) who undergo open-heart surgery are at risk of developmental impairment, including motor delay, which contributes to parental concerns. Additionally, parents experience prolonged stress associated with their child’s disease. There is a lack of early motor interventions in infants with CHD accounting for parental burdens. We developed a family-tailored early motor intervention (EMI-Heart), aiming to promote motor development in infants with CHD and family well-being. The primary aim was to evaluate the feasibility of the study design and the intervention. The secondary aim was to evaluate differences between the intervention and the control group in motor outcomes and family well-being at baseline (3–5 months), post-treatment (6–8 months), and at follow-up (12 months). Method In this single-centre feasibility randomized control trial (RCT), infants with CHD after open-heart surgery without genetic or major neurological comorbidities were randomly allocated to EMI-Heart or the control group (standard of care). EMI-Heart’s key elements promote postural functional activities and encourage parental sensitivity to infants’ motor and behaviour cues. Infants assigned to EMI-Heart received nine sessions of early motor intervention at home, in the hospital, and online for a duration of 3 months by a paediatric physiotherapist. We performed descriptive statistics for feasibility and secondary outcomes. Results The recruitment rate was 59% (10/17), all participating families completed the study (10/10), and the intervention duration was 3.9 months (± 0.54), including nine intervention sessions per family. Median acceptability to parents was 3.9 (1 = not agree–4 = totally agree, Likert scale). The paediatric physiotherapist considered the intervention as feasible. The comparison of motor outcomes did not show differences between groups. However, we detected improved reliable change scores in family well-being outcomes for families of the intervention group compared to the controls. Conclusions Our research indicates that EMI-Heart is a feasible intervention for infants with CHD after open-heart surgery. The intervention was highly acceptable both to parents and to the paediatric physiotherapist. Online treatment sessions offer a valuable alternative to home and hospital visits. This feasibility RCT provides a foundation for a future full trial. Trial registration ClinicalTrials.gov, NCTT04666857. Registered 23.11.2020.
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- 2024
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22. Early Mathematical Performance of Deaf and Hard of Hearing Toddlers in Family-Centred Early Intervention Programmes
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Loes Wauters, Claudia M. Pagliaro, Karen L. Kritzer, and Evelien Dirks
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Research indicates that establishing a strong foundation in early mathematics is essential for later academic learning. Previous research with students who are deaf or hard of hearing (DHH) has shown varying differences in the performance and achievement when compared to typically hearing (TH) students. While the majority of research in this area has been conducted in the United States, studies in other countries suggest that these differences may be global. The present study investigated the early mathematics abilities of 3-year-old DHH children enrolled in family-centred early intervention in the Netherlands. Fifty-three DHH and TH children were given an adapted version of the Early Mathematics Performance Diagnostic. Results showed that on average, the DHH and the TH children performed similarly on all domains, except for Measurement. Likewise, both groups showed similar mathematical knowledge in most early mathematics tasks measuring sub-concepts such as counting objects, shape matching, or measuring weight. Differences were identified in some basic tasks measuring the sub-concepts (e.g. rote counting, measuring time, solving puzzles), however, not on the more advanced tasks measuring these same sub-concepts. These findings are important for parents, teachers, and early interventionists.
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- 2024
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23. The STOIC2021 COVID-19 AI challenge: applying reusable training methodologies to private data
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Boulogne, Luuk H., Lorenz, Julian, Kienzle, Daniel, Schon, Robin, Ludwig, Katja, Lienhart, Rainer, Jegou, Simon, Li, Guang, Chen, Cong, Wang, Qi, Shi, Derik, Maniparambil, Mayug, Muller, Dominik, Mertes, Silvan, Schroter, Niklas, Hellmann, Fabio, Elia, Miriam, Dirks, Ine, Bossa, Matias Nicolas, Berenguer, Abel Diaz, Mukherjee, Tanmoy, Vandemeulebroucke, Jef, Sahli, Hichem, Deligiannis, Nikos, Gonidakis, Panagiotis, Huynh, Ngoc Dung, Razzak, Imran, Bouadjenek, Reda, Verdicchio, Mario, Borrelli, Pasquale, Aiello, Marco, Meakin, James A., Lemm, Alexander, Russ, Christoph, Ionasec, Razvan, Paragios, Nikos, van Ginneken, Bram, and Dubois, Marie-Pierre Revel
