cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Antimicrobial resistance dissemination driven by Klebsiella pneumoniae: the role of high-risk clones and high-risk plasmids
Creators: name: Andrey, Diego Olivier
Publisher: name: Université de Genève
Year: 2023
Subjects: info:eu-repo/classification/ddc/616
Plasmid
Klebsiella pneumoniae
ST258
ST16
ST11
Clones
Molecular epidemiology
Whole genome sequencing
AMR
WGS
Gram-negative

description:
Background. Carbapenem-resistant ESKAPE pathogen K. pneumoniae plays a critical role driving antimicrobial resistance dissemination. This is mainly mediated by two general fluxes, clonal spread of specific K. pneumoniae high-risk genetic lineages, and horizontal gene transfer through mobile genetic elements such as plasmids. Specific clones, such as ST258 and ST15, have successfully established themselves worldwide; others, as ST307 or ST16 are emerging. Among plasmids some backbones are closely linked to specific carbapenemase dissemination (such as IncFIB-pQIL-KPC and IncL-OXA-48), while other are ubiquitous. Another growing concern is plasmid-mediated hypervirulence, originally associated to distinct clones, converging into the same lineages as carbapenem resistance and vice-versa. Finally, when these lineages acquire last resort colistin or aminoglycoside resistance, it further complicates the epidemiological scenario and clinical management.

Results and Scientific publications. Five publications are presented here. Four are based on a retrospective cohort of 165 patients suffering bloodstream infections due to KPC-producing K. pneumoniae in a tertiary hospital in Latin America. The clinical and molecular description, using bacterial whole-genome sequencing (WGS), is provided. It showed a polyclonal distribution mainly driven by Clonal Complex 258 (ST258, ST11, ST437), the emergence of a ST16 lineage associated to high 30-day crude mortality, and minority cases provoked by other clones including ST15 and ST307. The scientific publications shown here further dissect the molecular features of carbapenemase-bearing plasmids including a unusual IncQ1 plasmid, horizontal spread of a 16SrRNA methylase, as well as chromosomally mediated colistin resistance in K. pneumoniae (sensu stricto) and K. pneumoniae complex subspecies K. variicola.

Discussion. These studies allowed to highlight the importance of the epidemic clone ST258 and its association with aminoglycoside and colistin resistance, and showed how horizontally-acquired and chromosomally vertically-encoded mechanisms co-exist. These publications also identify and describe an emergent ST16 lineage, associated with increased mortality; ST16 was subsequently described in the context of fatal outbreaks in Asia. These studies underscore how instrumental WGS has become to monitor these clonal dissemination patterns, and long-read sequencing technologies, thanks to recent advances, can now address the issue of plasmid transmission and their role in chains of transmission in healthcare settings. Plasmid monitoring is poised to become an important parameter to guide Infection Prevention and Control (IPC) practices.
Contribution of neuroradiology in the setting of multidisciplinary approach of disease
Creators: name: Fitsiori, Aikaterini
Publisher: name: Université de Genève
Year: 2023
Subjects: info:eu-repo/classification/ddc/616.0757
Neuroradiologie

description:
This thesis comprises five publications illustrating aspects of the application of neuroimaging studies in different kinds of pathologies and their contribution to the diagnostic approach in adults and the paediatric population. The aim of this selected work is to improve awareness of the numerous applications of neuroradiology, in order to achieve the best medical outcomes for patients. The benefit of choosing the appropriate neuroimaging modality under expert guidance is more likely to lead to a precise diagnosis, resulting in timely and appropriate treatment.
Symmetry, vol 9/2017
Creators: name: Smarandache, Florentin
name: Ye, Jun
Publisher: name: figshare
Year: 2018
Subjects: classificationCode: 490401
subject: Algebra and number theory

description: Neutrosophic sets and logic are generalizations of fuzzy and intuitionistic fuzzy sets and logic. Neutrosophic sets and logic are gaining significant attention in solving many real life decision making problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and indeterminacy. They have been applied in computational intelligence, multiple criteria decision making, image processing, medical diagnoses, etc.
Online Supplementary Materials and Method from The assembly of ant-farmed gardens: mutualism specialization via host broadening
Creators: name: Chomicki, Guillaume
name: Janda, Milan
name: Renner, Susanne S.
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences

