bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic inference using generative adversarial networks
Authors: Smith Megan L , Hahn Matthew W 
Published: September 2023

Abstract

Motivation
The application of machine learning approaches in phylogenetics has been impeded by the vast model space associated with inference. Supervised machine learning approaches require data from across this space to train models. Because of this, previous approaches have typically been limited to inferring relationships among unrooted quartets of taxa, where there are only three possible topologies. Here, we explore the potential of generative adversarial networks (GANs) to address this limitation. GANs consist of a generator and a discriminator: at each step, the generator aims to create data that is similar to real data, while the discriminator attempts to distinguish generated and real data. By using an evolutionary model as the generator, we use GANs to make evolutionary inferences. Since a new model can be considered at each iteration, heuristic searches of complex model spaces are possible. Thus, GANs offer a potential solution to the challenges of applying machine learning in phylogenetics.

Results
We developed phyloGAN, a GAN that infers phylogenetic relationships among species. phyloGAN takes as input a concatenated alignment, or a set of gene alignments, and infers a phylogenetic tree either considering or ignoring gene tree heterogeneity. We explored the performance of phyloGAN for up to 15 taxa in the concatenation case and 6 taxa when considering gene tree heterogeneity. Error rates are relatively low in these simple cases. However, run times are slow and performance metrics suggest issues during training. Future work should explore novel architectures that may result in more stable and efficient GANs for phylogenetics.

Availability and implementation
phyloGAN is available on github: https://github.com/meganlsmith/phyloGAN/.
Automated machine learning for genome wide association studies
Authors: Lakiotaki Kleanthi , Papadovasilakis Zaharias , Lagani Vincenzo , Fafalios Stefanos , Charonyktakis Paulos , Tsagris Michail , Tsamardinos Ioannis 
Published: September 2023

AbstractMotivationGenome-wide association studies (GWAS) present several computational and statistical challenges for their data analysis, including knowledge discovery, interpretability, and translation to clinical practice.ResultsWe develop, apply, and comparatively evaluate an automated machine learning (AutoML) approach, customized for genomic data that delivers reliable predictive and diagnostic models, the set of genetic variants that are important for predictions (called a biosignature), and an estimate of the out-of-sample predictive power. This AutoML approach discovers variants with higher predictive performance compared to standard GWAS methods, computes an individual risk prediction score, generalizes to new, unseen data, is shown to better differentiate causal variants from other highly correlated variants, and enhances knowledge discovery and interpretability by reporting multiple equivalent biosignatures.Availability and implementationCode for this study is available at: https://github.com/mensxmachina/autoML-GWAS. JADBio offers a free version at: https://jadbio.com/sign-up/. SNP data can be downloaded from the EGA repository (https://ega-archive.org/). PRS data are found at: https://www.aicrowd.com/challenges/opensnp-height-prediction. Simulation data to study population structure can be found at: https://easygwas.ethz.ch/data/public/dataset/view/1/.
Novel progestogenic androgens for male contraception: design, synthesis, and activity of C7 α-substituted testosterone
Authors: Lee Min S , Bunin Deborah I , Furimsky Anna M , Nguyen Donna , Parman Toufan , Kim Kyuri , Rausch Linda , Lin Ming-Teh , Gupta Pranab , Brown Jill E , Kroopnick Jeffrey M , Blithe Diana L 
Published: September 2023