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Challenges drive the state-of-the-art of automated medical image analysis. The quantity of public training data that they provide can limit the performance of their solutions. Public access to the training methodology for these solutions remains absent. This study implements the Type Three (T3) challenge format, which allows for training solutions on private data and guarantees reusable training methodologies. With T3, challenge organizers train a codebase provided by the participants on sequestered training data. T3 was implemented in the STOIC2021 challenge, with the goal of predicting from a computed tomography (CT) scan whether subjects had a severe COVID-19 infection, defined as intubation or death within one month. STOIC2021 consisted of a Qualification phase, where participants developed challenge solutions using 2000 publicly available CT scans, and a Final phase, where participants submitted their training methodologies with which solutions were trained on CT scans of 9724 subjects. The organizers successfully trained six of the eight Final phase submissions. The submitted codebases for training and running inference were released publicly. The winning solution obtained an area under the receiver operating characteristic curve for discerning between severe and non-severe COVID-19 of 0.815. The Final phase solutions of all finalists improved upon their Qualification phase solutions.HSUXJM-TNZF9CHSUXJM-TNZF9C
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- 2023
24. The implementation of EMI-Heart, a family-tailored early motor intervention in infants with complex congenital heart disease, in practice: a feasibility RCT
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Mitteregger, Elena, Dirks, Tineke, Theiler, Manuela, Kretschmar, Oliver, and Latal, Beatrice
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- 2024
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25. Establishment of primary prostate epithelial and tumorigenic cell lines using a non-viral immortalization approach
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Lange, Simon, Kuntze, Anna, Wüstmann, Neele, Reckers, Theresa, Humberg, Verena, Dirks, Wilhelm G., Huss, Sebastian, Vieler, Julia, Schrader, Andres Jan, Bögemann, Martin, Schlack, Katrin, and Bernemann, Christof
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- 2024
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26. Effects of a randomized-controlled and online-supported physical activity intervention on exercise capacity, fatigue and health related quality of life in patients with post-COVID-19 syndrome
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Kerling, Arno, Beyer, Sebastian, Dirks, Meike, Scharbau, Michèle, Hennemann, Ann-Katrin, Dopfer-Jablonka, Alexandra, Lampe, Viktoria, Salzmann, Jakob Heinrich Wolfgang, Tegtbur, Uwe, Drick, Nora, Pink, Isabell, and Haufe, Sven
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- 2024
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27. COVID Future panel survey: A unique public dataset documenting how U.S. residents’ travel-related choices changed during the COVID-19 pandemic
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Chauhan, R. S., Bhagat-Conway, M., Magassy, T. B., Corcoran, N., Rahimi, E., Dirks, A., Pendyala, R. M., Mohammadian, A., Derrible, S., and Salon, D.
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- 2024
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28. Evolutionary trajectories of small cell lung cancer under therapy
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George, Julie, Maas, Lukas, Abedpour, Nima, Cartolano, Maria, Kaiser, Laura, Fischer, Rieke N., Scheel, Andreas H., Weber, Jan-Philipp, Hellmich, Martin, Bosco, Graziella, Volz, Caroline, Mueller, Christian, Dahmen, Ilona, John, Felix, Alves, Cleidson Padua, Werr, Lisa, Panse, Jens Peter, Kirschner, Martin, Engel-Riedel, Walburga, Jürgens, Jessica, Stoelben, Erich, Brockmann, Michael, Grau, Stefan, Sebastian, Martin, Stratmann, Jan A., Kern, Jens, Hummel, Horst-Dieter, Hegedüs, Balazs, Schuler, Martin, Plönes, Till, Aigner, Clemens, Elter, Thomas, Toepelt, Karin, Ko, Yon-Dschun, Kurz, Sylke, Grohé, Christian, Serke, Monika, Höpker, Katja, Hagmeyer, Lars, Doerr, Fabian, Hekmath, Khosro, Strapatsas, Judith, Kambartel, Karl-Otto, Chakupurakal, Geothy, Busch, Annette, Bauernfeind, Franz-Georg, Griesinger, Frank, Luers, Anne, Dirks, Wiebke, Wiewrodt, Rainer, Luecke, Andrea, Rodermann, Ernst, Diel, Andreas, Hagen, Volker, Severin, Kai, Ullrich, Roland T., Reinhardt, Hans Christian, Quaas, Alexander, Bogus, Magdalena, Courts, Cornelius, Nürnberg, Peter, Becker, Kerstin, Achter, Viktor, Büttner, Reinhard, Wolf, Jürgen, Peifer, Martin, and Thomas, Roman K.
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- 2024
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29. A hydrogeological overview of the Upper Mega Aquifer System on the Arabian Platform
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Rausch, Randolf and Dirks, Heiko
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- 2024
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30. Genesis of copper mineralization in the polymetallic tin deposits from the Herberton Mineral Field, Queensland, Australia
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Kumar, Avish, Sanislav, Ioan, Martin, Laure, Aleshin, Matvei, and Dirks, Paul
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- 2024
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31. Verdier specialization and restrictions of Hodge modules
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Chen, Qianyu, Dirks, Bradley, and Saito, Morihiko
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Mathematics - Algebraic Geometry - Abstract
We give an explicit formula to express the cohomological pullback functors of Hodge modules under closed immersions of smooth varieties using Verdier specializations and $V$-filtrations of Kashiwara and Malgrange. This was locally obtained by the first two authors assuming the existence of global defining functions. We also give a quite simplified proof of the theorem reducing to the monodromical case via the Verdier specialization and using induction on codimension.
