bluuebunny/crossref_metadata_2025_split huggingface dataset:
A snapshot neural ensemble method for cancer-type prediction based on copy number variations
Authors: Karim Md. Rezaul , Rahman Ashiqur , Jares João Bosco , Decker Stefan , Beyan Oya 
Published: December 2019

AbstractAn accurate diagnosis and prognosis for cancer are specific to patients with particular cancer types and molecular traits, which needs to address carefully. The discovery of important biomarkers is becoming an important step toward understanding the molecular mechanisms of carcinogenesis in which genomics data and clinical outcomes need to be analyzed before making any clinical decision. Copy number variations (CNVs) are found to be associated with the risk of individual cancers and hence can be used to reveal genetic predispositions before cancer develops. In this paper, we collect the CNVs data about 8000 cancer patients covering 14 different cancer types from The Cancer Genome Atlas. Then, two different sparse representations of CNVs based on 578 oncogenes and 20,308 protein-coding genes, including genomic deletions and duplication across the samples, are prepared. Then, we train Conv-LSTM and convolutional autoencoder (CAE) networks using both representations and create snapshot models. While the Conv-LSTM can capture locally and globally important features, CAE can utilize unsupervised pretraining to initialize the weights in the subsequent convolutional layers against the sparsity. Model averaging ensemble (MAE) is then applied to combine the snapshot models in order to make a single prediction. Finally, we identify most significant CNVs biomarkers using guided-gradient class activation map plus (GradCAM++) and rank top genes for different cancer types. Results covering several experiments show fairly high prediction accuracies for the majority of cancer types. In particular, using protein-coding genes, Conv-LSTM and CAE networks can predict cancer types correctly at least 72.96% and 76.77% of the cases, respectively. Contrarily, using oncogenes gives moderately higher accuracies of 74.25% and 78.32%, whereas the snapshot model based on MAE shows overall 2.5% of accuracy improvement.
Clinical efficacy and safety of dotinurad, a novel selective urate reabsorption inhibitor, in Japanese hyperuricemic patients with or without gout: randomized, multicenter, double-blind, placebo-controlled, parallel-group, confirmatory phase 2 study
Authors: Hosoya Tatsuo , Sano Takafumi , Sasaki Tomomitsu , Fushimi Masahiko , Ohashi Tetsuo 
Published: December 2019

Abstract
Background
Dotinurad, a novel selective urate reabsorption inhibitor (SURI), reduces serum uric acid levels by selectively inhibiting urate transporter 1 (URAT1) for the treatment of hyperuricemia with or without gout. We confirmed the serum uric acid lowering effect and safety of dotinurad.

Methods
This was a confirmatory, 12-week, randomized, multicenter, double-blind, placebo-controlled, parallel-group, dose escalation, late phase 2 study. The study arms were dotinurad 0.5, 1, 2, or 4 mg and placebo. The primary endpoint was the percent change in serum uric acid level from the baseline to the final visit. The secondary endpoint was the percentage of patients achieving a serum uric acid level ≤ 6.0 mg/dL at the final visit.

Results
The study drugs were administered to 200 Japanese hyperuricemic patients with or without gout. The mean percent change in serum uric acid level from the baseline to the final visit in the dotinurad 0.5, 1, 2, and 4 mg groups and the placebo group was 21.81%, 33.77%, 42.66%, 61.09%, and − 2.83%, respectively. The percentage of patients achieving a serum uric acid level ≤ 6.0 mg/dL at the final visit in each group was 23.1%, 65.9%, 74.4%, 100%, and none, respectively. Regarding safety, the incidence of adverse events did not increase with dose escalation in the dotinurad groups. No significant differences were observed in the incidence of gouty arthritis in each group.

Conclusion
The serum uric acid lowering effect and safety of dotinurad were confirmed in hyperuricemic patients with or without gout.