description: Ant-gardens (AGs) are ant/plant mutualisms in which ants farm epiphytes in return for nest space and food rewards. They occur in the Neotropics and Australasia, but not in Africa, and their evolutionary assembly remains unclear. We here use phylogenetic frameworks for important AG lineages in Australasia, namely the ant genus Philidris and domatium-bearing ferns (Lecanopteris) and flowering plants in the Apocynaceae (Hoya and Dischidia) and Rubiaceae (Myrmecodia, Hydnophytum, Anthorrhiza, Myrmephytum and Squamellaria) to trace AG assembly in time and space. Our analyses revealed that in these clades, diaspore dispersal by ants evolved at least 13 times, five times in the Late Miocene and Pliocene in Australasia and seven times during the Pliocene in Southeast Asia, after Philidris ants had arrived there, with subsequent dispersal between these two areas. A uniquely specialized AG system evolved in Fiji at the onset of the Quaternary. The farming of other epiphytes that do not offer nest spaces in the same AGs suggests that a broadening of the ants' plant host spectrum drove the evolution of additional domatium-bearing AG-epiphytes by selecting on pre-adapted morphological traits. Consistent with this, we found a statistical correlation between the evolution of diaspore dispersal by ants and domatia in all three lineages. Our study highlights how host broadening by a symbiont has led to new farming mutualisms.
MOESM1 of Identification of serum proteins AHSG, FGA and APOA-I as diagnostic biomarkers for gastric cancer
Creators: name: Shi, Feiyu
name: Wu, Hong
name: Qu, Kai
name: Sun, Qi
name: Li, Fanni
name: Shi, Chengxin
name: Li, Yaguang
name: Xiong, Xiaofan
name: Qin, Qian
name: Yu, Tianyu
name: Jin, Xin
name: Cheng, Liang
name: Wei, Qingxia
name: Li, Yingchao
name: She, Junjun
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 1: Supplementary material figures S1â S10.
АДАПТИВНІ МЕТОДИ ОЦІНЮВАННЯ КОНЦЕНТРАЦІЇ РИНКУ
Creators: name: Титаренко, Валерій
Publisher: name: Zenodo
Year: 2024
Subjects: конкуренція, структура ринку, ринкова влада, конкурентоспроможність підприємств, рівень концентрації ринку, вимірювання концентрації ринку, коефіцієнт Джині.

description: Найбільш поширені формули оцінки ринкових структур, а саме: коефіцієнт концентрації та коефіцієнт Герфіндаля-Гіршмана, набули відомості, насамперед завдяки свій простоті в розрахунку та зрозумілості в сприйнятті. Саме вони використовуються на практиці в антимонопольному законодавстві ринкових економік, в тому числі Європейського Союзу та Сполучених Штатів Америки. Інші методи прямої оцінки концентрації ринку подібно до цих двох є відносно простими та не гнучкими.

Визначення типу ринку, складності його структури зазвичай не є ціллю наукового дослідження, це, як правило, тільки один з початкових його етапів. Для повного та глибокого вивчення ринку, його різних типів необхідно застосовувати більш спеціалізовані та ґрунтовні методи. Щоб охопити велике різноманіття об’єктів дослідження ринку та здобути глибші характеристики пропонується використовувати адаптивні методи оцінювання ринкових структур. Адаптивні методи мають інакше позиціонування, вони більш складні у прикладному використанні, але дають змогу отримати більше інформації щодо ринку.

Головною ознакою відмінності адаптивних методів від прямих методів дослідження ринку є можливість «налаштування» окремих параметрів в залежності від мети дослідження, типу ринку, рівня концентрації.

Адаптивні методи можуть допомогти під час аналізу часових рядів, пошуку «ядра» ринку, вирівнювання дослідження різноструктурованих ринків, вивчення ринку незалежно від рівня концентрації, виявлення ознак змов ринкових учасників.

