cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Investigation of the potential application of rhenium in medical imaging
Creators: name: De La Vega, José Carlos
Publisher: name: University of British Columbia
Year: 2018

description: Many thermodynamically stable coordination compounds have been synthesized using rhenium, a chemically versatile transition metal. Some of these rhenium complexes have been studied for utilization in nuclear medicine. However, many of their applications in medical imaging remain relatively unexplored and require further investigation. A comprehensive study was conducted in preclinical and clinical X-ray equipment to examine the use of rhenium as a contrast agent for X-ray imaging. Usually, there is a trade-off between image quality and radiation dose. This experimental work, along with theoretical Monte Carlo calculations, showed that it is feasible to preserve image quality and minimize radiation dose simultaneously when a rhenium-based formulation is utilized. This research provided thorough evidence of rhenium’s usefulness in X-ray imaging. Another application of rhenium was evaluated by producing a radiopaque, biodegradable electrospun scaffold containing a rhenium complex. Typically, catheterizations are performed under X-ray imaging guidance, but most catheters are radiolucent. After coating catheters with this scaffold, they became strongly radiopaque. Even a thin rhenium-doped coating has the potential of enhancing the contrast during catheterizations, which might be helpful in placing catheters more rapidly and precisely. Not only large medical devices, but also microsized carriers can be made radiopaque. An issue with embolic microspheres is their lack of contrast. To improve their visibility, potentially toxic contrast agents are co-administered in X-ray imaging-guided embolotherapy. Using a microfluidic technology, radiopaque, biodegradable microspheres made of a custom-synthesized polymer containing a rhenium complex were produced. Upon increasing the polymer’s rhenium concentration, these microspheres could be utilized in embolotherapy. Rhenium’s radioisotope Re¹⁸⁸ is a mixed beta and gamma emitter and can thus be exploited in another imaging modality: single photon emission computed tomography (SPECT). The biodistribution of microspheres labeled with Re¹⁸⁸ was evaluated in a hepatocellular carcinoma-bearing rat model. Although challenging in clinical practice, the radiation doses to the tumor and the healthy liver tissue were calculated. The radiation dose from the beta emissions yields these “imageable” microspheres theranostic, with quantifiable cancer radiotherapeutic potential. This work established the foundations to guide further research on the development of biodegradable devices doped with rhenium for medical imaging.
Kramers' law: Validity, derivations and generalisations
Creators: name: Berglund, Nils
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: Mathematical Physics (math-ph)
subject: History and Overview (math.HO)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 58J65, 60F10 (Primary) 60J45, 34E20 (Secondary)

description: Kramers' law describes the mean transition time of an overdamped Brownian particle between local minima in a potential landscape. We review different approaches that have been followed to obtain a mathematically rigorous proof of this formula. We also discuss some generalisations, and a case in which Kramers' law is not valid. This review is written for both mathematicians and theoretical physicists, and endeavours to link concepts and terminology from both fields.
description: 26 pages, 9 figures
Apparent diffusion coefficient measurements of the pancreas, pancreas carcinoma, and mass-forming focal pancreatitis
Creators: name: Wiggermann, Phillipp
name: Grützmann, Robert
name: Weissenböck, A.
name: Kamusella, P.
name: Dittert, D.-D.
name: Stroszczynski, Christian
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: MRI, diffusion-weighted imaging, apparent diffusion coefficient, abdominal imaging, pancreas
subject: 610 Medizin

description: Background Mass-forming focal pancreatitis (FP) may mimic pancreatic cancer (PC) on magnetic resonance (MR) imaging, and the preoperative differential diagnosis is often difficult. Recently, the usefulness of diffusion-weighted imaging (DWI) in the diagnosis of pancreatic cancer has been reported in several studies. Purpose To investigate if apparent diffusion coefficient (ADC) measurements based on diffusion-weighted echo-planar imaging (DW-EPI) may distinguish between normal pancreas parenchyma, mass-forming focal pancreatitis, and pancreas carcinoma. Material and Methods MRI was performed on 64 patients: 24 with pancreas carcinoma (PC), 20 with mass-forming focal pancreatitis (FP), three patients with other focal pancreatic disease as well as 17 controls without any known pancreatic disease. Diffusion-weighted sequence with ADC maps and T2-weighted sequence for anatomical information was performed. Apparent diffusion coefficient (ADC) maps were automatically created and analyzed using a dedicated user interface. In the group with pancreas disease the abnormal parenchyma was detected by using T1- and T2-weighted images and the region of interest (ROI) was transferred exactly to the ADC map and the coefficients were registered. In the control group the ROI was set to the head of the pancreas followed by a similar registration of the ADCs. Results ADC values for mass-forming FP and PC differed significantly from ADC values for normal pancreas parenchyma (P = 0.001/P = 0.002). Mean ADC values for mass-forming FP were 0.69 ± 0.18 × 10−3 mm2/s. ADC values for PC were 0.78 ± 0.11 × 10−3 mm2/s, compared to ADC values of 0.17 ± 0.06 × 10−3 mm2/s in the control group. However there was no significant difference in ADCs between PC and mass-forming FP (P = 0.15). Conclusion ADC measurements clearly differentiated between normal pancreatic tissue and abnormal pancreas parenchyma (PC and mass-forming FP). However there is an overlap in values of PC and mass-forming FP, with the consequent problem of their correct identification.
Round handles, logarithmic transforms, and smooth 4-manifolds
Creators: name: Baykur, R. Inanc
name: Sunukjian, Nathan
Publisher: name: arXiv
Year: 2010
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics

description: Round handles are affiliated with smooth 4-manifolds in two major ways: 5-dimensional round handles appear extensively as the building blocks in cobordisms between 4-manifolds, whereas 4-dimensional round handles are the building blocks of broken Lefschetz fibrations on them. The purpose of this article is to shed more light on these interactions. We prove that if X and X' are cobordant closed smooth 4-manifolds with the same euler characteristics, and if one of them is simply-connected, then there is a cobordism between them which is composed of round 2-handles only, and therefore one can pass from one to the other via a sequence of generalized logarithmic transforms along tori. As a corollary, we obtain a new proof of a theorem of Iwase's, which is a 4-dimensional analogue of the Lickorish-Wallace theorem for 3-manifolds: Every closed simply-connected 4-manifold can be produced by a surgery along a disjoint union of tori contained in a connected sum of copies of CP^2, -CP^2 and S^1 x S^3. These answer some of the open problems posted by Ron Stern, while suggesting more constraints on the cobordisms in consideration. We also use round handles to show that every infinite family of mutually non-diffeomorphic closed smooth oriented simply-connected 4-manifolds in the same homeomorphism class constructed up to date consists of members that become diffeomorphic after one stabilization with S^2 x S^2 if members are all non-spin, and with S^2 x S^2 # -CP^2 if they are spin. In particular, we show that simple cobordisms exist between knot surgered manifolds. We then show that generalized logarithmic transforms can be seen as standard logarithmic transforms along fiber components of broken Lefschetz fibrations, and show how changing the smooth structures on a fixed homeomorphism class of a closed smooth 4-manifold can be realized as relevant modifications of a broken Lefschetz fibration on it.
description: 17 pages, 1 figure. Submitted version; contains minor revisions and added references
Bedside diagnosis of pleural effusion with a latest generation hand-carried ultrasound device in intensive care patients
Creators: name: Schleder, Stephan
name: Dornia, Christian
name: Poschenrieder, Florian
name: Dendl, Lena Marie
name: Cojocaru, L.
name: Bein, Thomas
name: Schmid, Christof
name: Stroszczynski, Christian
name: Rennert, Janine
name: Jung, Ernst Michael
name: Heiss, P.
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: Ultrasound, pleura, conventional radiography, thorax
subject: 610 Medizin

description: Background: Further development established hand-carried ultrasound (HCU) imagers in daily clinical workflow providing several advantages such as fast bedside availability and prompt diagnosis. Purpose: To evaluate the diagnostic yield of a latest generation HCU imager compared to chest radiography (CR) for the detection of pleural effusion (PE) in intensive care patients. Material and Methods: Forty-eight hemithoraces of 24 patients on surgical intensive care units were enrolled in this study. All hemithoraces were evaluated using both HCU and CR. Definite diagnosis of PE was achieved using a high-end ultrasound system as standard of reference. Statistical analysis was performed using 2 × 2 tables and a McNemar test. A P value of <0.05 was considered statistically significant. Results: PE was present in 35 of 48 hemithoraces (73%). The HCU examination was carried out technically successfully in all hemithoraces. Sensitivity and specificity of HCU for the diagnosis of PE was 91% and 100%, respectively, whereas sensitivity and specificity of CR was 74% and 31%, respectively. The difference between HCU and CR was statistically significant with respect to specificity but not sensitivity (P = 0.008 and P = 0.11, respectively). Conclusion: Due to its ease of use and its high diagnostic yield HCU systems of the latest generation constitute a helpful technique for the primary assessment of PE.
The big de Rham-Witt complex
Creators: name: Hesselholt, Lars
Publisher: name: arXiv
Year: 2010
Subjects: subject: Number Theory (math.NT)
subject: Algebraic Geometry (math.AG)
subject: K-Theory and Homology (math.KT)
subject: FOS: Mathematics
subject: 19D35, 14F20, 19D55

description: This paper gives a new and direct construction of the multi-prime big de Rham-Witt complex which is defined for every commutative and unital ring; the original construction by the author and Madsen relied on the adjoint functor theorem and accordingly was very indirect. (The construction given here also corrects the 2-torsion which was not quite correct in the original version.) The new construction is based on the theory of modules and derivations over a lambda-ring which is developed first. The main result in this first part of the paper is that the universal derivation of a lambda-ring is given by the universal derivation of the underlying ring together with an additional structure depending on the lambda-ring structure in question. In the case of the ring of big Witt vectors, this additional structure gives rise to divided Frobenius operators on the module of Kähler differentials. It is the existence of these divided Frobenius operators that makes the new construction of the big de Rham-Witt complex possible. It is further shown that the big de Rham-Witt complex behaves well with respect to étale maps, and finally, the big de Rham-Witt complex of the ring of integers is explicitly evaluated. The latter complex may be interpreted as the complex of differentials along the leaves of a foliation of Spec Z.
description: 63 pages
Cerebrovascular and ventilatory responses to acute normobaric hypoxia in girls and women
Creators: name: Morris, Laura
Publisher: name: University of British Columbia
Year: 2017