ClinicalTrials.gov Identifier
NCT02416167
NorthEuraLex: a wide-coverage lexical database of Northern Eurasia
Authors: Dellert Johannes , Daneyko Thora , Münch Alla , Ladygina Alina , Buch Armin , Clarius Natalie , Grigorjew Ilja , Balabel Mohamed , Boga Hizniye Isabella , Baysarova Zalina , Mühlenbernd Roland , Wahle Johannes , Jäger Gerhard 
Published: December 2019

AbstractThis article describes the first release version of a new lexicostatistical database of Northern Eurasia, which includes Europe as the most well-researched linguistic area. Unlike in other areas of the world, where databases are restricted to covering a small number of concepts as far as possible based on often sparse documentation, good lexical resources providing wide coverage of the lexicon are available even for many smaller languages in our target area. This makes it possible to attain near-completeness for a substantial number of concepts. The resulting database provides a basis for rich benchmarks that can be used to test automated methods which aim to derive new knowledge about language history in underresearched areas.
Renal cell carcinoma in young FH mutation carriers: case series and review of the literature
Authors: Hol J. A. , Jongmans M. C. J. , Littooij A. S. , de Krijger R. R. , Kuiper R. P. , van Harssel J. J. T. , Mensenkamp A. , Simons M. , Tytgat G. A. M. , van den Heuvel-Eibrink M. M. , van Grotel M. 
Published: December 2019

AbstractHereditary Leiomyomatosis and Renal Cell Cancer (HLRCC) is an autosomal dominant syndrome caused by heterozygous pathogenic germline variants in the fumarate hydratase (FH) gene. It is characterized by cutaneous and uterine leiomyomas and an increased risk of developing renal cell carcinoma (RCC), which is usually adult-onset. HLRCC-related RCC tends to be aggressive and can metastasize even when the primary tumor is small. Data on children and adolescents are scarce. Herein, we report two patients from unrelated Dutch families, with HLRCC-related RCC at the ages of 15 and 18 years, and a third patient with an FH mutation and complex renal cysts at the age of 13. Both RCC’s were localized and successfully resected, and careful MRI surveillance was initiated to monitor the renal cysts. One of the patients with RCC subsequently developed an ovarian Leydig cell tumor. A review of the literature identified 10 previously reported cases of HLRCC-related RCC in patients aged younger than 20 years, five of them presenting with metastatic disease. These data emphasize the importance of recognizing HLRCC in young patients to enable early detection of RCC, albeit rare. They support the recommendations from the 2014 consensus guideline, in which genetic testing for FH mutations, and renal MRI surveillance, is advised for HLRCC family members from the age of 8–10 years onwards.
Experienced Severity of Imprisonment Among Fathers and Non-Fathers
Authors: Reef Joni , Dirkzwager Anja 
Published: December 2019

Abstract
Objectives
Even though 90% of the prison population is male, fatherhood among prisoners is an overlooked topic. Previous studies suggest that experienced severity of detention is different between fathers and non-fathers in prison because there is a unique deprivation strain related to fatherhood. There are criminological arguments and arguments in the legal context why we need more knowledge on the experience of detention by incarcerated fathers.

Methods
We studied longitudinal data of 785 males in pre-trial detention in the Netherlands from the nationwide Prison Project study population: 329 fathers were compared with 456 non-fathers for experienced severity, adjustment patterns (i.e. mental distress and misconduct), and deprivations strains.

Results
We found differences between fathers and non-fathers, both in adjustment and deprivation strains. Fathers reported less adjustment problems and different deprivation strains than non-fathers. Missing children during pre-trial detention was associated with depressive behavior (β = 0.158, p < 0.005) and anxiety among fathers (β = 0.128, p < 0.05).

Conclusions
Our results underline the importance of designing interventions for fathers in prison and educating sentencers about this topic. Proportional sentencing of fathers in the criminal justice system could only be validated as long as sufficient attention will be paid to their unique deprivation strain, which is, missing their children. During pre-trial detention, care for the child-father relation may not only lead to father’s emotional wellbeing during pre-trial detention, but may also lead to strengthened family bonds and children’s wellbeing on the long term.
Intra-residue methyl–methyl correlations for valine and leucine residues in large proteins from a 3D-HMBC-HMQC experiment
Authors: Siemons Lucas , Mackenzie Harold W. , Shukla Vaibhav Kumar , Hansen D. Flemming 
Published: November 2019