Поряд з тим слабкою стороною даних методів є високі вимоги до фахівців, які їх використовують, зокрема в галузі економіки, математики та статистики. Для прикладу коефіцієнт Джині чи U індекс, потребують не тільки вибору окремих параметрів для розрахунку, а вибору окремих формул, рівнянь чи способів обчислення.

В статті наведено головні адаптивні методи оцінки концентрації ринкової структури, підготовлено порівняльну таблицю із рекомендаціями щодо їх застосування, запропоновано уточнену редакцію деяких формул.
Additional file 1: of Position-specific intron retention is mediated by the histone methyltransferase SDG725
Creators: name: Wei, Gang
name: Liu, Kunpeng
name: Shen, Ting
name: Shi, Jinlei
name: Liu, Bing
name: Han, Miao
name: Peng, Maolin
name: Fu, Haihui
name: Song, Yifan
name: Zhu, Jun
name: Dong, Aiwu
name: Ni, Ting
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S1. The quantification of H3K36 methylation in 725Ri-1. and WT plants. Figure S2. Differential gene expression between 725Ri-1. and WT rice. Figure S3. Accumulative plot of up-regulated (725Ri-1._IRI_up) and down-regulated (725Ri-1._IRI_down) IR events with different intron length coverage. Figure S4. Distribution of up-regulated (red.) and down-regulated (blue.) intron retention (IR) events between 725Ri-1. and wild-type (WT) rice (a) and between 708Ri-1. and WT (b). Figure S5. Schematic diagram illustrating the way to transform the H3K36 methylation changes between the 725Ri-1. and wild-type plants at individual gene level. Figure S6. Box plot for levels of H3K36 methylations at IRI-up or IRI-down introns. Figure S7. qPCR validation of quality of cellular fractionation in wild-type rice. Figure S8. Box plot for expression level of transcripts with premature termination codon. Figure S9. Box plot of gene expression before and after cycloheximide (CHX) treatment in either wild-type or 725Ri-1. rice. Figure S10. H3K36 methylations associate with gene expression levels. Figure S11. Distribution of up-regulated (red.) and down-regulated (blue.) intron retention (IR) events in genes with no obvious changes (≤ 2-fold) in total levels of H3K36me2 (a) or H3K36me3 (b). Figure S12. Box plot for intron length in two groups of introns by distinct methods in calculating the degree of intron retention. Figure S13. Box plot for GC percentage in two groups of introns. Figure S14. Box plot for maximum entropy score of 5′ splice site (a) and 3′ splice site (b) in two groups of introns. Figure S15. Comparison of H3K36me2/me3 distribution across gene body between rice (a) and Arabidopsis (b). (DOCX 2596 kb)
Electronic supplementary material - continent no legend, figure 1 from Life-history evolution in ants: the case of Cardiocondyla
Creators: name: Heinze, Jürgen
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: Phylogeny of the ant genus Cardiocondyla and reconstruction of the most parsimonious ancestral geographic origin of the genus (Southeast Asia: green; Wallacea / Australia: blue; Sub-Saharan Africa: yellow; Madagascar: red; Palearctic: black; unknown: hatched grey). For the phylogenetic analysis previously published data sets (1415bp of CO I / CO II including tLeu, [1, 2, 3]) were extended by adding complete or partial sequences of several additional taxa. Sequences were aligned in BioEdit 7.2.3 [4] using the Clustal W algorithm and ambiguous regions were manually corrected. As large gaps appeared between positions 816 and 838 this part of the sequences was deleted to facilitate alignment. The data were analyzed with MrBayes version 3.2.2 [5] using GTR+G+I as DNA model and the default settings of four Markov chains (three heated, one cold). The heating parameter was set at 0.2. Each analysis was conducted with a Markov Chain Monte Carlo method with 3,000,000 generations and sampled every 1000 generations. The consensus tree was created discarding the first 25% of the sampled trees (the burn-in). The most parsimonious ancestral character states were estimated by Mesquite, 3.0.4 [6]. 1. Heinze J, Trindl A, Seifert B, Yamauchi K. 2005 Evolution of male morphology in the ant genus Cardiocondyla. Mol. Phylogenet. Evol. 37, 278–288. (doi: 10.1016/j.ympev.2005.04.005) 2. Oettler J, Suefuji M, Heinze J. 2010. The evolution of alternative reproductive tactics in male Cardiocondyla ants. Evolution 64, 3310–3317. (doi: 10.1111/j.1558-5646.2010.01090.x) 3. Heinze J, Seifert B, Zieschank V. in press Massacre of the innocents in Cardiocondyla thoracica: manipulation by adult ant males incites workers to kill their immature rivals. Entomol. Sci. (doi: 10.1111/ens.12194) 4. Hall TA. 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/96/NT. Nucl. Acids Symp. Ser. 41, 95–98. 5. Huelsenbeck JP, Ronquist F. 2001 MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17, 745–755. 6. Maddison WP, Maddison DR. 2015 Mesquite: a modular system for evolutionary analysis. Version 3.04. http://mesquiteproject.org
Additional file 2: of Position-specific intron retention is mediated by the histone methyltransferase SDG725
Creators: name: Wei, Gang
name: Liu, Kunpeng
name: Shen, Ting
name: Shi, Jinlei
name: Liu, Bing
name: Han, Miao
name: Peng, Maolin
name: Fu, Haihui
name: Song, Yifan
name: Zhu, Jun
name: Dong, Aiwu
name: Ni, Ting
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
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: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology

description: Table S1. Summary of the RNA-seq libraries. Table S2. Alternative splicing events discovered between rice RNA-seq data sets in this study compared with annotation by using SplAdder. Table S3. Primers used for validating intron-retention events. Table S4. The numbers of IRI changed introns and genes. Table S5. Summary of the ChIP-seq libraries. Table S6. Primers used to validate intron retention in the same gene by qRT-PCR and those used to validate H3K36me2 by ChIP-PCR. Table S7. Number of retained introns for previously identified IRI changed introns in nucleus or cytoplasm. Table S8. Expression changes of annotated rice splicing factors in our data. Table S9. Detailed information for ChIP-seq and RNA-seq data sets. (DOCX 43Â kb)
Table S1 from Phytoplankton growth rate modelling: can spectroscopic cell chemotyping be superior to physiological predictors?
Creators: name: Fanesi, Andrea
name: Wagner, Heiko
name: Wilhelm, Christian
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Environmental Science
subject: Plant Biology

description: Percentage of variance explained by each single principal component (PC) of the PLSR model. The explained variance is reported both for the X (efficiency of light utilization) and for the Y (growth rate) matrix.
Supporting Information from Dictating anisotropic electric conductivity of a transparent copper nanowire coating by the surface structure of wood
Creators: name: Guo, Huizhang
name: Büchel, Martin
name: Li, Xing
name: Wäckerlin, Aneliia
name: Chen, Qing
name: Burgert, Ingo
Publisher: name: The Royal Society
Year: 2018