description: Physiological responses to hypoxia in children are incompletely understood. We aimed to characterize cerebrovascular and ventilatory responses to normobaric hypoxia in girls and women. Methods: Ten healthy girls (9.9 +/- 1.7y; mean +/- SD; Tanner stage 1 and 2) and their mothers (43.9 +/- 3.5y) participated. Internal carotid (ICA) and vertebral artery (VA) velocity, diameter and flow (Duplex ultrasound) was recorded pre- and post-1h of hypoxic exposure (FIO₂=0.126;~4000m) in a normobaric chamber. Ventilation (VE) and respiratory drive (VT/TI) expressed as delta change from baseline (∆%), and end-tidal carbon-dioxide (PETCO₂) were collected at baseline (BL) and 5, 30 and 60 minutes of hypoxia (5/30/60 HYP). Heart rate (HR) and oxygen saturation (SpO₂) were also collected at these time-points. Results: SpO₂ declined similarly in girls (BL-97%; 60HYP-80%, P<0.05) and women (BL-97%; 60HYP-83%, P<0.05). Global cerebral blood flow (gCBF) increased in both girls (BL-687; 60HYP-912 ml.min-¹, P<0.05) and women (BL-472; 60HYP-651 ml.min-¹, P<0.01), though the ratio of ICA:VA (%) contribution to gCBF differed significantly (girls, 75:25%; women, 61:39%). The relative increase in VE peaked at 30HYP in both girls (27%, P<0.05) and women (19%, P<0.05), as did ∆%VT/TI (girls, 41%; women, 27%, P’s<0.05). Tidal volume (VT) increased in both girls and women at 5HYP, remaining elevated above baseline in girls at 30 and 60HYP, but declined back toward baseline in women. Conclusion: Girls elicit similar increases in gCBF and ventilatory parameters in response to acute hypoxia as women, though the pattern of these responses appear developmentally divergent.
The Challenge for Innovation in Direct Restorative Materials
Creators: name: Bayne, S.
name: Petersen, P. E.
name: Schmalz, Gottfried
name: Meyer, D.
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: dental caries, prevention, alternative restorative material, WHO, risk assessment, recycling, dental amalgam
subject: 610 Medizin

description: During the past 50 years, a series of key UN conferences have established a framework to minimize human health risks from environmental exposures to key chemicals. In January 2013, more than 140 countries agreed to the text of new treaty to minimize Hg effects on the environment (the Minamata Convention). Dental caries is omnipresent around the globe, affecting 60% to 90% of school children and most adults, and producing discomfort that affects quality of life. Dental amalgam is frequently used to treat carious lesions and its use releases mercury into the environment. The best way to avoid the use of dental amalgam is to emphasize caries prevention. Alternatives to amalgam are suitable in some applications, but no replacement for amalgam has been found for large posterior restorations. For any restorative material, safety and environmental impacts are part of clinical risk assessment. Safety is freedom from unacceptable risks. Risk is a combination of probability of exposure and severity of harm. Best management practices are crucial to manage dental amalgam, but these impose additional that are disproportionately more for developing countries. The Minamata Convention seeks a phase-out of all mercury-based products except dental amalgam, where a phase-down is the present goal. For dentistry, the most important focus is the promotion of caries prevention and research on new materials.
Un-reduction
Creators: name: Bruveris, Martins
name: Ellis, David C. P.
name: Gay-Balmaz, Francois
name: Holm, Darryl D.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 37K05, 37K65

description: This paper provides a full geometric development of a new technique called un-reduction, for dealing with dynamics and optimal control problems posed on spaces that are unwieldy for numerical implementation. The technique, which was originally concieved for an application to image dynamics, uses Lagrangian reduction by symmetry in reverse. A deeper understanding of un-reduction leads to new developments in image matching which serve to illustrate the mathematical power of the technique.
description: 25 pages, revised version
Six operations and Lefschetz-Verdier formula for Deligne-Mumford stacks
Creators: name: Zheng, Weizhe
Publisher: name: arXiv
Year: 2010
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14F20 (Primary) 14A20, 18D05 (Secondary)