Abstract
Methyl-TROSY based NMR experiments have over the last two decades become one of the most important means to characterise dynamics and functional mechanisms of large proteins and macromolecular machines in solution. The chemical shift assignment of methyl groups in large proteins is, however, still not trivial and it is typically performed using backbone-dependent experiments in a ‘divide and conquer’ approach, mutations, structure-based assignments or a combination of these. Structure-based assignment of methyl groups is an emerging strategy, which reduces the time and cost required as well as providing a method that is independent of a backbone assignment. One crucial step in available structure-based assignment protocols is linking the two prochiral methyl groups of leucine and valine residues. This has previously been achieved by recording NOESY spectra with short mixing times or by comparing NOESY spectra. Herein, we present a method based on through-bond scalar coupling transfers, a 3D-HMBC-HMQC experiment, to link the intra-residue methyl groups of leucine and valine. It is shown that the HMBC-HMQC method has several advantages over solely using NOESY spectra since a unique intra-residue cross-peak is observed. Moreover, overlap in the methyl-TROSY HMQC spectrum can easily be identified with the HMBC-HMQC experiment, thereby removing possible ambiguities in the assignment.
Drivers of and barriers to partner switch in interfirm alliances: a conceptual model
Authors: Hampl Nina 
Published: December 2019

AbstractHistorically, research on alliance termination assumes that alliance partners only withdraw from alliances in the event of alliance failure (failure-driven alliance termination). However, recent research on the dissolution of alliances shows that firms also withdraw from alliances through alliance partner switch when they find options with higher match quality than the current partner (option-driven alliance termination). This paper builds on previous work in that field and develops a comprehensive conceptual model of drivers of and barriers to partner switch in interfirm alliances. Based on matching theory, the rectification of alliance partner fit is defined in relation to strategic need, social status and social power as the main drivers and switching costs, social embeddedness and social norms as the main barriers to partner switch. Furthermore, it is argued that market uncertainty and behavioural uncertainty as well as the financial strength and social status of the focal firm have a moderating effect on such drivers and barriers.
Is it Necessary to Perform Sentinel Lymph Node Biopsy in Thin Melanoma? A Retrospective Single Center Analysis
Authors: Kocsis A. , Karsko L. , Kurgyis Zs. , Besenyi Zs. , Pavics L. , Dosa-Racz E. , Kis E. , Baltas E. , Ocsai H. , Varga E. , Bende B. , Varga A. , Mohos G. , Korom I. , Varga J. , Kemeny L. , Nemeth I. B. , Olah J. 
Published: December 2019

AbstractSentinel lymph node biopsy (SLNB) is a standard procedure for regional lymph node staging and still has the most important prognostic value for the outcome of patients with thin melanoma. In addition to ulceration, SLNB had to be considered even for a single mitotic figure in thin (<1 mm) melanoma according to AJCC7th guideline, therefore, a retrospective review was conducted involving 403 pT1 melanoma patients. Among them, 152 patients suffered from pT1b ulcerated or mitotic rate ≥ 1/ mm2melanomas according to the AJCC7th staging system. SLNB was performed in 78 cases, of which nine (11.5%) showed SLN positivity. From them, interestingly, we found a relatively high positive sentinel rate (6/78–8%) in the case of thin primary melanomas ˂0.8 mm. Moreover, the presence of regression increased the probability of sentinel positivity by 5.796 fold. After reassessing pT stage based on the new AJCC8th, 37 pT1b cases were reordered into pT1a category. There was no significant relation between other characteristics examined (age, gender, Breslow, Clark level, and mitosis index) and sentinel node positivity. Based on our data, we suggest that mitotic rate alone is not a sufficiently powerful predictor of SLN status in thin melanomas. If strict histopathological definition criteria are applied, regression might be an additional adverse feature that aids in identifying T1 patients most likely to be SLN-positive. After reassessing of pT1b cases according to AJCC8thregression proved to be independent prognostic factor on sentinel lymph node positivity. Our results propose that sentinel lymph node biopsy might also be considered at patients with regressive thin (˂0.8 mm) melanomas.
Human adaptation to invasive species: A conceptual framework based on a case study metasynthesis
Authors: Howard Patricia L. 
Published: November 2019

