Stacked Penalized Logistic Regression for Selecting Views in Multi-View Learning

In biomedical research, many different types of patient data can be collected, such as various types of omics data and medical imaging modalities. Applying multi-view learning to these different sources of information can increase the accuracy of medical classification models compared with single-view procedures. However, collecting biomedical data can be expensive and/or burdening for patients, so that it is important to reduce the amount of required data collection. It is therefore necessary to develop multi-view learning methods which can accurately identify those views that are most important for prediction. In recent years, several biomedical studies have used an approach known as multi-view stacking (MVS), where a model is trained on each view separately and the resulting predictions are combined through stacking. In these studies, MVS has been shown to increase classification accuracy. However, the MVS framework can also be used for selecting a subset of important views. To study the view selection potential of MVS, we develop a special case called stacked penalized logistic regression (StaPLR). Compared with existing view-selection methods, StaPLR can make use of faster optimization algorithms and is easily parallelized. We show that nonnegativity constraints on the parameters of the function which combines the views play an important role in preventing unimportant views from entering the model. We investigate the performance of StaPLR through simulations, and consider two real data examples. We compare the performance of StaPLR with an existing view selection method called the group lasso and observe that, in terms of view selection, StaPLR is often more conservative and has a consistently lower false positive rate.Comment: 26 pages, 9 figures. Accepted manuscrip

Analyzing hierarchical multi-view MRI data with StaPLR: An application to Alzheimer's disease classification

Multi-view data refers to a setting where features are divided into feature sets, for example because they correspond to different sources. Stacked penalized logistic regression (StaPLR) is a recently introduced method that can be used for classification and automatically selecting the views that are most important for prediction. We introduce an extension of this method to a setting where the data has a hierarchical multi-view structure. We also introduce a new view importance measure for StaPLR, which allows us to compare the importance of views at any level of the hierarchy. We apply our extended StaPLR algorithm to Alzheimer's disease classification where different MRI measures have been calculated from three scan types: structural MRI, diffusion-weighted MRI, and resting-state fMRI. StaPLR can identify which scan types and which derived MRI measures are most important for classification, and it outperforms elastic net regression in classification performance.Comment: 36 pages, 9 figures. Accepted manuscrip

Early CT and FDG-metabolic tumour volume changes show a significant correlation with survival in stage I-III small cell lung cancer: A hypothesis generating study

BACKGROUND: Many patients with stage I–III small cell lung cancer (SCLC) experience disease progression short after the completion of concurrent chemoradiotherapy (CRT). The purpose of the current study was to evaluate whether CT or FDG metabolic response early after the start of chemotherapy, but before the beginning of chest RT, is predictive for survival in SCLC. METHODS: Fifteen stage I–III SCLC patients treated with concurrent CRT with an FDG-PET and CT scan available before the start of chemotherapy and after or during the first cycle of chemotherapy, but before the start of radiotherapy, were selected. The metabolic volume (MV) was defined both within the primary tumour and in the involved nodal stations using the 40% (MV40) and 50% (MV50) threshold of the maximum SUV. Metabolic and CT response was assessed by the relative change in MV and CT volume, respectively, between both time points. The association between response and overall survival (OS) was analysed by univariate cox regression analysis. The minimum follow-up was 18 months. RESULTS: Reductions in MV40 and MV50 were −36 ± 38% (126.4 to 68.7 cm(3)) and −44 ± 38% (90.2 to 27.8 cm(3)), respectively. The median CT volume reduction was −40 ± 64% (190.6 to 113.8 cm(3)). MV40 and MV50 changes showed a significant association with survival (HR = 1.02, 95% CI: 1.00–1.04 (p = 0.042); HR = 1.02, 95% CI: 1.00–1.04 (p = 0.048), respectively), indicating a 2% increase in survival probability for 1% reduction in metabolic volume. The CT volume change was also significantly correlated with survival (HR = 1.01, 95% CI: 1.00–1.03, p = 0.007). CONCLUSIONS: This hypothesis generating study shows that both the early CT and the MV changes show a significant correlation with survival in SCLC. A prospective study is planned in a larger patient cohort to allow multivariate analysis, with the final aim to select patients early during treatment that could benefit from dose intensification or alternative treatment

Hot-water immersion does not increase postprandial muscle protein synthesis rates during recovery from resistance-type exercise in healthy, young males