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- 2023
32. Subclinical infection and potential shedding routes of equine parvovirus‐hepatitis among hospitalized horses in Austria
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Dilara Lale, Esther E. Dirks, Irina Preining, Manolis Lyrakis, Andre Gömer, Eike Steinmann, Jessika‐M. V. Cavalleri, and Anna Sophie Ramsauer
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hepatic viruses ,horizontal transmission ,horse ,hospital hygiene ,prevalence ,Theiler's disease ,Veterinary medicine ,SF600-1100 - Abstract
Abstract Background Equine parvovirus hepatitis (EqPV‐H) can cause Theiler's disease and subclinical hepatitis in horses. Objectives Assess the frequency of subclinical EqPV‐H infection in hospitalized horses and to study viral transmission by investigating potential shedding routes. Animals One hundred sixteen equids, that presented to the University Equine Hospital of the University of Veterinary Medicine Vienna between February 2021 and March 2022, for causes other than hepatopathy. Methods In this cross‐sectional study, samples (serum, feces, nasal, and buccal swabs) of hospitalized horses were collected. Sera were screened for the presence of anti‐EqPV‐H antibodies by a luciferase immunoprecipitation system assay. Quantitative PCR was used for the detection of EqPV‐H DNA in the samples and a nested PCR was used for further validation. Results Seroprevalence was 10.3% (12/116) and viremia occurred in 12.9% (15/116) of the serologically positive horses. The detected viral load in serum varied from non‐quantifiable amount to 1.3 × 106 genome equivalents per milliliter of serum. A low viral load of EqPV‐H DNA was detected in 2 nasal swabs and 1 fecal sample. Conclusion and Clinical Importance EqPV‐H DNA was detected in nasal secretions and feces of viremic horses, which could pose a risk to naive hospitalized horses. It is advisable to screen hospitalized horses that are potential donors of blood or plasma to reduce the risk of iatrogenic EqPV‐H transmission.
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- 2024
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33. Establishment of primary prostate epithelial and tumorigenic cell lines using a non-viral immortalization approach
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Simon Lange, Anna Kuntze, Neele Wüstmann, Theresa Reckers, Verena Humberg, Wilhelm G. Dirks, Sebastian Huss, Julia Vieler, Andres Jan Schrader, Martin Bögemann, Katrin Schlack, and Christof Bernemann
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Prostate cancer ,Primary (cancer) cell lines ,Non-viral immortalization ,Oncogenic transformation ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Research on prostate cancer is mostly performed using cell lines derived from metastatic disease, not reflecting stages of tumor initiation or early progression. Establishment of cancer cell lines derived from the primary tumor site has not been described so far. By definition, cancer cells are able to be cultured indefinitely, whereas normal epithelial cells undergo senescence in vitro. Epithelial cells can be immortalized, accomplished by using viral integration of immortalization factors. Viral approaches, however, might be impaired by regulatory and safety issues as well as random integration into regulatory genetic elements, modifying precise gene expression. We intend to use surgical specimen of prostate cancer patients to (i) prove for establishment of cancer cell lines, and (ii) perform non-viral, Sleeping Beauty (SB) transposase-based immortalization of prostate epithelial cells. Methods Radical prostatectomy samples of prostate cancer patients (n = 4) were dissociated and cultured in vitro. Cells were cultivated either without or after non-viral, Sleeping-Beauty transposase-based stable transfection with immortalization factors SV40LT and hTERT. Established cell lines were analyzed in vitro and in vivo for characteristics of prostate (cancer) cells. Results Initial cell cultures without genetic manipulation underwent senescence within ≤ 15 passages, demonstrating inability to successfully derive primary prostate cancer cell lines. By using SB transposase-based integration of immortalization factors, we were able to establish primary prostate cell lines. Three out of four cell lines displayed epithelial characteristics, however without expression of prostate (cancer) characteristics, e.g., androgen receptor. In vivo, one cell line exhibited tumorigenic potential, yet characteristics of prostate adenocarcinoma were absent. Conclusion Whereas no primary prostate cancer cell line could be established, we provide for the first-time immortalization of primary prostate cells using the SB transposase system, thereby preventing regulatory and molecular issues based on viral immortalization approaches. Although, none of the newly derived cell lines demonstrated prostate cancer characteristics, tumor formation was observed in one cell line. Given the non-prostate adenocarcinoma properties of the tumor, cells have presumably undergone oncogenic transformation rather than prostate cancer differentiation. Still, these cell lines might be used as a tool for research on prostate cancer initiation and early cancer progression.
