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Use of diagnostic likelihood ratio of outcome to evaluate misclassification bias in the planning of database studies

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BMC MEdICAL INFOrMATICS ANd dECISION MAKING 2022年第1期22卷 19-19页

作者： Ii, Yoichi Hiro, Shintaro Nakazuru, Yoshiomi Pfizer R&D Biometr & Data Management Dev Japan Shibuya Ku 3-22-7 Yoyogi Tokyo 1518589 Japan

Background The diagnostic likelihood ratio (dLr) and its utility are well-known in the field of medical diagnostic testing. However, its use has been limited in the context of an outcome validation study. We considered that wider recognition of the utility of dLr would enhance the practices surrounding database studies. This is particularly timely and important since the use of healthcare-related databases for pharmacoepidemiology research has greatly expanded in recent years. In this paper, we aimed to advance the use of dLr, focusing on the planning of a new database study. Methods Theoretical frameworks were developed for an outcome validation study and a comparative cohort database study;these two were combined to form the overall relationship. Graphical presentations based on these relationships were used to examine the implications of validation study results on the planning of a database study. Additionally, novel uses of graphical presentations were explored using some examples. results Positive dLr was identified as a pivotal parameter that connects the expected positive-predictive value (PPV) with the disease prevalence in the planned database study, where the positive dLr is equal to sensitivity/(1-specificity). Moreover, positive dLr emerged as a pivotal parameter that links the expected risk ratio with the disease risk of the control group in the planned database study. In one example, graphical presentations based on these relationships provided a transparent and informative summary of multiple validation study results. In another example, the potential use of a graphical presentation was demonstrated in selecting a range of positive dLr values that best represented the relevant validation studies. Conclusions Inclusion of the dLr in the results section of a validation study would benefit potential users of the study results. Furthermore, investigators planning a database study can utilize the dLr to their benefit. Wider recognition of the full utility

关键词： Claims database study Healthcare Likelihood ratio Outcome Predictive values risk ratio Sensitivity Specificity Validation study

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Why estimands are needed to define treatment effects in clinical trials

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BMC MEdICINE 2023年第1期21卷 276-276页

作者： Keene, Oliver N. Lynggaard, Helle Englert, Stefan Lanius, Vivian Wright, david KeeneONStat Maidenhead England Biostatistics Novo Nord A S Bagsvaerd Denmark Janssen Cilag GmbH Stat Modeling & Methodol Janssen R&D Neuss Germany Stat & Data Insights Bayer AG Wuppertal Germany Stat Innovat Data Sci & Artificial Intelligence Biopharmaceut R&D AstraZeneca Cambridge England

BackgroundThe estimand for a clinical trial is a precise definition of the treatment effect to be estimated. Traditionally, estimates of treatment effects are based on either an ITT analysis or a per-protocol analysis. However, there are important clinical questions which are not addressed by either of these analyses. For example, consider a trial where patients take a rescue medication. The ITT analysis includes data after use of rescue, while the per-protocol analysis excludes these patients altogether. Neither of these analyses addresses the important question of what the treatment effect would have been if patients did not take rescue *** textTrial estimands provide a broader perspective compared to the limitations of ITT and per-protocol analysis. Trial treatment effects depend on how events occurring after treatment initiation such as use of alternative medication or discontinuation of the intervention are included in the definition. These events can be accounted for in different ways, depending on the clinical question of *** estimand framework is an important step forward in improving the clarity and transparency of clinical trials. The centrality of estimands to clinical trials is currently not reflected in methods recommended by the Cochrane group or the CONSOrT statement, the current standard for reporting clinical trials in medical journals. We encourage revisions to these guidelines.