AbstractSpecies invasions are a major driver of ecological change, are very difficult to control or reverse, and will increase with climate change and global trade. Invasion sciences consider how species in invaded environments adapt, but neither scientists nor policy makers consider human adaptation to invasive species and how this affects ecosystems and well-being. To address this, a framework conceptualising autochthonous human adaptation to invasions was developed based on the Human Adaptation to Biodiversity Change framework and a case study metasynthesis. Results show that adaptation occurs within different spheres of human activity and organisation at different social-ecological scales; responses have feedbacks within and across these spheres. Adaptation to invasives and other drivers is a set of highly contextual, complex, non-linear responses that make up pathways pursued over time. Most invasive species management and adaptation occurs ‘from below,’ and policies and planned control efforts should support autochthonous adaptation, rather than undermining it.
Conjugate gradient variants for $${\ell}_{p}$$-regularized image reconstruction in low-field MRI
Authors: de Leeuw den Bouter Merel L. , van Gijzen Martin B. , Remis Rob F. 
Published: December 2019

AbstractWe consider the MRI physics in a low-field MRI scanner, in which permanent magnets are used to generate a magnetic field in the millitesla range. A model describing the relationship between measured signal and image is derived, resulting in an ill-posed inverse problem. In order to solve it, a regularization penalty is added to the least-squares minimization problem. We generalize the conjugate gradient minimal error (CGME) algorithm to the weighted and regularized least-squares problem. Analysis of the convergence of generalized CGME (GCGME) and the classical generalized conjugate gradient least squares (GCGLS) shows that GCGME can be expected to converge faster for ill-conditioned regularization matrices. The$${\ell}_{p}$$ℓp-regularized problem is solved using iterative reweighted least squares for$$p=1$$p=1and$$p=\frac{1}{2}$$p=12, with both cases leading to an increasingly ill-conditioned regularization matrix. Numerical results show that GCGME needs a significantly lower number of iterations to converge than GCGLS.
Adaptive risk consensus models: simulations and applications
Authors: Mitic Peter 
Published: December 2019

AbstractA simulation framework that implements adaptive agent–agent interaction is developed, such that agent behaviour typical of complex adaptive systems is observed. Within this framework, agents monitor the state of the system they inhabit, and adapt their actions so as to optimise a local utility. No central control is present. The context for state is intended to be very general, but is interpreted as risk state, in which optimisation implies a minimisation of risk. Three adaptive interaction modes are proposed. In each, there is a trade-off between simplicity and effectiveness. Additionally a fourth ‘counter-adaptive’ mode is proposed to model situations of a prolonged high risk state. Corresponding ‘real’ examples from recent events are proposed.
Frequency, Determinants, and Satisfaction of Breast Augmentation in Trans Women Receiving Hormone Treatment
Authors: de Blok Christel J.M. , Staphorsius Annemieke S. , Wiepjes Chantal M. , Smit Jan Maerten , Nanayakkara Prabath W.B. , den Heijer Martin 
Published: December 2019