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- 2024
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34. Correction: Comprehensive Assessment of Risk-Based Quality Management Adoption in Clinical Trials
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Dirks, Abigail, Florez, Maria, Torche, Francois, Young, Steve, Slizgi, Brian, and Getz, Kenneth
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- 2024
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35. The minimal exponent and $k$-rationality for local complete intersections
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Chen, Qianyu, Dirks, Bradley, and Mustaţă, Mircea
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Mathematics - Algebraic Geometry ,14F10, 14B05, 14J17, 32S35 - Abstract
We show that if $Z$ is a local complete intersection subvariety of a smooth complex variety $X$, of pure codimension $r$, then $Z$ has $k$-rational singularities if and only if $\widetilde{\alpha}(Z)>k+r$, where $\widetilde{\alpha}(Z)$ is the minimal exponent of $Z$. We also characterize this condition in terms of the Hodge filtration on the intersection cohomology Hodge module of $Z$. Furthermore, we show that if $Z$ has $k$-rational singularities, then the Hodge filtration on the local cohomology sheaf $\mathcal{H}^r_Z(\mathcal{O}_X)$ is generated at level $\dim(X)-\lceil \widetilde{\alpha}(Z)\rceil-1$ and, assuming that $k\geq 1$ and $Z$ is singular, of dimension $d$, that $\mathcal{H}^k(\underline{\Omega}_Z^{d-k})\neq 0$. All these results have been known for hypersurfaces in smooth varieties., Comment: 21 pages. Comments are welcome!; v2: small changes and some typos are fixed
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- 2022
36. Multi-epoch variability of AT 2000ch (SN 2000ch) in NGC 3432 -- A radio continuum and optical study
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Müller, Ancla, Frohn, Vanessa, Dirks, Lukas, Stein, Michael, Adebahr, Björn, Bomans, Dominik J., Weis, Kerstin, and Dettmar, Ralf-Jürgen
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
AT 2000ch is a highly variable massive star and supernova imposter in NGC 3432 first detected in 2000. It is similar and often compared to SN 2009ip, and it is therefore expected to undergo a core-collapse supernova -- a SN imposter of similar brightness -- in the near future. We characterize the long-term variability of AT 2000ch in the radio and optical regimes with archival data reaching back to the year 1984. We use these newly reduced observations in addition to observations in the literature to restrict the mass-loss rates of AT 2000ch at multiple epochs based on different approaches, and to infer the general properties of its circumstellar nebula with respect to the detected radio brightness. We extend the known optical light curve of AT 2000ch up to the beginning of 2022 by performing point spread function photometry on archival data from the Palomar Transient Factory and the Zwicky Transient Facility. We reduced archival radio continuum observations obtained with the Very Large Array using standard calibration and imaging methods and complemented these with pre-reduced \changes observations as well as observations obtained with the Westerbork Synthesis Radio Telescope and LOw Frequency ARray. For the analysis of AT 2000ch, we consider the optical light curve and color evolution, its radio continuum brightness at different frequencies and times, and the corresponding spectral indices. We estimated mass-loss rates and optical depths based on radio continuum brightnesses and Ha fluxes. We report two newly detected outbursts of AT 2000ch similar to those found in the 2000s and 13 re-brightening events, of which at least four are not conclusively detected because of insufficient sampling of the light curve. The dates of all outbursts and significant, well-sampled re-brightening events are consistent with a period of $\sim 201 \pm 12\,$days over a total time-span of two decades. Such a behavior has never been found for any SN imposter, especially not for candidate SN~2009ip analogs. During 2010 to 2012 and 2014 to 2018, we only have a few detections, which is insufficient to come to any conclusion as to a possible less eruptive phase of the transient. We find steady dimming after the most recent re-brightening events and possible evidence of porosity in the circumstellar envelope, suggesting AT~2000ch may currently be in transition to a state of relative calm. We identified a second, unrelated source at a projected distance of $\sim 23\,$pc ($\sim0.5^{\prime\prime}$) that has contaminated the optical measurements of AT~2000ch at its minimum luminosity over the last two decades probably on a $5\%-10\,\%$ level, but this does not affect our overall findings and is negligible during re-brightening. We are able to restrict the mass-loss rate of AT~2000ch to range between several $10^{-6}\,\textrm{M}_{\odot}/\textrm{yr}$ and several $10^{-5}\,\textrm{M}_{\odot}/\textrm{yr}$. The fresh ejecta appear to be optically thick to radio continuum emission at least within the first $\sim 25\,$days after significant re-brightening., Comment: Accepted for publication on A&A on 23/10/2022
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- 2022
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37. Deletion of arrestin-3 does not reduce drug-seeking behavior in a longitudinal paradigm of oral morphine self-administration