description: Laszlo and Olsson constructed Grothendieck's six operations for constructible complexes on Artin stacks in étale cohomology under an assumption of finite cohomological dimension, with base change established on the level of sheaves. In this article we give a more direct construction of the six operations for complexes on Deligne-Mumford stacks without the finiteness assumption and establish base change theorems in derived categories. One key tool in our construction is the theory of gluing finitely many pseudofunctors developed in arXiv:1211.1877. As an application, we prove a Lefschetz-Verdier formula for Deligne-Mumford stacks. We include both torsion and $\ell$-adic coefficients.
description: 62 pages. v5, v4: minor improvements; v3: added a Lefschetz-Verdier formula; v2: moved the appendix in v1 to arXiv:1211.1877
Safety and efficacy of defibrotide for the treatment of severe hepatic veno-occlusive disease
Creators: name: Richardson, Paul M.
name: Ho, Vincent T.
name: Giralt, Sergio
name: Arai, Sally
name: Mineishi, Shin
name: Cutler, C.
name: Antin, Joseph H.
name: Stavitzski, N.
name: Niederwieser, N.
name: Holler, Ernst
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: defibrotide, sinusoidal obstruction syndrome, veno-occlusive disease
subject: 610 Medizin

description: Hepatic veno-occlusive disease (VOD), also known as sinusoidal obstruction syndrome, is a potentially life-threatening complication of chemotherapeutic conditioning used in preparation for hematopoietic stem-cell transplantation (SCT). VOD may occur in up to 62% of patients undergoing SCT, with onset generally within the first month after SCT. In severe cases, 100-day mortality is in excess of 80%. Current management consists of best supportive care, with no agents to date approved for treatment in the USA or the EU. Defibrotide, a polydisperse oligonucleotide, has been shown in phase II and III trials to improve complete response and survival in patients undergoing SCT with severe VOD. This article reviews our current understanding of VOD, and examines recent clinical findings on defibrotide for the treatment and prophylaxis of VOD.
Optimal scaling and diffusion limits for the Langevin algorithm in high dimensions
Creators: name: Pillai, Natesh S.
name: Stuart, Andrew M.
name: Thiéry, Alexandre H.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: Statistics Theory (math.ST)
subject: Computation (stat.CO)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: The Metropolis-adjusted Langevin (MALA) algorithm is a sampling algorithm which makes local moves by incorporating information about the gradient of the logarithm of the target density. In this paper we study the efficiency of MALA on a natural class of target measures supported on an infinite dimensional Hilbert space. These natural measures have density with respect to a Gaussian random field measure and arise in many applications such as Bayesian nonparametric statistics and the theory of conditioned diffusions. We prove that, started in stationarity, a suitably interpolated and scaled version of the Markov chain corresponding to MALA converges to an infinite dimensional diffusion process. Our results imply that, in stationarity, the MALA algorithm applied to an N-dimensional approximation of the target will take $\mathcal{O}(N^{1/3})$ steps to explore the invariant measure, comparing favorably with the Random Walk Metropolis which was recently shown to require $\mathcal{O}(N)$ steps when applied to the same class of problems.
description: Published in at http://dx.doi.org/10.1214/11-AAP828 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Arakelov motivic cohomology I
Creators: name: Holmstrom, Andreas
name: Scholbach, Jakob
Publisher: name: arXiv
Year: 2010
Subjects: subject: Number Theory (math.NT)
subject: Algebraic Geometry (math.AG)
subject: K-Theory and Homology (math.KT)
subject: FOS: Mathematics
subject: 14G40, 14F42, 19F99

description: This paper introduces a new cohomology theory for schemes of finite type over an arithmetic ring. The main motivation for this Arakelov-theoretic version of motivic cohomology is the conjecture on special values of $L$-functions and zeta functions formulated by the second author. Taking advantage of the six functors formalism in motivic stable homotopy theory, we establish a number of formal properties, including pullbacks for arbitrary morphisms, pushforwards for projective morphisms between regular schemes, localization sequences, $h$-descent. We round off the picture with a purity result and a higher arithmetic Riemann-Roch theorem.
description: final version, to appear in Journal of Algebraic Geometry
Paramedics experiences and expectations concerning advance directives: A prospective, questionnaire-based, bi-centre study
Creators: name: Taghavi, Mahmoud
name: Simon, A.
name: Kappus, Stefan
name: Meyer, Nicole
name: Lassen, Christoph L.
name: Klier, Tobias
name: Ruppert, David
name: Graf, Bernhard
name: Hanekop, Gerd G.
name: Wiese, Christoph H.
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: Advance directives, palliative care, paramedics, prehospital emergency care
subject: 610 Medizin