AbstractIntroductionAs breast development in trans women (male sex assigned at birth, female gender identity) who receive gender-affirming hormone treatment is often moderate, they may choose breast augmentation as part of their treatment.AimThe aim of the study was to investigate the frequency, determinants, and satisfaction of breast augmentation among trans women receiving hormone treatment.MethodsTrans women who started hormone treatment between 1972 and 2018 at our center received an anonymous questionnaire.Main Outcome MeasureThe questionnaire contained questions about the start date of hormone treatment, the current age of the respondent, whether or not she underwent breast augmentation, what her considerations in this decision were, and, if the respondent did have breast implants, whether she was satisfied with the result and/or experienced health complaints she attributed to her breast implants.ResultsA total of 3,073 questionnaires were distributed, of which 773 were retrieved back (median age of the respondents: 50 years, interquartile range: 35–59). Age and year of start of hormone treatment was comparable between responders and nonresponders. The frequency of breast augmentation varied from 70% in trans women who started hormone treatment between 1980 and 2000 to 20% in those who started between 2010 and 2015. Trans women underwent breast augmentation median 2 years after the start of hormone treatment (interquartile range: 2–4), and 80% was satisfied with the result. Approximately one-third experienced health complaints they attributed to their breast implants. People who considered breast augmentation reported financial limitations as an important reason not to undergo breast augmentation.Clinical ImplicationsThis study shows that it is important to discuss pros and cons of breast augmentation to support trans women in making a well-informed decision.Strengths & LimitationsThis is the largest study performed on the frequency and satisfaction of breast augmentation among trans women, which also includes health complaints and considerations in the decision whether or not to undergo breast augmentation. One of the limitations was that we were unable to link other clinical data.Conclusion4 of 5 trans women either chose or considered breast augmentation as part of their gender-affirming treatment. Most of the trans women who underwent breast augmentation were satisfied with the result, although approximately one-third experienced health complaints they attributed to their breast implants. Reasons not to undergo breast augmentation included financial limitations. This study shows that it is important to discuss with trans women the positive effects and possible side-effects of breast augmentation to help them make a well-informed decision whether or not to undergo breast augmentation.
Automated Ionospheric Scattering Layer Hypothesis Generation for Detected and Classified Auroral Global Positioning System Scintillation Events
Authors: Sreenivash Vaishnavi , Su Yang , Datta‐Barua Seebany 
Published: November 2019

AbstractWe describe a method to detect and classify global positioning system (GPS) scintillation, and then hypothesize a possible ionospheric layer scattering the signal. The objective is to routinely identify events of interest to investigate in detail in future work. Scintillation types include amplitude, phase, or both amplitude and phase. A scintillation event is one for which a scintillation index remains above a threshold across a majority of closely spaced receivers viewing a single satellite. Events are categorized by signal frequency and scintillation type. An event is then hypothesized to be due to the E or F layer using an independent data source. Data from the scintillation auroral GPS array located in Poker Flat Research Range, Alaska, are used to analyze L1 and L2C frequencies in 2014 and 2015. The irregularity layer associated with each scintillation event is hypothesized to be due to the activity in the E layer of the ionosphere (below 150 km) or in the F layer (above 195 km) using collocated Poker Flat Incoherent Scatter Radar electron density measurements. Events in a transition layer (150–195 km) and inconclusive results are also recorded. We find that nearly all of the over 4,000 events are phase scintillations. The majority of the events are hypothesized to occur when the peak density is at E‐layer altitudes. This indicates that E‐layer‐related scintillation may be quite common at auroral latitudes and that GPS receivers are sensitive to the irregularities occurring both there and at F layer altitudes.
Forecasting Residential Water Consumption in California: Rethinking Model Selection
Authors: Buck Steven , Auffhammer Maximilian , Soldati Hilary , Sunding David 
Published: November 2019

AbstractUrban water managers use forecasts of water consumption to determine management decisions and investment choices. Public reports show that water utilities rely on forecast models that are not selected based on their out‐of‐sample prediction performance; further, these reports frequently only present a single forecast instead of a range of forecasts. In our review of the academic literature on forecasting long‐term water consumption, only a few analyses consider out‐of‐sample prediction performance measures to assess prediction ability. In none of these analyses did out‐of‐sample prediction performance drive model selection. Ensemble‐type long‐term forecasts based on multiple models were also lacking. Using annual data on single‐family residential water consumption in Southern California, we show that predictive ability varies drastically depending on how the forecast model is selected. As an illustration of how forecast performance is affected when the criteria for model selection does support forecasting objectives, we compare statistical models with the best in‐sample and out‐of‐sample prediction performance. We find that the models with the best in‐sample performance over‐estimate consumption five years out by 10%‐25% compared to actual consumption. In contrast, the top 1% of models selected based on out‐of‐sample prediction performance came within 1% of actual consumption. Finally, we compare the performance of our ensemble‐type forecasts to those reported in public documents derived from models selected based on non‐out‐of‐sample prediction performance criteria. Our results highlight the benefits of (i) using an out‐of‐sample evaluation criterion to guide model selection and (ii) reporting ensemble forecasts in lieu of a single forecast.