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Sarah Warren Gooding, Lindsey Felth, Randi Foxall, Zachary Rosa, Kyle Ireton, Izabella Sall, Joshua Gipoor, Anirudh Gaur, Madeline King, Noah Dirks, Cheryl Allyne Whistler, and Jennifer Lynne Whistler
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mu opioid receptor ,morphine ,arrestin ,signaling bias ,substance use disorder ,Therapeutics. Pharmacology ,RM1-950 - Abstract
IntroductionOpioid drugs are potent analgesics that mimic the endogenous opioid peptides, endorphins and enkephalins, by activating the µ-opioid receptor. Opioid use is limited by side effects, including significant risk of opioid use disorder. Improvement of the effect/side effect profile of opioid medications is a key pursuit of opioid research, yet there is no consensus on how to achieve this goal. One hypothesis is that the degree of arrestin-3 recruitment to the µ-opioid receptor impacts therapeutic utility. However, it is not clear whether increased or decreased interaction of the µ-opioid receptor with arrestin-3 would reduce compulsive drug-seeking.MethodsWe utilized three genotypes of mice with varying abilities to recruit arrestin-3 to the µ-opioid receptor in response to morphine in a novel longitudinal operant self-administration model. We also created a quantitative method to define compulsivity in drug-seeking based on a multi-variate analysis of several operant response variables.ResultsWe demonstrate that arrestin-3 knockout and wild type mice have highly variable drug-seeking behavior with few genotype differences. In contrast, in mice where the µ-opioid receptor strongly recruits arrestin-3, drug-seeking behavior is much less varied. We found that mice lacking arrestin-3 were more likely to meet the criteria for compulsivity whereas mice with enhanced arrestin-3 recruitment did not develop a compulsive phenotype.ConclusionThese experiments show that a lack of arrestin-3 is not protective against the abuse liability of morphine in an operant self-administration context. Our data also suggest that opioids that engage both G protein and arrestin-3, recapitulating the endogenous signaling pattern, will reduce abuse liability.
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- 2024
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38. Home-based long-term physical endurance and inspiratory muscle training in children and adults with Fontan circulation
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Lena Walzer, Hannes Sallmon, Marcus Kelm, Stefan Dirks, Michael Meyer, Peter Kramer, Bernd Wolfarth, Thomas Thouet, Stanislav Ovroutski, Felix Berger, and Anastasia Schleiger
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home-based training ,physical endurance training ,inspiratory muscle training ,Fontan circulation ,pediatric and adult Fontan patients ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background and study aimRegular physical activity is highly recommended for patients with Fontan hemodynamics. Our aim was to investigate the effects of a long-term individualized home-based endurance training (IHET) on a bicycle ergometer in combination with inspiratory muscle training (IMT) in pediatric and adult patients after Fontan palliation. Additionally, factors influencing the trainability of Fontan palliated patients were analyzed.MethodsFrom 2018 to 2021 a single-center prospective study was performed initially including 25 Fontan palliated patients. During study period nine patients were excluded due to incompliance. A Magbike® bicycle ergometer (DKN Technology, France) was used for IHET and a POWERbreathe® Medic plus device (HaB GmbH, Germany) was utilized for the IMT. Over the study period, bike training was increased from 90 min of basic endurance training per week to additional 25 min of interval training per week. IMT consisted of 30 breaths per day for 6–7 days per week with pressure adaption over time. Patients underwent cardiopulmonary exercise testing (CPET) and body plethysmography including measurement of respiratory muscle strength at baseline and at follow-up examinations at 4, 10 and 22 months.ResultsFollow-up examinations were completed by 18/25 patients (72.0%) at 4 and 10 months and 16/25 patients (64.0%) at 22 months. Median exercise capacity slightly increased by 0.13 W/kg from baseline to last follow-up (p = 0.055, 95%CI: 0.0–0.36). However, a significant increase of oxygen pulse of 0.7 ml/beat (p = 0.006, 95%CI: 0.38–2.22) was detectable. IMT significantly improved respiratory function with an increase of inspiratory vital capacity (VCin/reference) by 4.0% (p = 0.016, 95%CI: 0.8–8). Median maximal inspiratory pressure increased by 1.2 kPa (p = 0.003, 95%CI: 0.64–3.19) and expiratory pressure by 1.5 kPa (p = 0.036, 95%CI: 0.08–2.29). No adverse events or unplanned interventions occurred during the study. Patients' subjective quality of life did not significantly change over the study period.ConclusionIn Fontan palliated patients, IHET in combination with IMT leads to a significant increase in oxygen pulse, inspiratory vital capacity as well as median maximal inspiratory and expiratory pressure but not to significant improvement of quality of life. Fontan patients should be encouraged to perform regular home-based exercise training.