description: Background: Advance directives and palliative crisis cards are means by which palliative care patients can exert their autonomy in end-of-life decisions. Aim: To examine paramedics’ attitudes towards advance directives and end-of-life care. Design: Questionnaire-based investigation using a self-administered survey instrument. Setting/participants: Paramedics of two cities (Hamburg and Goettingen, Germany) were included. Participants were questioned as to (1) their attitudes about advance directives, (2) their clinical experiences in connection with end-of-life situations (e.g. resuscitation), (3) their suggestions in regard to advance directives, ‘Do not attempt resuscitation’ orders and palliative crisis cards. Results: Questionnaires were returned by 728 paramedics (response rate: 81%). The majority of paramedics (71%) had dealt with advance directives and end-of-life decisions in emergency situations. Most participants (84%) found that cardiopulmonary resuscitation in end-of-life patients is not useful and 75% stated that they would withhold cardiopulmonary resuscitation in the case of legal possibility. Participants also mentioned that more extensive discussion of legal aspects concerning advance directives should be included in paramedic training curricula. They suggested that palliative crisis cards should be integrated into end-of-life care. Conclusions: Decision making in prehospital end-of-life care is a challenge for all paramedics. The present investigation demonstrates that a dialogue bridging emergency medical and palliative care issues is necessary. The paramedics indicated that improved guidelines on end-of-life decisions and the termination of cardiopulmonary resuscitation in palliative care patients may be essential. Participants do not feel adequately trained in end-of-life care and the content of advance directives. Other recent studies have also demonstrated that there is a need for training curricula in end-of-life care for paramedics.
Random walks in random environments without ellipticity
Creators: name: Lenci, Marco
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 60G50, 60K37, 37A50, 37A20, 60G42, 60F17

description: We consider random walks in random environments on Z^d. Under a transitivity hypothesis that is much weaker than the customary ellipticity condition, and assuming an absolutely continuous invariant measure on the space of the environments, we prove the ergodicity of the annealed process w.r.t. the dynamics "from the point of view of the particle". This implies in particular that the environment viewed from the particle is ergodic. As an example of application of this result, we give a general form of the quenched Invariance Principle for walks in doubly stochastic environments with zero local drift (martingale condition).
description: Final version for Stochastic Process. Appl., 18 pages, 1 figure
Clinical outcomes and safety of rituximab treatment for patients with systemic lupus erythematosus (SLE) - results from a nationwide cohort in Germany (GRAID)
Creators: name: Witt, M.
name: Grunke, M.
name: Proft, F.
name: Bäuerle, M.
name: Aringer, M.
name: Burmester, G.
name: Chehab, B.
name: Fiehn, C.
name: Fischer-Betz, R.
name: Fleck, Martin
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: Systemic lupus erythematosus; rituximab; efficacy; safety;Blymphocytes; cohort studies
subject: 610 Medizin

description: Objective The objective of this article is to evaluate the safety and clinical outcome of rituximab treatment in systemic lupus erythematosus (SLE) patients refractory to standard of care therapy in a real-life setting in Germany. Methods The GRAID registry included patients with different autoimmune diseases who were given off-label treatment with rituximab. Data on safety and clinical response were collected retrospectively. In SLE patients, clinical parameters included tender and swollen joint counts, fatigue, myalgia, general wellbeing, Raynaud’s and the SLEDAI index. Laboratory tests included dsDNA antibody titres, complement factors, hematologic parameters and proteinuria. Finally, the investigators rated their patients as non-, partial or complete responders based on clinical grounds. Results Data from 85 SLE patients were collected, 69 female and 16 male, with a mean disease duration of 9.8 years. The mean follow-up period was 9.6 ± 7.4 months, resulting in 66.8 patient years of observation. A complete response was reported in 37 patients (46.8%), partial response in 27 (34.2%), no response in 15 (19.0%). On average, major clinical as well as laboratory efficacy parameters improved substantially, with the SLEDAI decreasing significantly from 12.2 to 3.3 points. Concerning safety, one infusion reaction leading to discontinuation of treatment occurred. Infections were reported with a rate of 19.5 (including six severe infections) per 100 patient years. Conclusion With the restrictions of a retrospective data collection, the results of this study confirm data of other registries, which suggest a favourable benefit-risk ratio of rituximab in patients with treatment-refractory SLE.
Selecting normalization genes for small diagnostic microarrays
Creators: name: Jaeger, J.
name: Spang, Rainer
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: 610 Medizin

description: Background Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normalization strategies to diagnostic microarrays causes new normalization problems. Results In this paper we point out the differences of normalizing large microarrays and small diagnostic microarrays. We suggest to include additional normalization genes on the small diagnostic microarrays and propose two strategies for selecting them from genomewide microarray studies. The first is a data driven univariate selection of normalization genes. The second is multivariate and based on finding a balanced diagnostic signature. Finally, we compare both methods to standard normalization protocols known from large microarrays. Conclusion Not including additional genes for normalization on small microarrays leads to a loss of diagnostic information. Using house keeping genes from the literature for normalization fails to work for certain datasets. While a data driven selection of additional normalization genes works well, the best results were obtained using a balanced signature.
High-Velocity Estimates and Inverse Scattering for Quantum N-Body Systems with Stark Effect
Creators: name: Valencia, Gerardo Daniel
name: Weder, Ricardo
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 81U40, 35P25, 35Q40, 35R30

description: In an N-body quantum system with a constant electric field, by inverse scattering, we uniquely reconstruct pair potentials, belonging to the optimal class of short-range potentials and long-range potentials, from the high-velocity limit of the Dollard scattering operator. We give a reconstruction formula with an error term.
description: In this published version we have added remarks and we have edited the paper
Selecting quality indicators for pulmonary rehabilitation programs in Canada : a modified RAND Appropriateness Method study
Creators: name: Cheung, Walden A.
Publisher: name: University of British Columbia
Year: 2017