关键词： Estimand Treatment effect Intercurrent event ITT Per-protocol PICO CONSOrT

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Novel approaches to develop community-built biological network models for potential drug discovery

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EXPErT OPINION ON drUG dISCOVErY 2017年第8期12卷 849-857页

作者： Talikka, Marja Bukharov, Natalia Hayes, William S. Hofmann-Apitius, Martin Alexopoulos, Leonidas Peitsch, Manuel C. Hoeng, Julia Philip Morris Prod SA Philip Morris Int R&D Neuchatel Switzerland Clarivate Analyt Translat Data Management Serv Boston MA USA Appl Dynam Solut LLC Data Sci Rahway NJ USA Fraunhofer Inst Algorithms & Sci Comp Dept Bioinformat Schloss Birlinghoven Sankt Augustin Germany Natl Tech Univ Athens Syst Bioengn Lab Zografos Greece Protavio Ltd Stevenage Herts England

Introduction: Hundreds of thousands of data points are now routinely generated in clinical trials by molecular profiling and NGS technologies. A true translation of this data into knowledge is not possible without analysis and interpretation in a well-defined biology context. Currently, there are many public and commercial pathway tools and network models that can facilitate such analysis. At the same time, insights and knowledge that can be gained is highly dependent on the underlying biological content of these resources. Crowdsourcing can be employed to guarantee the accuracy and transparency of the biological content underlining the tools used to interpret rich molecular data. Areas covered: In this review, the authors describe crowdsourcing in drug discovery. The focal point is the efforts that have successfully used the crowdsourcing approach to verify and augment pathway tools and biological network models. Technologies that enable the building of biological networks with the community are also described. Expert opinion: A crowd of experts can be leveraged for the entire development process of biological network models, from ontologies to the evaluation of their mechanistic completeness. The ultimate goal is to facilitate biomarker discovery and personalized medicine by mechanistically explaining patients' differences with respect to disease prevention, diagnosis, and therapy outcome.

关键词： Mechanistic pathway network model crowd sourcing ontology Biological Expression Language

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Enzymatic treatment for preventing biofilm formation in the paper industry

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APPLIEd MICrOBIOLOGY ANd BIOTECHNOLOGY 2011年第1期92卷 95-103页

作者： Esperanza Torres, Claudia Lenon, Giles Craperi, delphine Wilting, reinhard Blanco, Angeles Univ Complutense Dept Chem Engn Fac Chem E-28040 Madrid Spain Ctr Tech Ind Papiers Cartons & Celluloses CTP CTPs Gen Direct F-38044 Grenoble France Ctr Tech Ind Papiers Cartons & Celluloses CTP Format Coordinat Dept F-38044 Grenoble France Novozymes AS Dept Head R&D Data Management DK-2880 Bagsvaerd Denmark

Microbiological control programmes at industrial level should aim at reducing both the detrimental effects of microorganisms on the process and the environmental impact associated to the use of biocides as microbiological control products. To achieve this target, new efficient and environmentally friendly products are required. In this paper, 17 non-specific, commercial enzymatic mixtures were tested to assess their efficacy for biofilm prevention and control at laboratory and pilot plant scale. Pectin methylesterase, an enzyme found in the formulation of two of the mixtures tested, was identified as an active compound able to reduce biofilm formation by 71% compared to control tests.

关键词： Enzymes Biofilm Microbiological control Pectin methylesterase Paper industry

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Changes in Prescription of Psychotropic drugs After Introduction of Polypharmacy reduction Policy in Japan Based on a Large-Scale Claims database

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CLINICAL drUG INVESTIGATION 2019年第11期39卷 1077-1092页

作者： Hirano, Yoko Ii, Yoichi Kitasato Univ Grad Sch Pharmaceut Sci Dept Clin Med Pharmaceut Med Minato Ku 5-9-1 Shirokane Tokyo 1088641 Japan Pfizer Pharmaceut KK Rare Dis Therapeut Area Med Affairs Shibuya Ku Tokyo Japan Pfizer R&D Japan GK Biometr & Data Management Shibuya Ku Tokyo Japan