The purpose of this study was to assess the impact of postexercise hot-water immersion on postprandial myofibrillar protein synthesis rates during recovery from a single bout of resistance-type exercise in healthy, young men. Twelve healthy, adult men (age: 23 ± 1 y) performed a single bout of resistance-type exercise followed by 20 min of water immersion of both legs. One leg was immersed in hot water [46°C: hot-water immersion (HWI)], while the other leg was immersed in thermoneutral water (30°C: CON). After water immersion, a beverage was ingested containing 20 g intrinsically L-[1-13C]-phenylalanine and L-[1-13C]-leucine labeled milk protein with 45 g of carbohydrates. In addition, primed continuous L-[ring-2H5]-phenylalanine and L-[1-13C]-leucine infusions were applied, with frequent collection of blood and muscle samples to assess myofibrillar protein synthesis rates in vivo over a 5-h recovery period. Muscle temperature immediately after water immersion was higher in the HWI compared with the CON leg (37.5 ± 0.1 vs. 35.2 ± 0.2°C; P < 0.001). Incorporation of dietary protein-derived L-[1-13C]-phenylalanine into myofibrillar protein did not differ between the HWI and CON leg during the 5-h recovery period (0.025 ± 0.003 vs. 0.024 ± 0.002 MPE; P = 0.953). Postexercise myofibrillar protein synthesis rates did not differ between the HWI and CON leg based upon L-[1-13C]-leucine (0.050 ± 0.005 vs. 0.049 ± 0.002%/h; P = 0.815) and L-[ring-2H5]-phenylalanine (0.048 ± 0.002 vs. 0.047 ± 0.003%/h; P = 0.877), respectively. Hot-water immersion during recovery from resistance-type exercise does not increase the postprandial rise in myofibrillar protein synthesis rates. In addition, postexercise hot-water immersion does not increase the capacity of the muscle to incorporate dietary protein-derived amino acids in muscle tissue protein during subsequent recovery

Visually guided inspiration breath-hold facilitated with nasal high flow therapy in locally advanced lung cancer

Background and purpose Reducing breathing motion in radiotherapy (RT) is an attractive strategy to reduce margins and better spare normal tissues. The objective of this prospective study (NCT03729661) was to investigate the feasibility of irradiation of non-small cell lung cancer (NSCLC) with visually guided moderate deep inspiration breath-hold (IBH) using nasal high-flow therapy (NHFT). Material and methods Locally advanced NSCLC patients undergoing photon RT were given NHFT with heated humidified air (flow: 40 L/min with 80% oxygen) through a nasal cannula. IBH was monitored by optical surface tracking (OST) with visual feedback. At a training session, patients had to hold their breath as long as possible, without and with NHFT. For the daily cone beam CT (CBCT) and RT treatment in IBH, patients were instructed to keep their BH as long as it felt comfortable. OST was used to analyze stability and reproducibility of the BH, and CBCT to analyze daily tumor position. Subjective tolerance was measured with a questionnaire at 3 time points. Results Of 10 included patients, 9 were treated with RT. Seven (78%) completed the treatment with NHFT as planned. At the training session, the mean BH length without NHFT was 39 s (range 15-86 s), and with NHFT 78 s (range 29-223 s) (p = .005). NHFT prolonged the BH duration by a mean factor of 2.1 (range 1.1-3.9s). The mean overall stability and reproducibility were within 1 mm. Subjective tolerance was very good with the majority of patients having no or minor discomfort caused by the devices. The mean inter-fraction tumor position variability was 1.8 mm (-1.1-8.1 mm;SD 2.4 mm). Conclusion NHFT for RT treatment of NSCLC in BH is feasible, well tolerated and significantly increases the breath-hold duration. Visually guided BH with OST is stable and reproducible. We therefore consider this an attractive patient-friendly approach to treat lung cancer patients with RT in BH

Groene keuzes voor de Nederlandse basisindustrie: Klimaatneutrale productie in een circulaire economie

Dit rapport schetst hoe de Nederlandse basisindustrie in 2050 klimaatneutraal en circulair kan produceren. Het is gebaseerd op discussies binnen het Sustainable Industry Lab vanaf medio 2021. De transitie van de basisindustrie is uitdagend, maar de ligging aan de Noordzee en het netwerk van industriële bedrijven, toeleveranciers en kennisinstellingen, maken het plausibel en wenselijk dat Nederland een flinke basisindustrie behoudt. Dat vraagt echter om keuzes, waarover de meningen uiteen lopen. We schetsen daarom ook hoe verschillende sociaal-maatschappelijke toekomstbeelden deze keuzes beïnvloeden

The challenge of unprecedented floods and droughts in risk management

Risk management has reduced vulnerability to floods and droughts globally1,2, yet their impacts are still increasing3. An improved understanding of the causes of changing impacts is therefore needed, but has been hampered by a lack of empirical data4,5. On the basis of a global dataset of 45 pairs of events that occurred within the same area, we show that risk management generally reduces the impacts of floods and droughts but faces difficulties in reducing the impacts of unprecedented events of a magnitude not previously experienced. If the second event was much more hazardous than the first, its impact was almost always higher. This is because management was not designed to deal with such extreme events: for example, they exceeded the design levels of levees and reservoirs. In two success stories, the impact of the second, more hazardous, event was lower, as a result of improved risk management governance and high investment in integrated management. The observed difficulty of managing unprecedented events is alarming, given that more extreme hydrological events are projected owing to climate change3