description: In this article, a robust, air-stable, flexible and transparent copper (Cu) nanowire (NW) network coating on the surface of the wood is presented, based on a fusion welding of the Cu NWs by photonic curing. Thereby, an anisotropic conductivity can be achieved, which is originating from the structural organization of the wood body and its surface. Furthermore, the Cu NWs are protected from oxidation or wear by a commercially available paraffin wax—polyolefin, which also results in surface water repellency. The developed processing steps present a facile and flexible routine for applying Cu NW transparent conductors to abundant biomaterials and solve current manufacturing obstacles for corrosion-resistant circuits while keeping the natural appearance of the substrate. It may open a venue for more extensive utilization of materials from renewable resources such as wood for electronic devices in smart buildings or mobility applications.
Supplementary Information from Earliest filter-feeding pterosaur from the Jurassic of China and ecological evolution of Pterodactyloidea
Creators: name: Zhou, Chang-Fu
name: Gao, Ke-Qin
name: Hongyu Yi
name: Jinzhuang Xue
name: Quanguo Li
name: Fox, Richard C.
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Pterosaurs were a unique clade of flying reptiles that were contemporaries of dinosaurs in Mesozoic ecosystems. The Pterodactyloidea as the most species-diverse group of pterosaurs dominated the sky during Cretaceous time, but earlier phases of their evolution remain poorly known. Here, we describe a 160 Myr filter-feeding pterosaur from western Liaoning, China, representing the geologically oldest record of the Ctenochasmatidae, a group of exclusive filter feeders characterized by an elongated snout and numerous fine teeth. The new pterosaur took the lead of a major ecological transition in pterosaur evolution from fish-catching to filter-feeding adaptation, prior to the Tithonian (145–152 Myr) diversification of the Ctenochasmatidae. Our research shows that the rise of ctenochasmatid pterosaurs was followed by the burst of eco-morphological divergence of other pterodactyloid clades, which involved a wide range of feeding adaptations that considerably altered the terrestrial ecosystems of the Cretaceous world.
Supplementary Material from Ant circadian activity associated with brood care type
Creators: name: Fujioka, Haruna
name: Abe, Masato S.
name: Fuchikawa, Taro
name: Tsuji, Kazuki
name: Shimada, Masakazu
name: Okada, Yasukazu
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: Supplementary Methods and Figs. S1 S2 S3
The ecological public goods game (EPGG) predicts many features of the yeast sucrose system. from Cooperators trade off ecological resilience and evolutionary stability in public goods games
Creators: name: Rauch, Joseph
name: Kondev, Jane
name: Sanchez, Alvaro
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60114 Systems Biology
subject: 60113 Synthetic Biology

description: A comparison between growth rates predicted by the Ecological Public Goods Game (EPGG) [1,2] on the left, and a reproduced plot from Sanchez and Gore [3] (Copyright 2013 CC-BY) showing experimental growth rates of yeast on the right. In the experiments, cooperators are haploid yeast cells that contain and express the “public good” gene SUC2, which codes for an enzyme that extracellularly breaks down sucrose into glucose and fructose. Freeloaders have a null allele mutant of this gene, and thus enjoy the fructose and glucose produced by the cooperators, without paying the metabolic costs associated to it. Both the prediction by the EPGG and the experimental observations indicate an allee effect, with low growth rates at high and low population densities, and high growth rates at intermediate population densities.
Myeloproliferative neoplasms in young patients: clinical features and specific management
Creators: name: Beauverd, Yan
Publisher: name: Université de Genève
Year: 2024
Subjects: info:eu-repo/classification/ddc/616

description: Myeloproliferative neoplasms (MPN) are a group of clonal haematopoietic stem cell diseases usually associated with increased production of blood cells (red blood cells, white blood cells, and platelets), splenomegaly, and other symptoms (fatigue, pruritus, night seat, early satiety, abdominal discomfort, weight loss, and recurrent fever). In addition, the main complications of MPN involve thrombotic (venous and arterial) events and less frequent progression to acute leukaemia and death. Usually, MPN are diagnosed during the 6th decade, but it is now wellrecognised that a small proportion of patients (<20%) are diagnosed below the age of 40 years. The diagnosis of MPN in young patients, in addition to the extension of life expectancy, has revealed emergent questions regarding thrombotic risk, progression, disease evolution, and pregnancies. Data on young MPN are limited, and this original thesis presents three papers illustrating two aspects of this population. The first two papers focus on the description of this population regarding characteristics of diagnosis, management, and prognosis. Moreover, the first paper presents the largest real-world study of young patients diagnosed with MPN and provides reliable information on this population. Finally, the third paper focused on the management of pregnancy in this population. MPN are associated with a high risk of foetal and maternal complications. The use of interferon is part of the treatment to reduce complications during pregnancy. This paper presents the first and largest series of patients treated with peginterferon alfa-2a during pregnancy, a more recently developed form of interferon with better tolerance than the previously used interferon alfa-2a. This selected work is put into perspective with the current knowledge of this rare population of young patients with MPN and its management.
Multimodal Immunomonitoring of Hematopoietic Stem Cell Transplantation and Cellular Therapies for Hematological Malignancies
Creators: name: Simonetta, Federico
Publisher: name: Université de Genève
Year: 2023
Subjects: info:eu-repo/classification/ddc/616