Background and Objectives In Japan, polypharmacy reduction policy, which reduces the reimbursement of medical cost, was introduced to address unnecessary psychotropic polypharmacy. The rule was applied to the prescriptions of three or more anxiolytics or three or more hypnotics in the policy introduced in 2012. The prescriptions of four or more antidepressants or four or more antipsychotics were added to the rule in the policy revised in 2014. Furthermore, the prescriptions of three or more drugs of anxiolytics, hypnotics, antidepressants, or antipsychotics were subject to the reduction criteria of the policy revision in 2016. Benzodiazepine receptor agonists (BZs) are classified both into anxiolytics and hypnotics, and the reduction rule was not applied to the category of BZs before April 2018. This study aimed to examine the effect of the policy on the prescriptions of four drug categories as well as BZs from the point of view of the number of drugs and doses. Methods This was a retrospective observational study using a large-scale Japanese health insurance claims database. Patients who were prescribed at least one psychotropic drug (anxiolytic, hypnotic, antidepressant, or antipsychotic) during the study period (from April 2011 to March 2017) were selected. Segmented regression analysis was used to analyze the proportions of patients with three or more or four or more drugs as well as patients above clinically recommended doses, and the means of the average daily doses by drug category. results A total of 312,167 patients were identified as a study population. The proportions of patients with three or more drugs in anxiolytics, hypnotics, antidepressants, and antipsychotics significantly decreased after the introduction or revisions of the policy, but not BZs. The proportions of patients with three or more drugs in March 2017 were 0.9%, 2.0%, 1.2%, 2.4%, and 8.9% in anxiolytics, hypnotics, antidepressants, antipsychotics, and BZs, respectively. The effect of the

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Knowledge inheritance in disciplines: Quantifying the successive and distant reuse of references

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JOUrNAL OF THE ASSOCIATION FOr INFOrMATION SCIENCE ANd TECHNOLOGY 2023年第13期74卷 1515-1531页

作者： Zhou, Hongyu dong, Ke Xia, Yikun Univ Antwerp Fac Social Sci Ctr R&D Monitoring ECOOM Antwerp Belgium Nanjing Univ Res Inst Data Management Innovat Suzhou Peoples R China Nanjing Univ Sch Informat Management Nanjing Peoples R China Nanjing Univ Res Inst Data Management & Innovat Suzhou 215163 Jiangsu Peoples R China

How the knowledge base of disciplines grows, renews, and decays informs their distinct characteristics and epistemology. Here we track the evolution of knowledge bases of 19 disciplines for over 45 years. We introduce the notation of knowledge inheritance as the overlap in the set of references between years. We discuss two modes of knowledge inheritance of disciplines-successive and distant. To quantify the status and propensity of knowledge inheritance for disciplines, we propose two indicators: one descriptively describes knowledge base evolution, and one estimates the propensity of knowledge inheritance. When observing the continuity in knowledge bases for disciplines, we show distinct patterns for STEM and SS & H disciplines: the former inherits knowledge bases more successively, yet the latter inherits significantly from distant knowledge bases. We further discover stagnation or revival in knowledge base evolution where older knowledge base ceases to decay after 10 years (e.g., Physics and Mathematics) and are increasingly reused (e.g., Philosophy). regarding the propensity of inheriting prior knowledge bases, we observe unanimous rises in both successive and distant knowledge inheritance. We show that knowledge inheritance could reveal disciplinary characteristics regarding the trajectory of knowledge base evolution and interesting insights into the metabolism and maturity of scholarly communication.