バレイショ近縁種における種の分化 XIII. S.acaule X S.demissumより得た7倍雑種の染色体行動と両親ゲノムの類縁関係

中央アンデス産Acaulia群4倍種S. acaule (acl, 2n=48)とメキシコ産Demissa群6倍種S. demissum (dms, 2n=72)のゲノムの類縁関係を明らかにするために, 前者を母本として得た7倍雑種(2n=84)の還元分裂における染色体行動と稔性を調べた。以下その結果を要約する。両種間の交雑は極めて困難で, aclを母とした時のみ受粉花数当り0.02の低率で雑種が得られたにすぎない。得られた雑種は, 両親との形態的比較から, aclの非還元性卵とdmsの還元性花粉の受精に起因するものと推定された。この雑種の第1中期における染色体対合行動は甚だしく多様であったが, その対合型のモードは(12)_+(20)_+8_I, その平均対合頻度は(0.18)_V+(1.11)_+(11.73)_+(18.11)_+(7.26)_Iで, 著しく高頻度の3価形成を示す点が特徴的であった。このような対合行動はその後の染色体行動にも反映し, 第1後期では観察細胞のすべてに平均4.8の遅滞染色体がみられ, 第2中期では94%の細胞が分散染色体を示し, 数的平衡核板頻度は0.6%にすぎなかった。稔性は極めて低く, 調査花粉粒数の27%が一見正常であったが, 自殖及び戻交配のいずれにおいても全く種子を生じなかった。上記の観察結果, 特に高頻度で出現した3価染色体の成因を考察して次の知見を得た。すでにaclはAAA^aA^a, dmsはA^dA^dC_1C_1C_2C_2のゲノム型をもつことが知られているので, 当雑種のゲノム型はAAA^aA^aA^dC_1C_2となる。A^dゲノムは若干の構造的差異はもつもののAゲノム群に属することも知られている。したがって, 当雑種にみられる3価形成は, 主に, aclからのAAとdmsからのA^dの3ゲノム間の染色体対合に由来すると推論でき, 両種はこれらのゲノムの相同性によって相互に関係づけられているものと考えられる。 / Meiotic behavior and fertility were studied in a heptaploid F_1 hybrid (2n=84) obtained from crossing S. acaule (acl, 2n=48) with S. demissum (dms, 2n=72), with the aim of assessing a genomic relationship between the parent species. Crossability between the two species was very low, the number of hybrid plants per pollination being only 0.02. Morphological evidence indicated that the hybrid arose through the union of an unreduced egg of acl and a reduced pollen grain of dms. The hybrid had the mean pairing frequency of (0.18)_V+(1.11)_+(11.73)_+(18.11)_+(7.26)_I per cell at metaphase I, with (12)_+(20)_+8_I as the modal configuration. Its subsequent behaviors were extremely irregular, showing several laggards in all the cells and chromatid bridges in occasional cells at anaphase I and also scattered chromosomes in 94% of the cells at metaphase II. The hybrid gave only 27% stainable pollen and no seed either on selfing or on backcrossing with both parents. The pattern of chromosome pairing found in the hybrid was interpreted in terms of genomic relationship between both parent species. From this, it was suggested that one (A) of the two genomes (designated AA^a) which acl possess in its gametes seems to be closely similar to, but not identical with, one (A^d) of the three genomes (A^dC_1C_2) which dms possess in its gemetes

Twenty-three unsolved problems in hydrology (UPH) – a community perspective

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through on-line media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focussed on process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come

Panta Rhei benchmark dataset: socio-hydrological data of paired events of floods and droughts

As the adverse impacts of hydrological extremes increase in many regions of the world, a better understanding of the drivers of changes in risk and impacts is essential for effective flood and drought risk management and climate adaptation. However, there is currently a lack of comprehensive, empirical data about the processes, interactions and feedbacks in complex human-water systems leading to flood and drought impacts. Here we present a benchmark dataset containing socio-hydrological data of paired events, i.e., two floods or two droughts that occurred in the same area. The 45 paired events occurred in 42 different study areas and cover a wide range of socio-economic and hydro-climatic conditions. The dataset is unique in covering both floods and droughts, in the number of cases assessed, and in the quantity of socio-hydrological data. The benchmark dataset comprises: 1) detailed review style reports about the events and key processes between the two events of a pair; 2) the key data table containing variables that assess the indicators which characterise management shortcomings, hazard, exposure, vulnerability and impacts of all events; 3) a table of the indicators-of-change that indicate the differences between the first and second event of a pair. The advantages of the dataset are that it enables comparative analyses across all the paired events based on the indicators-of-change and allows for detailed context- and location-specific assessments based on the extensive data and reports of the individual study areas. The dataset can be used by the scientific community for exploratory data analyses e.g. focused on causal links between risk management, changes in hazard, exposure and vulnerability and flood or drought impacts. The data can also be used for the development, calibration and validation of socio-hydrological models. The dataset is available to the public through the GFZ Data Services (Kreibich et al. 2023, link for review: https://dataservices.gfz-potsdam.de/panmetaworks/review/923c14519deb04f83815ce108b48dd2581d57b90ce069bec9c948361028b8c85/).</p