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- 2024
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39. A clinical protocol for a German birth cohort study of the Maturation of Immunity Against respiratory viral Infections (MIAI)
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Carina R. Hartmann, Robin Khan, Jennifer Schöning, Maximilian Richter, Maike Willers, Sabine Pirr, Julia Heckmann, Johannes Dirks, Henner Morbach, Monika Konrad, Elena Fries, Magdalene Winkler, Johanna Büchel, Silvia Seidenspinner, Jonas Fischer, Claudia Vollmuth, Martin Meinhardt, Janina Marissen, Mirco Schmolke, Sibylle Haid, Thomas Pietschmann, Simone Backes, Lars Dölken, Ulrike Löber, Thomas Keil, Peter U. Heuschmann, Achim Wöckel, Sagar, Thomas Ulas, Sofia K. Forslund-Startceva, Christoph Härtel, and Dorothee Viemann
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birth cohort ,respiratory viral infection ,IAV ,RSV ,SARS-CoV-2 ,multi-omics data ,Immunologic diseases. Allergy ,RC581-607 - Abstract
IntroductionRespiratory viral infections (RVIs) are a major global contributor to morbidity and mortality. The susceptibility and outcome of RVIs are strongly age-dependent and show considerable inter-population differences, pointing to genetically and/or environmentally driven developmental variability. The factors determining the age-dependency and shaping the age-related changes of human anti-RVI immunity after birth are still elusive. MethodsWe are conducting a prospective birth cohort study aiming at identifying endogenous and environmental factors associated with the susceptibility to RVIs and their impact on cellular and humoral immune responses against the influenza A virus (IAV), respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The MIAI birth cohort enrolls healthy, full-term neonates born at the University Hospital Würzburg, Germany, with follow-up at four defined time-points during the first year of life. At each study visit, clinical metadata including diet, lifestyle, sociodemographic information, and physical examinations, are collected along with extensive biomaterial sampling. Biomaterials are used to generate comprehensive, integrated multi-omics datasets including transcriptomic, epigenomic, proteomic, metabolomic and microbiomic methods. DiscussionThe results are expected to capture a holistic picture of the variability of immune trajectories with a focus on cellular and humoral key players involved in the defense of RVIs and the impact of host and environmental factors thereon. Thereby, MIAI aims at providing insights that allow unraveling molecular mechanisms that can be targeted to promote the development of competent anti-RVI immunity in early life and prevent severe RVIs.Clinical trial registrationhttps://drks.de/search/de/trial/, identifier DRKS00034278.
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- 2024
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40. Protocol for the derivation of primary cancer stem cell lines from human ependymal tumors
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Cory M. Richman, Peter B. Dirks, Michael D. Taylor, and Kulandaimanuvel Antony Michealraj
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Cell Biology ,Cancer ,Stem Cells ,Cell Differentiation ,Science (General) ,Q1-390 - Abstract
Summary: Cancer stem cells (CSCs) established from surgical biopsies closely mimic the human context and can be used to investigate disease mechanisms, genetic fitness, and therapeutic evaluation. Here, we present a protocol for the derivation of primary patient-derived CSC lines from ependymal tumors. We describe the necessary steps, from surgical intervention and biopsy to the dissociation of ependymomas to derive cultures. We then detail procedures for cell line propagation and define the characteristics of these primary cancer cell lines.For complete details on the use and execution of this protocol, please refer to Michealraj et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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- 2024
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41. The effect of dietary supplementation of a Bacillus-based direct fed-microbial on Pekin duck performance and welfare
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Jessica J. Rocha, Hector Leyva-Jimenez, Yemi Burden, Brian Dirks, and Gregory S. Archer
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direct-fed microbial ,Pekin duck ,stress ,welfare ,performance ,Animal culture ,SF1-1100 ,Food processing and manufacture ,TP368-456 - Abstract
SUMMARY: The objective of this study was to evaluate the effect of a commercially available Bacillus-based direct fed microbial (DFM, Amnil®, United Animal Health, Sheridan, IN) on Pekin duck performance and welfare. The study consisted of 5 dietary treatments, each consisting of 10 replicate pens and 25 straight-run day-of-hatch ducks/pen. The treatments included a commercial-type basal diet (CON), or the basal diet supplemented with 125 ppm (A-125), or 250 ppm (A-250), or 500 ppm (A-500), or 750 ppm (A-750) DFM. On D 14 and 35 performance was evaluated. Gait scores (GS), footpad lesions (FPL), complete cell blood counts, nitrogen digestibility, and total plasma corticosterone levels (CORT) were measured at D 35. The average daily feed intake (ADFI) and feed conversion ratio (FCR) overall were higher in the CON than all other treatments. Body weights did not differ between treatments. The H/L Ratio and total plasma corticosterone levels for CON were higher than all of treatments. Nitrogen digestibility for CON was lower than all other treatments. Gait Scores and Footpad Lesion Scores did not differ between treatments. Utilization of the DFM at any inclusion rate improved feed efficiency, reduced stress susceptibility, and improved nitrogen digestibility. While gait scores, footpad scores, and body weights were not affected by supplementation, feeding this DFM to Pekin ducks can improve their performance and welfare.