关键词： Knowledge based systems

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Computational Assessment of Chemical Saturation of Analogue Series under Varying Conditions

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ACS OMEGA 2018年第11期3卷 15799-15808页

作者： Yonchev, dimitar Vogt, Martin Stumpfe, dagmar Kunimoto, ryo Miyao, Tomoyuki Bajorath, Juergen Rheinische Friedrich Wilhelms Univ LIMES Program Unit Chem Biol & Med Chem Dept Life Sci Informat B IT Endenicher Allee 19c D-53115 Bonn Germany Nara Inst Sci & Technol Data Sci Ctr 8916-5 Takayama Cho Nara 6300192 Japan Nara Inst Sci & Technol Grad Sch Sci & Technol 8916-5 Takayama Cho Nara 6300192 Japan Daichi Sankyo Co Ltd Shinagawa R&D Ctr R&D Div Shinagawa KuMed Chem Management GrpRes Funct 1-2-58 Hiromachi Tokyo 1408710 Japan

Assessing the degree to which analogue series are chemically saturated is of major relevance in compound optimization. decisions to continue or discontinue series are typically made on the basis of subjective judgment. Currently, only very few methods are available to aid in decision making. We further investigate and extend a computational concept to quantitatively assess the progression and chemical saturation of a series. To these ends, existing analogues and virtual candidates are compared in chemical space and compound neighborhoods are systematically analyzed. A large number of analogue series from different sources are studied, and alternative chemical space representations and virtual analogues of different designs are explored. Furthermore, evolving analogue series are distinguished computation-ally according to different saturation levels. Taken together, our findings provide a basis for practical applications of computational saturation analysis in compound optimization.

关键词： Saturation Medicinal chemistry Structure activity relationship Testing and assessment Optimization

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Bayesian optimization design for dose-finding based on toxicity and efficacy outcomes in phase I/II clinical trials

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PHArMACEUTICAL STATISTICS 2021年第3期20卷 422-439页

作者： Takahashi, Ami Suzuki, Taiji Tokyo Inst Technol Sch Comp Dept Math & Comp Sci 2-12-1 Ookayama Meguro Tokyo 1528550 Japan Pfizer R&D Japan Clin Stat Biometr & Data Management Tokyo Japan Univ Tokyo Grad Sch Informat Sci & Technol Dept Math Informat Tokyo Japan RIKEN Ctr Adv Intelligence Project Tokyo Japan

In phase I trials, the main goal is to identify a maximum tolerated dose under an assumption of monotonicity in dose-response relationships. On the other hand, such monotonicity is no longer applied to biologic agents because a different mode of action from that of cytotoxic agents potentially draws unimodal or flat dose-efficacy curves. Therefore, biologic agents require an optimal dose that provides a sufficient efficacy rate under an acceptable toxicity rate instead of a maximum tolerated dose. Many trials incorporate both toxicity and efficacy data, and drugs with a variety of modes of actions are increasingly being developed;thus, optimal dose estimation designs have been receiving increased attention. Although numerous authors have introduced parametric model-based designs, it is not always appropriate to apply strong assumptions in dose-response relationships. We propose a new design based on a Bayesian optimization framework for identifying optimal doses for biologic agents in phase I/II trials. Our proposed design models dose-response relationships via nonparametric models utilizing a Gaussian process prior, and the uncertainty of estimates is considered in the dose selection process. We compared the operating characteristics of our proposed design against those of three other designs through simulation studies. These include an expansion of Bayesian optimal interval design, the parametric model-based EffTox design, and the isotonic design. In simulations, our proposed design performed well and provided results that were more stable than those from the other designs, in terms of the accuracy of optimal dose estimations and the percentage of correct recommendations.

关键词： Bayesian optimization biological agent dose‐ finding nonparametric method optimal dose

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Efficacy of denosumab co-administered with vitamin d and Ca by baseline vitamin d status

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JOUrNAL OF BONE ANd MINErAL METABOLISM 2020年第6期38卷 848-858页

作者： Sugimoto, Toshitsugu Matsumoto, Toshio Hosoi, Takayuki Shiraki, Masataka Kobayashi, Makiko Okubo, Naoki Takami, Hideo Nakamura, Toshitaka Eikokai Ono Hosp Tenjincho 973 Ono Hyogo 6751316 Japan Tokushima Univ Fujii Mem Inst Med Sci Inst Adv Med Sci Tokushima Japan Kenkoin Clin Tokyo Japan Res Inst & Practice Involut Dis Nagano Japan Daiichi Sankyo Co Ltd Med Sci Dept Med Affairs Div Tokyo Japan Daiichi Sankyo Co Ltd Biostat & Data Management Dept R&D Div Tokyo Japan Daiichi Sankyo Co Ltd Dev Funct R&D Div Tokyo Japan Touto Sangenjaya Rehabil Hosp Tokyo Japan