description:
Allogeneic hematopoietic stem cell transplantation (HSCT) and other cellular therapies are a broadly used therapeutic strategy employed against a wide range of hematological malignancies. However, these therapies are associated with significant toxicities and their efficacy is still not optimal. Our ability to study the immune system at steady state, during physiological responses and in immunopathological diseases greatly increased during the last decades thanks to the technological advances coming from different fields including cytometry, genomics and molecular imaging. In this work, we will discuss the application of these techniques to the study of the immune system after allogeneic HSCT and cellular therapies. In particular, we will see how these approaches can be applied to the understanding of new diagnostic and therapeutic strategies and exploited for their optimization. We will discuss the development of molecular imaging strategies for the immunomonitoring of T cells during GvHD. We will apply the use of multiple genomic techniques to the understanding of GvHD suppression by immune-regulatory T cells, namely regulatory T cells (Treg) and invariant natural killer T (iNKT) cells. We will study the immunomodulatory effects of engineered CAR iNKT cells on host immune-cells leading to an amplification of their antitumoral effect. We will apply high-throughput T cell receptor (TCR) sequencing to the understanding of the immunological defects during anti-SARS-CoV-2 responses in allogeneic HSCT. Finally, we will discuss the future applications of this acquired knowledge to improve the efficacy and safety of allogeneic HSCT and cellular therapies.
MOESM1 of Heterologous expression of Spathaspora passalidarum xylose reductase and xylitol dehydrogenase genes improved xylose fermentation ability of Aureobasidium pullulans
Creators: name: Guo, Jian
name: Huang, Siyao
name: Chen, Yefu
name: Guo, Xuewu
name: Xiao, Dongguang
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Plant Biology

description: Additional file 1: Table S1. Primers used for genetic manipulation of A. pullulans var. melanogenum CBS 110374.
Theory, mathematical appendix, and figure captions from Cooperators trade off ecological resilience and evolutionary stability in public goods games
Creators: name: Rauch, Joseph
name: Kondev, Jane
name: Sanchez, Alvaro
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60114 Systems Biology
subject: 60113 Synthetic Biology

description: Microbial populations often rely on the cooperative production of extracellular ‘public goods’ molecules. The cooperative nature of public good production may lead to minimum viable population sizes, below which populations collapse. In addition, ‘cooperator’ public goods producing individuals face evolutionary competition from non-producing mutants, or ‘freeloaders’. Thus, public goods cooperators should be resilient not only to the invasion of freeloaders, but also to ecological perturbations that may push their populations below a sustainable threshold. Through a mathematical analysis of the Ecological Public Goods Game, we show that game parameters that improve the cooperating population's stability to freeloader invasion also lead to a low ecological resilience. Complex regulatory strategies mimicking those used by microbes in nature may allow cooperators to beat this trade-off and become evolutionary stable to invading freeloaders while at the same time maximizing their ecological resilience. Our results thus identify the coupling between resilience to evolutionary and ecological challenges as a key factor for the long-term viability of public goods cooperators.
Qualitative assessment of the control arm in oncology randomized clinical trials
Creators: name: Olivier, Timothée
Publisher: name: Université de Genève
Year: 2024
Subjects: info:eu-repo/classification/ddc/616
Randomized controlled trials (RCTs)
Control arm
Evaluation framework

description:
This thesis focuses on the pivotal, yet frequently underappreciated aspect of randomized controlled trials (RCTs) – the control arm. Our research highlights the critical importance of rigorously designing and implementing this component within RCTs.