description: Pulmonary rehabilitation (PR) is a comprehensive intervention of self-management education and exercise training that improves quality of life, exercise tolerance, symptoms of dyspnea, and reduces the risk of hospitalization in patients living with chronic respiratory diseases such as chronic obstructive pulmonary disease, asthma, lung cancer, and interstitial lung disease. Despite the proven benefit of pulmonary rehabilitation, recent studies have found notable inconsistencies in its organization and delivery. Inconsistencies within clinical practice are likely to affect the quality in the delivery of pulmonary rehabilitation. Quality indicators (QIs) are tools similar to a checklist that can potentially remediate these concerns. While other jurisdictions have created quality indicators for pulmonary rehabilitation programs, their methodological approach to developing these quality indicators is questionable. This study developed 56 quality indicators with a rigorous approach using a modified RAND Appropriateness Method. A panel comprising twelve PR healthcare professionals and stakeholders was created to create a list of QIs. The panel rated each indicator based on four criteria (importance, scientific soundness, reliability, and feasibility) and listed which indicator they believed could determine a quality pulmonary rehabilitation program. This study recommends that the 56 QIs, based upon consensus, be used for operationalizing the evaluation and auditing of PR programs as well as for establishing clinical benchmarks.
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures
Creators: name: Kostka, Dennis
name: Spang, Rainer
Publisher: name: Universität Regensburg
Year: 2008
Subjects: subject: 610 Medizin

description: Microarray gene expression signatures hold great promise to improve diagnosis and prognosis of disease. However, current documentation standards of such signatures do not allow for an unambiguous application to study-external patients. This hinders independent evaluation, effectively delaying the use of signatures in clinical practice. Data from eight publicly available clinical microarray studies were analyzed and the consistency of study-internal with study-external diagnoses was evaluated. Study-external classifications were based on documented information only. Documenting a signature is conceptually different from reporting a list of genes. We show that even the exact quantitative specification of a classification rule alone does not define a signature unambiguously. We found that discrepancy between study-internal and study-external diagnoses can be as frequent as 30% (worst case) and 18% (median). By using the proposed documentation by value strategy, which documents quantitative preprocessing information, the median discrepancy was reduced to 1%. The process of evaluating microarray gene expression diagnostic signatures and bringing them to clinical practice can be substantially improved and made more reliable by better documentation of the signatures.
Implementation of ICON 10km global coupled demonstrator and performance analysis (D2.12)
Creators: name: Neumann, Philipp
name: Serradell, Kim
Publisher: name: Zenodo
Year: 2019

description: We have evaluated and improved the performance of a 5km-5km coupled ocean-atmosphere ICON set up. The set up makes use of ECHAM physics for the atmosphere component, but abstains from parameterisations for convection and gravity waves.

The work was accomplished to enable simulations on bigger node counts, and column-blocking parameter tuning was carried out. Throughput on O(500) nodes suggests a performance of ca. 20 simulated days per day.

Although the provided investigations are rather preliminary results than the end of the story on performance investigation for coupled high-resolution ICON simulations, the measured throughput rate is expected to already enable the investigation of selected science cases in the near future. Besides, the technical and modelling achievement lies in the fact that a 5km-5km coupled simulation could successfully be established.

Yet, more work is required to enable simulations on even bigger node counts, that is beyond 550 nodes on the supercomputer Mistral
description: ESiWACE has received funding from the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No 675191
Modeling and analyzing software ecosystems
Creators: name: Schwichtenberg, Bahar
Publisher: name: Universität Paderborn
Year: 2021

description: Heutzutage erreichen erfolgreiche Softwareunternehmen ihre Geschäftsziele, indem sie Software-Ökosysteme schaffen, wo die Software-Plattformen für Tausende von Drittanbietern geöffnet geworden sind. Bei der Erstellung von Software-Ökosystemen müssen viele architektonische Designentscheidungen getroffen werden. Die Menge an Entscheidungen führt zu einem überwältigenden Gestaltungsraum architektonischer Variabilitäten. Bisher gibt es keine Architekturrichtlinien und -werkzeuge, die das Design der Ökosystemarchitektur explizit erfassen. Dadurch fehlt systematisches Wissen; Plattformanbieter müssen auf ad-hoc Entscheidungen zurückgreifen; dies hat Folgen wie ungesunde Ökosysteme mit Ausfallrisiken und Mehrkosten. Der Mangel an Architekturwissen manifestiert sich konkret in zwei großen Gruppen von Herausforderungen: Herausforderungen im Zusammenhang mit fehlender Architekturwissens- basis und Herausforderungen im Zusammenhang mit fehlendem Methodenwissen. Eine Architekturwissensbasis würde Orientierungshilfen zu den Bestandteilen von Software- Ökosystemen und deren Abhängigkeiten geben, während methodisches Wissen die Erstellung dieser Systeme erleichtern würde.
description: Nowadays, successful software companies attain enhanced business objectives by creating software ecosystems by opening their platforms to thousands of third-party providers. When creating software ecosystems, many architectural design decisions have to be made. The set of decisions results in an overwhelming design space of architectural variabilities. Until now, there are no architectural guidelines and tools that explicitly capture the design of ecosystem architecture. As a result, systematic knowledge is missing; platform providers have to fall back to ad-hoc decision-making; this bears consequences such as unhealthy ecosystems with risks of failure and extra costs. The lack of architectural knowledge is specifically manifested in two major groups of challenges: challenges related to a lack of an architectural knowledge base and challenges related to a lack of methodical knowledge. An architectural knowledge base would provide guidance on constituents of software ecosystems and their interdependencies while methodical knowledge would facilitate the creation of these systems.
Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring
Creators: name: Toedling, J.
name: Rhein, P.
name: Ratei, R.
name: Karawajew, L.
name: Spang, Rainer
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: 610 Medizin