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- 2024
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42. Assessing the net financial benefits of employing digital endpoints in clinical trials
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Joseph A. DiMasi, Abigail Dirks, Zachary Smith, Sarah Valentine, Jennifer C. Goldsack, Thomas Metcalfe, Upinder Grewal, Lada Leyens, Ute Conradi, Daniel Karlin, Lesley Maloney, Kenneth A. Getz, and Bert Hartog
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Therapeutics. Pharmacology ,RM1-950 ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract In the last few decades, developers of new drugs, biologics, and devices have increasingly leveraged digital health technologies (DHTs) to assess clinical trial digital endpoints. To our knowledge, a comprehensive assessment of the financial net benefits of digital endpoints in clinical trials has not been conducted. We obtained data from the Digital Medicine Society (DiMe) Library of Digital Endpoints and the US clinical trials registry, ClinicalTrials.gov. The benefit metrics are changes in trial phase duration and enrollment associated with the use of digital endpoints. The cost metric was obtained from an industry survey of the costs of including digital endpoints in clinical trials. We developed an expected net present value (eNPV) model of the cash flows for new drug development and commercialization to assess financial value. The value measure is the increment in eNPV that occurs when digital endpoints are employed. We also calculated a return on investment (ROI) as the ratio of the estimated increment in eNPV to the mean digital endpoint implementation cost. For phase II trials, the increase in eNPV varied from $2.2 million to $3.3 million, with ROIs between 32% and 48% per indication. The net benefits were substantially higher for phase III trials, with the increase in eNPV varying from $27 million to $40 million, with ROIs that were four to six times the investment. The use of digital endpoints in clinical trials can provide substantial extra value to sponsors developing new drugs, with high ROIs.
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- 2024
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43. Auto-Encoder Neural Network Incorporating X-Ray Fluorescence Fundamental Parameters with Machine Learning
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Dirks, Matthew and Poole, David
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Computer Science - Machine Learning - Abstract
We consider energy-dispersive X-ray Fluorescence (EDXRF) applications where the fundamental parameters method is impractical such as when instrument parameters are unavailable. For example, on a mining shovel or conveyor belt, rocks are constantly moving (leading to varying angles of incidence and distances) and there may be other factors not accounted for (like dust). Neural networks do not require instrument and fundamental parameters but training neural networks requires XRF spectra labelled with elemental composition, which is often limited because of its expense. We develop a neural network model that learns from limited labelled data and also benefits from domain knowledge by learning to invert a forward model. The forward model uses transition energies and probabilities of all elements and parameterized distributions to approximate other fundamental and instrument parameters. We evaluate the model and baseline models on a rock dataset from a lithium mineral exploration project. Our model works particularly well for some low-Z elements (Li, Mg, Al, and K) as well as some high-Z elements (Sn and Pb) despite these elements being outside the suitable range for common spectrometers to directly measure, likely owing to the ability of neural networks to learn correlations and non-linear relationships., Comment: X-Ray Spectrometry 2023
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- 2022
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44. Automatic Neural Network Hyperparameter Optimization for Extrapolation: Lessons Learned from Visible and Near-Infrared Spectroscopy of Mango Fruit
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Dirks, Matthew and Poole, David
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Machine Learning - Abstract
Neural networks are configured by choosing an architecture and hyperparameter values; doing so often involves expert intuition and hand-tuning to find a configuration that extrapolates well without overfitting. This paper considers automatic methods for configuring a neural network that extrapolates in time for the domain of visible and near-infrared (VNIR) spectroscopy. In particular, we study the effect of (a) selecting samples for validating configurations and (b) using ensembles. Most of the time, models are built of the past to predict the future. To encourage the neural network model to extrapolate, we consider validating model configurations on samples that are shifted in time similar to the test set. We experiment with three validation set choices: (1) a random sample of 1/3 of non-test data (the technique used in previous work), (2) using the latest 1/3 (sorted by time), and (3) using a semantically meaningful subset of the data. Hyperparameter optimization relies on the validation set to estimate test-set error, but neural network variance obfuscates the true error value. Ensemble averaging - computing the average across many neural networks - can reduce the variance of prediction errors. To test these methods, we do a comprehensive study of a held-out 2018 harvest season of mango fruit given VNIR spectra from 3 prior years. We find that ensembling improves the state-of-the-art model's variance and accuracy. Furthermore, hyperparameter optimization experiments - with and without ensemble averaging and with each validation set choice - show that when ensembling is combined with using the latest 1/3 of samples as the validation set, a neural network configuration is found automatically that is on par with the state-of-the-art.