Abstract
Male contraceptive development has included use of testosterone (T) with or without a progestin or the use of a single molecule such as progestogenic androgens (PA) for suppression of testicular T production. Expanding upon the vast amount of data accumulated from nortestosterone (NT), NT analogs, and their prodrugs, a new series of PA, the C7 methyl, and ethyl α-substituted T analogs 7α-Methyltestosterone (7α-MT) and 7α-Ethyltestosterone (7α-ET), respectively, were hypothesized and designed to have superior androgenic and progestogenic activities when compared with parent T. Results from androgen receptor and progesterone receptor competitive binding and transcriptional activation assays showed favorable activities for these T analogs. Additionally, 7α-MT and 7α-ET were shown to be active substrates for aromatase in vitro, mitigating a potential negative impact on bone mineral density with long-term use. In conjunction with this observation, the diminished metabolism of these T analogs by 5α-reductase may reduce potential concerns for prostatic growth. In the Hershberger in vivo rat bioassay, 7α-MT and 7α-ET showed superior androgenic and anabolic activities as compared with T. These C7 α-substituted T analogs also showed clear progestogenic activity in the McPhail bioassay which evaluated endometrial glandular arborization in a rabbit model. The discovery of aromatizable molecules with reduced metabolism by 5α-reductase that have androgenic, anabolic, and progestogenic properties indicates that the core and/or prodrugs of 7α-MT and 7α-ET are promising molecules for further development as male contraceptive PAs.
Novel variant in CADM3 causes Charcot–Marie–Tooth disease
Authors: Yalcouyé Abdoulaye , Rebelo Adriana P , Cissé Lassana , Rives Lynette , Bamba Salia , Cogan Joy , Esoh Kevin , Diarra Salimata , Ezell Kimberly M , Taméga Abdoulaye , Guinto Cheick O , Dohrn Maike F , Hamid Rizwan , Fischbeck Kenneth H , Zuchner Stephan , Landouré Guida 
Published: September 2023

Abstract
CADM3 has been recently reported causing a rare axonal Charcot–Marie–Tooth disease in three independent Caucasian families carrying a recurrent change. We describe the first alternative causative mutation in CADM3 in a family from black African and also observed de novo in a patient of Caucasian ancestry. The disease inheritance was consistent with autosomal dominant and sporadic patterns, respectively. Eight patients and their relatives were enroled from both families. The mean age at diagnosis was 33.9 years, and walking difficulty was commonly the first symptom. Neurological examination showed distal muscle weakness and atrophy, sensory loss and foot and hand deformities. A high clinical variability was noted, but as seen in CADM3-associated neuropathy, symptoms were more pronounced in the arms in some patients. Nerve conduction studies showed no response in most of the examined nerves, and an axonal type of neuropathy, where recorded. Whole exome sequencing revealed a novel missense variant (c.1102G&gt;T; Gly368Cys) in CADM3, segregating with the disease. Functional analyses showed a significant decrease in CADM3-Gly368Cys protein levels in the membrane and major structural changes in its predicted secondary structure. Therefore, we extend the genotype spectrum of CADM3, underlining the need for genetic studies in underrepresented populations like in Africa.
Analysis of quantile graphs in EGC data from elderly and young individuals using machine learning and deep learning
Authors: Pineda Aruane M , Alves Caroline L , Möckel Michael , Toutain Thaise G L de O , Moura Porto Joel Augusto , Rodrigues Francisco A 
Published: September 2023

Abstract
Heart disease, also known as cardiovascular disease, encompasses a variety of heart conditions that can result in sudden death for many people. Examples include high blood pressure, ischaemia, irregular heartbeats and pericardial effusion. Electrocardiogram (ECG) signal analysis is frequently used to diagnose heart diseases, providing crucial information on how the heart functions. To analyse ECG signals, quantile graphs (QGs) is a method that maps a time series into a network based on the time-series fluctuation proprieties. Here, we demonstrate that the QG methodology can differentiate younger and older patients. Furthermore, we construct networks from the QG method and use machine-learning algorithms to perform the automatic diagnosis, obtaining high accuracy. Indeed, we verify that this method can automatically detect changes in the ECG of elderly and young subjects, with the highest classification performance for the adjacency matrix with a mean area under the receiver operating characteristic curve close to one. The findings reported here confirm the QG method’s utility in deciphering intricate, nonlinear signals like those produced by patient ECGs. Furthermore, we find a more significant, more connected and lower distribution of information networks associated with the networks from ECG data of the elderly compared with younger subjects. Finally, this methodology can be applied to other ECG data related to other diseases, such as ischaemia.
Digest: Urbanization shapes selection altering food webs
Authors: Williams Magie 
Published: September 2023