description: BACKGROUND: Identification of minor cell populations, e.g. leukemic blasts within blood samples, has become increasingly important in therapeutic disease monitoring. Modern flow cytometers enable researchers to reliably measure six and more variables, describing cellular size, granularity and expression of cell-surface and intracellular proteins, for thousands of cells per second. Currently, analysis of cytometry readouts relies on visual inspection and manual gating of one- or two-dimensional projections of the data. This procedure, however, is labor-intensive and misses potential characteristic patterns in higher dimensions. RESULTS: Leukemic samples from patients with acute lymphoblastic leukemia at initial diagnosis and during induction therapy have been investigated by 4-color flow cytometry. We have utilized multivariate classification techniques, Support Vector Machines (SVM), to automate leukemic cell detection in cytometry. Classifiers were built on conventionally diagnosed training data. We assessed the detection accuracy on independent test data and analyzed marker expression of incongruently classified cells. SVM classification can recover manually gated leukemic cells with 99.78% sensitivity and 98.87% specificity. CONCLUSION: Multivariate classification techniques allow for automating cell population detection in cytometry readouts for diagnostic purposes. They potentially reduce time, costs and arbitrariness associated with these procedures. Due to their multivariate classification rules, they also allow for the reliable detection of small cell populations.
Implementation of NEMO global 1km ocean-only demonstrator and performance analysis (D2.10)
Creators: name: Maisonnave, Eric
name: Levy, Claire
name: Masson, Sebastien
Publisher: name: Zenodo
Year: 2019

description: Popularity of one kilometre scale global geophysical models is continuously growing in Europe. In this study, we increase the resolution of the NEMO ocean model, to better identify technical limitations of the present implementation and deduce, from the performance measured on one of our top supercomputers, the hardware characteristics needed to routinely use a global ocean one kilometre configuration. 24,000 Intel Broadwell cores of the Météo-France supercomputer are required to measure the performance of a simplified version of NEMO global kilometre scale. From them, assuming a perfect scaling up to 9,000,000 (nine million) computing cores, we infer that we could target a maximum speed of approximately 2 SYPD with the ORCA-Km global model.
description: ESiWACE has received funding from the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No 675191
A relation between Dieudonne displays and crystalline Dieudonne theory
Creators: name: Lau, Eike
Publisher: name: arXiv
Year: 2010
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 14L05, 14F30

description: We discuss the relation between crystalline Dieudonne theory and Dieudonne displays, with special emphasis on the case p=2. The theory of Dieudonne displays is extended to this case without restriction, which implies that the classification of finite flat group schemes by Breuil-Kisin modules holds for p=2 as well.
description: 47 pages, final version
The role of inflammatory mediators in the synergistic toxicity of ozone and 1-nitronaphthalene in rat airways
Creators: name: Schmelzer, K. R.
name: Wheelock, A. M.
name: Dettmer, Katja
name: Morin, D.
name: Hammock, B. D.
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: 1-nitronaphthalene, arachidonic acid, cyclooxygenase, inflammatory mediators, linoleic acid, lipoxygenase, ozone
subject: 610 Medizin