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- 2022
45. COVID Future Panel Survey: A Unique Public Dataset Documenting How U.S. Residents' Travel Related Choices Changed During the COVID-19 Pandemic
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Chauhan, Rishabh Singh, Bhagat-Conway, Matthew Wigginton, Magassy, Tassio, Corcoran, Nicole, Rahimi, Ehsan, Dirks, Abbie, Pendyala, Ram, Mohammadian, Abolfazl, Derrible, Sybil, and Salon, Deborah
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Computer Science - Computers and Society ,Statistics - Methodology - Abstract
The COVID-19 pandemic is an unprecedented global crisis that has impacted virtually everyone. We conducted a nationwide online longitudinal survey in the United States to collect information about the shifts in travel-related behavior and attitudes before, during, and after the pandemic. The survey asked questions about commuting, long distance travel, working from home, online learning, online shopping, pandemic experiences, attitudes, and demographic information. The survey has been deployed to the same respondents thrice to observe how the responses to the pandemic have evolved over time. The first wave of the survey was conducted from April 2020 to June 2021, the second wave from November 2020 to August 2021, and the third wave from October 2021 to November 2021. In total, 9,265 responses were collected in the first wave; of these, 2,877 respondents returned for the second wave and 2,728 for the third wave. Survey data are publicly available. This unique dataset can aid policy makers in making decisions in areas including transport, workforce development, and more. This article demonstrates the framework for conducting this online longitudinal survey. It details the step-by-step procedure involved in conducting the survey and in curating the data to make it representative of the national trends.
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- 2022
46. V-filtrations and minimal exponents for locally complete intersection singularities
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Chen, Qianyu, Dirks, Bradley, Mustaţă, Mircea, and Olano, Sebastián
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Mathematics - Algebraic Geometry ,14F10, 14B05, 14J17 - Abstract
We define and study a notion of minimal exponent for a locally complete intersection subscheme $Z$ of a smooth complex algebraic variety $X$, extending the invariant defined by Saito in the case of hypersurfaces. Our definition is in terms of the Kashiwara-Malgrange $V$-filtration associated to $Z$. We show that the minimal exponent describes how far the Hodge filtration and order filtration agree on the local cohomology $H^r_Z({\mathcal O}_X)$, where $r$ is the codimension of $Z$ in $X$. We also study its relation to the Bernstein-Sato polynomial of $Z$. Our main result describes the minimal exponent of a higher codimension subscheme in terms of the invariant associated to a suitable hypersurface; this allows proving the main properties of this invariant by reduction to the codimension $1$ case. A key ingredient for our main result is a description of the Kashiwara-Malgrange $V$-filtration associated to any ideal $(f_1,\ldots,f_r)$ in terms of the microlocal $V$-filtration associated to the hypersurface defined by $\sum_{i=1}^rf_iy_i$., Comment: 34 pages; v.2: new, simpler argument for Theorem 1.4. V.3: final version, to appear in Crelle's Journal
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- 2022
47. Pan-cancer ion transport signature reveals functional regulators of glioblastoma aggression
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Bahcheli, Alexander T, Min, Hyun-Kee, Bayati, Masroor, Zhao, Hongyu, Fortuna, Alexander, Dong, Weifan, Dzneladze, Irakli, Chan, Jade, Chen, Xin, Guevara-Hoyer, Kissy, Dirks, Peter B, Huang, Xi, and Reimand, Jüri
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- 2024
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48. Pre-pandemic Executive Function Protects Against Pandemic Anxiety in Children with and Without Autism Spectrum Disorder
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Romero, Celia, Kupis, Lauren, Goodman, Zachary T., Dirks, Bryce, Baez, Adriana, Beaumont, Amy L., Cardona, Sandra M., Parlade, Meaghan V., Alessandri, Michael, Nomi, Jason S., Perry, Lynn K., and Uddin, Lucina Q.
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- 2023
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49. SAGES/AHPBA guidelines for the use of microwave and radiofrequency liver ablation for the surgical treatment of hepatocellular carcinoma or colorectal liver metastases less than 5 cm
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Ceppa, Eugene P., Collings, Amelia T., Abdalla, Moustafa, Onkendi, Edwin, Nelson, Daniel W., Ozair, Ahmad, Miraflor, Emily, Rahman, Faique, Whiteside, Jake, Shah, Mihir M., Ayloo, Subhashini, Dirks, Rebecca, Kumar, Sunjay S., Ansari, Mohammed T., Sucandy, Iswanto, Ali, Kchaou, Douglas, Sam, Polanco, Patricio M., Vreeland, Timothy J., Buell, Joseph, Abou-Setta, Ahmed M., Awad, Ziad, Kwon, Choon Hyuck, Martinie, John B., Sbrana, Fabio, Pryor, Aurora, Slater, Bethany J., Richardson, William, Jeyarajah, Rohan, and Alseidi, Adnan
- Published
- 2023
- Full Text
- View/download PDF
50. Can contralateral lymph-node metastases be ruled out in prostate cancer patients with only unilaterally positive prostate biopsy?
- Author
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Michalik, Bianca, Engels, Svenja, Kampmeier, Leonie, Dirks, Lena, Henke, R.-Peter, Wawroschek, Friedhelm, and Winter, Alexander
- Published
- 2023
- Full Text
- View/download PDF
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