Abstract
How has urbanization altered the relationships between species and selection on phenotypes? To address this question, Palacio and Ordano measured trait and frugivore selection in blue passionflower (Passiflora caerulea) in three different localities. Their analysis revealed changes in avian selection with urbanization, which altered population phenotypes.
Quantifying assays: inhibition of signalling pathways of cancer
Authors: Anguelov Roumen , Manjunath G , Phiri Avulundiah E , Nyakudya Trevor T , Bipath Priyesh , C. Serem June , N. Hlophe Yvette 
Published: September 2023

Abstract
Inhibiting a signalling pathway concerns controlling the cellular processes of a cancer cell’s viability, cell division and death. Assay protocols created to see if the molecular structures of the drugs being tested have the desired inhibition qualities often show great variability across experiments, and it is imperative to diminish the effects of such variability while inferences are drawn. In this paper, we propose the study of experimental data through the lenses of a mathematical model depicting the inhibition mechanism and the activation-inhibition dynamics. The method is exemplified through assay data obtained from an experimental study of the inhibition of the chemokine receptor 4 (CXCR4) and chemokine ligand 12 (CXCL12) signalling pathway of melanoma cells. The quantitative analysis is conducted as a two step process: (i) deriving theoretically from the model the cell viability as a function of time depending on several parameters; (ii) estimating the values of the parameters by using the experimental data. The cell viability is obtained as a function of concentration of the inhibitor and time, thus providing a comprehensive characterization of the potential therapeutic effect of the considered inhibitor, e.g. $IC_{50}$ can be computed for any time point.
Interspecific Variation in the Inner Ear Maculae of Sharks
Authors: Sauer Derek J , Yopak Kara E , Radford Craig A 
Published: September 2023

SynopsisThere is well-documented diversity in the organization of inner ear hair cells in fishes; this variation is thought to reflect the differing functional requirements of species across a range of ecological niches. However, relatively little is known about interspecific variation (and its potential ecological implications) in the number and density of inner ear hair cells in elasmobranchs (sharks, skates, and rays). In this study, we quantified inner ear hair cells in the saccule, lagena, utricle, and macula neglecta of 9 taxonomically and ecologically distinct shark species. Using phylogenetically informed comparative approaches, sharks that feed in the water column had significantly greater hair cell density and total number of hair cells in the lagena and macula neglecta (i.e., vertically oriented maculae) compared to species that feed primarily on the seafloor. In addition, sharks within Carcharhinidae seemingly possess a specialized macula neglecta compared to other shark species. Overall, findings suggest that, similar to bony fishes, there is considerable variation in hair cell organization of shark inner ears, which may be tied to variation in ecology and/or specialized behaviors between different species.
Food Insecurity and Unrest Participation: Evidence from Johannesburg, South Africa
Authors: Rudolfsen Ida 
Published: September 2023