Introduction In anti-osteoporosis drug trials, vitamin d and calcium (Ca) are common supplements;however, the optimal dose of each is unclear. Using data from the randomized, double-blind, placebo-controlled dIrECT trial, we assessed whether baseline serum 25-hydroxy vitamin d (25[OH]d) level influences the efficacy of denosumab co-administered with vitamin d and Ca. Materials and methods In this prespecified sub-analysis, subjects with primary osteoporosis who received denosumab or placebo, plus vitamin d (>= 400 IU/day) and Ca (>= 600 mg/day), were classified as 25(OH)d deficient (< 20 ng/mL), insufficient (>= 20 to < 30 ng/mL), and sufficient (>= 30 ng/mL). Study endpoints included absolute serum 25(OH)d level at baseline, 12 months, and 24 months;change in serum 25(OH)d and bone mineral density (BMd) status from baseline;and incidence of new vertebral fractures at 24 months. results In 475 denosumab-treated and 481 placebo-treated subjects, proportions with deficient/insufficient/sufficient 25(OH)d at baseline were 53.1%/37.1%/9.9% and 50.9%/42.0%/7.1%, respectively. Supplementation significantly increased mean serum 25(OH)d levels;at 24 months, mean levels were > 30 ng/mL (sufficient) in both treatment groups. Increase in BMd over time was higher in the denosumab group vs. placebo group in all three vitamin d status groups. At month 24, denosumab-treated subjects with deficient/insufficient baseline 25(OH)d had a significantly lower risk of new vertebral fracture vs. placebo-treated subjects. Conclusion Among dIrECT trial subjects supplemented with >= 400 IU/day of vitamin d and >= 600 mg/day of Ca, baseline 25(OH)d sufficiency may not influence the efficacy of denosumab in increasing BMd or preventing vertebral fractures.

关键词： Bone mineral density deficiency denosumab Fracture Vitamin d insufficiency

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EVAdyr: A New dynamic resampling Algorithm for Auto-Tuning Noisy High Performance Computing Systems

SSRN

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SSrN 2023年

作者： robert, Sophie Zertal, Soraya Couvée, Philippe Atos BDS R&D Data Management Echirolles38130 France Li-PaRAD UPSaclay-UVSQ Guyancourt78297 France

Black-box auto-tuning methods have been proven to be efficient for tuning configurable computer appliance, including those encountered within the High Performance Computing (HPC) ecosystem. However, because of the shared nature of HPC clusters and the complexity of the software and hardware stacks, the measurement of the performance function can be tainted by noise during the tuning process, which can reduce and sometimes prevent the benefit of the tuning approach. An usual choice for performing the tuning in spite of these interference is to add a resampling step at each iteration to reduce uncertainty, but this approach can be time-consuming and must be done carefully. In this paper, we propose a new resampling and filtering algorithm called EVAdyr (Efficient Value Aware dynamic resampling). Compared to the state of the art, it finds a better exploration versus exploitation trade-off by resampling only promising parametrization and increases the level of confidence around the suggested solution as the tuning process advances. This algorithm was able to tune efficiently two I/O accelerators highly sensitive to interference, in two different scenarios. Compared to Standard Error dynamic resampling (SEdr), a state of the art noise reduction strategy, we show that EVAdyr is able to reduce the distance to the optimum by 93.5% and 24.7% for the two I/O accelerators respectively, as well as speed-up the experiment duration by 45.8% and 58.1% because less iterations are needed to reach the found optimum. Our results prove the importance of using noise reduction strategies whenever tuning systems running in production. © 2023, The Authors. All rights reserved.

关键词： Noise abatement

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