description: Ambient air is polluted with a mixture of pulmonary toxicants. Previous studies indicate that prior exposure to atmospheric oxidant pollutants such as ozone may significantly alter the response to other pollutants, such as 1-nitronaphthalene (1-NN). 1-NN, a component of the particulate exhaust from diesel engines, has been found at low concentrations in ambient air. Using a metabolomic approach, we investigated inflammatory responses in arachidonic and linoleic acid biochemical cascades (35 metabolites) and the expression of 19 cytokines/chemokines at three time points (2, 6, and 24 hr) following exposure to 1-NN with and without prior long-term O3 exposure. Long-term O3 exposure is associated with biochemical changes that have been shown to render the lung resistant to further O3 exposure. This study indicates that airways of O3-tolerant rats exhibited a low level of chronic inflammation, rendering the lungs more susceptible to other environmental pollutants such as 1-NN. Specifically, a 12.5-mg/kg dose of 1-NN to O3-tolerant rats produced significantly higher levels of cysteinyl-leukotrienes in bronchiolar lavage fluid even when compared to a 50-mg/kg dose of 1-NN in rats exposed to filtered air. Collectively, these results indicate that the combination of exposures as encountered in polluted ambient air are considerably more injurious to the lung than would be anticipated from previous studies employing single exposures. The observed synergism between O3 and 1-NN may be causally related to a shift in a T-helper 1 to T-helper 2 immune response in the airways.
Packing triangles in weighted graphs
Creators: name: Chapuy, Guillaume
name: DeVos, Matt
name: McDonald, Jessica
name: Mohar, Bojan
name: Scheide, Diego
Publisher: name: arXiv
Year: 2010
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: Tuza conjectured that for every graph $G$, the maximum size $ν$ of a set of edge-disjoint triangles and minimum size $τ$ of a set of edges meeting all triangles satisfy $τ\leq 2ν$. We consider an edge-weighted version of this conjecture, which amounts to packing and covering triangles in multigraphs. Several known results about the original problem are shown to be true in this context, and some are improved. In particular, we answer a question of Krivelevich who proved that $τ\leq 2ν^*$ (where $ν^*$ is the fractional version of $ν$), and asked if this is tight. We prove that $τ\leq 2ν^*-\frac{1}{\sqrt{6}}\sqrt{ν^*}$ and show that this bound is essentially best possible.
description: v2: 20 pages, corrected version (from 2013) following referee reports
Enhancing geodatabases operability: advanced human-computer interaction through rag and multi-agent systems
Creators: name: Peng, Ziming
name: Kuai, Xi
name: Ke, Shuisong
name: Dong, Xuehui
name: Guo, Renzhong
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: The increasing demand for efficient geographic data querying has underscored the need to improve both the speed and accuracy of such operations. This study presents a novel approach that combines Retrieval-Augmented Generation (RAG) with a Large Language Model (LLM)-based Multi-Agent System (MAS) to address this challenge. By leveraging Geographic Information System (GIS) metadata, the method transforms natural language queries into precise SQL queries, enhancing the functionality of LLMs in geospatial database management. RAG enriches the model’s responses with relevant external knowledge, while the MAS framework decomposes complex queries into manageable subtasks, each handled by a dedicated agent. This ensures the generation of syntactically accurate and contextually relevant SQL queries, improving query precision. Rigorous experimentation shows that the approach achieves over 80% SQL generation accuracy, surpassing traditional LLM-based techniques, even with large-scale geospatial datasets and complex queries. Additionally, the average query execution time is only 11.74 seconds, demonstrating the method’s efficiency. The practical applicability of our method has been validated through its implementation and user testing in an urban planning platform. This has made geospatial database access more accessible and user-friendly, regardless of the user’s expertise in database management or SQL, thus facilitating more efficient geospatial data interaction.
Gain of chromosome region 18q21 including the MALT1 gene is associated with the activated B-cell-like gene expression subtype and increased BCL2 gene dosage and protein expression in diffuse large B-cell lymphoma
Creators: name: Dierlamm, J.
name: Murga Penas, E. M.
name: Bentink, Stefan
name: Wessendorf, S.
name: Berger, H.
name: Hummel, M.
name: Klapper, W.
name: Lenze, D.
name: Rosenwald, A.
name: Haralambieva, E.
name: Ott, G.
name: Cogliatti, S. B.
name: Möller, Peter
name: Schwaenen, C.
name: Stein, H.
name: Löffler, M.
name: Spang, Rainer
name: Trumper, L.
name: Siebert, Reiner
Publisher: name: Universität Regensburg
Year: 2008
Subjects: subject: 610 Medizin

description: BACKGROUND: The aim of this study was to determine the impact of a gain of the MALT1 gene on gene expression and clinical parameters in diffuse large B-cell lymphoma. DESIGN AND METHODS: We analyzed 116 cases of diffuse large B-cell lymphoma by fluorescence in situ hybridization, array-based comparative genomic hybridization, and transcriptional profiling. RESULTS: A gain of 18q21 including MALT1 was detected in 44 cases (38%) and was accompanied by a gain of BCL2 in 43 cases. All cases with a 18q21/MALT1 gain showed BCL2 protein whereas 79% in the group without a 18q21/MALT1 gain did so (p<0.001). Cases with 18q21/MALT1 gain more frequently showed an activated B-cell-like (ABC) gene expression signature (65%) than a germinal center B-cell-like (GCB) one (23%) (p<0.001). Ninety-eight genes including MALT1, BCL2, and some selected nuclear factor-kappaB target genes were differentially expressed between the two genetic groups of diffuse large B-cell lymphoma. By global testing of each chromosome, we identified 33 genes, all located on chromosome 18q, which were differentially expressed between the two genetic groups independently of the ABC/GCB status. In multivariate analysis, the 18q21/MALT1 status represented an independent negative prognostic factor for overall survival (p=0.03). CONCLUSIONS: In diffuse large B-cell lymphoma, gain of 18q21 including MALT1 is significantly associated with differential expression of genes located on 18q, the ABC gene expression subtype, increased BCL2 gene and protein expression and might indicate an unfavorable prognosis.