AbstractThis study assesses the claim that food insecurity leads to participation in unrest. I argue that insecure access to food can provide a motivational force to engage in urban unrest. But individuals must also have the capacity to partake in collective action, and acute food insecurity may undermine mobilization potential. Further, food insecurity is a mundane and widespread grievance often seen as an apolitical issue. I therefore suggest that organizational networks could facilitate the occurrence of unrest, as they provide both an existing mobilizing structure and the potential to politicize an individual-level grievance. The article explores the relationship between food access and unrest participation on the individual level in the context of Johannesburg, South Africa. I find that food insecurity increases the likelihood of unrest participation and that some types of organizational networks are catalysts of such effects.
The 2023 Impact of Inflammatory Bowel Disease in Canada: The Influence of Sex and Gender on Canadians Living With Inflammatory Bowel Disease
Authors: Targownik Laura E , Bollegala Natasha , Huang Vivian W , Windsor Joseph W , Kuenzig M Ellen , Benchimol Eric I , Kaplan Gilaad G , Murthy Sanjay K , Bitton Alain , Bernstein Charles N , Jones Jennifer L , Lee Kate , Peña-Sánchez Juan-Nicolás , Rohatinsky Noelle , Ghandeharian Sara , Davis Tal , Weinstein Jake , Im James H B , Jannati Nazanin , Khan Rabia , Matthews Priscilla , Jones May Tyrel , Tabatabavakili Sahar , Jogendran Rohit , Hazan Elias , Browne Mira , Meka Saketh , Vukovic Sonya , Jogendran Manisha , Hu Malini , Osei Jessica Amankwah , Wang Grace Y , Sheekha Tasbeen Akhtar , Dahlwi Ghaida , Goddard Quinn , Gorospe Julia , Nisbett Cyanne , Gertsman Shira , Sousa James , Morganstein Taylor , Stocks Taylor , Weber Ann , Seow Cynthia H 
Published: September 2023

Abstract
Sex (the physical and physiologic effects resulting from having specific combinations of sex chromosomes) and gender (sex-associated behaviours, expectations, identities, and roles) significantly affect the course of inflammatory bowel disease (IBD) and the experience of living with IBD. Sex-influenced physiologic states, like puberty, the menstrual cycle, pregnancy, and andropause/menopause may also impact and be impacted by IBD.
While neither Crohn’s disease nor ulcerative colitis is commonly considered sex-determined illnesses, the relative incidence of Crohn’s disease and ulcerative colitis between males and females varies over the life cycle. In terms of gender, women tend to use healthcare resources at slightly higher rates than men and are more likely to have fragmented care. Women are more commonly prescribed opioid medications and are less likely than men to undergo colectomy. Women tend to report lower quality of life and have higher indirect costs due to higher rates of disability. Women are also more likely to take on caregiver roles for children with IBD. Women with IBD are more commonly burdened with adverse mental health concerns and having poor mental health has a more profound impact on women than men.
Pregnant people with active IBD have higher rates of adverse outcomes in pregnancy, made worse in regions with poor access to IBD specialist care. The majority of individuals with IBD in Canada do not have access to a pregnancy-in-IBD specialist; access to this type of care has been shown to allay fears and increase knowledge among pregnant people with IBD.
The 2023 Impact of Inflammatory Bowel Disease in Canada: Treatment Landscape
Authors: Murthy Sanjay K , Weizman Adam V , Kuenzig M Ellen , Windsor Joseph W , Kaplan Gilaad G , Benchimol Eric I , Bernstein Charles N , Bitton Alain , Coward Stephanie , Jones Jennifer L , Lee Kate , Peña-Sánchez Juan-Nicolás , Rohatinsky Noelle , Ghandeharian Sara , Sabrie Nasruddin , Gupta Sarang , Brar Gurmun , Khan Rabia , Im James H B , Davis Tal , Weinstein Jake , St-Pierre Joëlle , Chis Roxana , Meka Saketh , Cheah Eric , Goddard Quinn , Gorospe Julia , Kerr Jack , Beaudion Kayla D , Patel Ashley , Russo Sophia , Blyth Jonathan , Blyth Stephanie , Charron-Bishop Diane , Targownik Laura E 
Published: September 2023

Abstract
The therapeutic landscape for inflammatory bowel disease (IBD) has changed considerably over the past two decades, owing to the development and widespread penetration of targeted therapies, including biologics and small molecules. While some conventional treatments continue to have an important role in the management of IBD, treatment of IBD is increasingly moving towards targeted therapies given their greater efficacy and safety in comparison to conventional agents. Early introduction of these therapies—particularly in persons with Crohn’s disease—combining targeted therapies with traditional anti-metabolite immunomodulators and targeting objective markers of disease activity (in addition to symptoms), have been shown to improve health outcomes and will be increasingly adopted over time. The substantially increased costs associated with targeted therapies has led to a ballooning of healthcare expenditure to treat IBD over the past 15 years. The introduction of less expensive biosimilar anti-tumour necrosis factor therapies may bend this cost curve downwards, potentially allowing for more widespread access to these medications. Newer therapies targeting different inflammatory pathways and complementary and alternative therapies (including novel diets) will continue to shape the IBD treatment landscape. More precise use of a growing number of targeted therapies in the right individuals at the right time will help minimize the development of expensive and disabling complications, which has the potential to further reduce costs and improve outcomes.
The 2023 Impact of Inflammatory Bowel Disease in Canada: COVID-19 and IBD
Authors: Kaplan Gilaad G , Kuenzig M Ellen , Windsor Joseph W , Bernstein Charles N , Bitton Alain , Coward Stephanie , Jones Jennifer L , Lee Kate , Murthy Sanjay K , Targownik Laura E , Peña-Sánchez Juan-Nicolás , Ghandeharian Sara , Rohatinsky Noelle , Weinstein Jake , Jones May Tyrel , Browne Mira , Jannati Nazanin , Tabatabavakili Sahar , Im James H B , Meka Saketh , Vukovic Sonya , Davis Tal , Goddard Quinn , Gorospe Julia , Stocks Taylor , Caplan Léa , Kanaan Najla , Stuart Daniel , Ramsay Tesa , Robinson Kelly J , Charron-Bishop Diane , Benchimol Eric I 
Published: September 2023

Abstract
The COVID-19 pandemic had a monumental impact on the inflammatory bowel disease (IBD) community. At the beginning of the pandemic, knowledge on the effect of SARS-CoV-2 on IBD was lacking, especially in those with medication-suppressed immune systems. Throughout the pandemic, scientific literature exponentially expanded, resulting in clinical guidance and vaccine recommendations for individuals with IBD. Crohn’s and Colitis Canada established the COVID-19 and IBD Taskforce to process and communicate rapidly transforming knowledge into guidance for individuals with IBD and their caregivers, healthcare providers, and policy makers. Recommendations at the onset of the pandemic were based on conjecture from experience of prior viruses, with a precautionary principle in mind. We now know that the risk of acquiring COVID-19 in those with IBD is the same as the general population. As with healthy populations, advanced age and comorbidities increase the risk for severe COVID-19. Individuals with IBD who are actively flaring and/or who require high doses of prednisone are susceptible to severe COVID-19 outcomes. Consequently, sustaining maintenance therapies (e.g., biologics) is recommended. A three-dose mRNA COVID-19 vaccine regimen in those with IBD produces a robust antibody response with a similar adverse event profile as the general population. Breakthrough infections following vaccine have been observed, particularly as the virus continues to evolve, which supports receiving a bivalent vaccine booster. Limited data exist on the impact of IBD and its therapies on long-term outcomes following COVID-19. Ongoing research is necessary to address new concerns manifesting in those with IBD throughout the evolving pandemic.
Algorithmic Personalized Pricing with the Right to Explanation
Authors: Zhao Zeyu 
Published: September 2023

Abstract
Personalized pricing by algorithms has been widely deployed by digital platforms. Although this strategy provides economic efficiencies and benefits consumers, it precipitates discriminatory, exploitative, and exclusionary effects on the market. If massive market power and certain information asymmetry exist, this pricing behavior could be illegal as the negatives could outweigh the positives. The negatives could nevertheless not be fully addressed by current ex-post and ex-ante antitrust, consumer protection, and anti-discrimination approaches because the sloping pricing information between platforms and consumers based on data will not be effectively rebalanced considering these approaches. Data protection measures should be underlined, despite the flaws of some data rights. This article shows how the right to explanation as a synthetic right of data protection mitigates the damaging effects by providing consumers with the access to the result of algorithmic decision-making to optimize the information distribution, despite the application limits due to technological and cognitive immatureness of ‘explanation’.