The rise of the randomized controlled trial as one of the most robust methods for estimating the effect of a medical intervention is born out of a long history of ideas, particularly in statistical and medical sciences. Randomization has three main advantages: balancing potential confounding factors (known and unknown), avoiding or at least limiting the issue of analytic flexibility, and finally determining a time-zero - the time of randomization - which avoids numerous biases which can affect observational studies. The principle of equipoise, and uncertainty about the result of an experiment, is crucial as it justifies conducting a randomized trial. Estimates suggest that the frequency of suboptimal control arms, within modern clinical trials in oncology, varies from 11% to 17%.

However, based on our works, this proportion may be underestimated, as no systematic framework has been applied to assess for control arm’s quality. Beyond factors classically assessed for, we described specific features which can unfavorably affect the control arm. For instance, when the control arm is left to the “physician's discretion”, this choice may seem optimal, yet we show that it was restricted in 85% of cases, and such restriction can deprive the patients of essential treatment options. We also demonstrate that the treatment duration in the control arm, when compared to the duration in previous clinical trials in identical settings, can decrease. This raises the question of whether investigators are less incentivized to promote the control treatment, particularly in open-label trials. Lastly, we show that a majority (55%) of head- to-head registration clinical trials in oncology have dose modification rules or supportive care usage that penalize the control arm.

In the conclusion, we higlight that the qualitative analysis of the control arm is not taken into consideration by professional society evaluation scores (such as ASCO and ESMO) and other systematic evaluation methodologies from the evidence-based medicine (EBM) movement. We propose an evaluation framework that could prove beneficial to clinicians, patients, Health Technology Assessment (HTA) agencies, and regulators.
Variation of diameter of V3 for 30 min from Variation in wall shear stress in channel networks of zebrafish models
Creators: name: Woorak Choi
name: Kim, Hye Mi
name: Sungho Park
name: Eunseop Yeom
name: Junsang Doh
name: Lee, Sang Joon
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Biological Engineering
subject: 110601 Biomechanics
subject: FOS: Health sciences

description: Variation of the diameter of V3 for 30 minutes after blocking ISV2. (n=5)
Additional file 1: of The dual blockade of MET and VEGFR2 signaling demonstrates pronounced inhibition on tumor growth and metastasis of hepatocellular carcinoma
Creators: name: Zhang, Yu
name: Gao, Xiaomei
name: Zhu, Ying
name: Kadel, Dhruba
name: Sun, Haoran
name: Chen, Jing
name: Luo, Qin
name: Sun, Haoting
name: Yang, Luyu
name: Yang, Jing
name: Sheng, Yuanyuan
name: Zheng, Yan
name: Zhu, Kejin
name: Dong, Qiongzhu
name: Qin, Lunxiu
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Astronomical and Space Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Table S1. Primary Antibodies for WB, IF and IHC. Table S2. Clinicopathological characteristics of HCC patients for analyzing the clinical significance of MET mRNA expression (n = 109). Table S3. Clinicopathological characteristics of HCC patients for detecting MET protein expression by IHC staining(n = 122). Table S4. Clinicopathological characteristics of HCC Patients for isolating primary HCC cells (n = 16). Table S5. Univariate and multivariate analyses of factors associated with OS and TTR. Table S6. Pharmacokinetic characteristics of NZ001 in mouse. Table S7. The analysis of correlation between MET gene amplification and MET protein expression in the 16 HCC samples. Table S8. The analysis of correlation between MET gene amplification and P-MET protein expression in the 16 HCC samples. (DOCX 39 kb)
Will new technologies be able to reduce the rate of post-operative hypoparathyroidism in thyroid surgery?
Creators: name: Demarchi, Marco Stefano
Publisher: name: Université de Genève
Year: 2024
Subjects: info:eu-repo/classification/ddc/617

description: Hypoparathyroidism is the most frequent complication in thyroid surgery. Technology improvements in medical field tends to help reducing complication in surgery and in recent years fluorescence-guided surgery technology has been largely developed and has been used in many different surgical fields. In endocrine surgery a recent but actively researched field is near infrared fluorescence imaging and several groups have each detailed their methodology and reported on the observed utility of their approach. Overall fluorescence-guided surgery has been shown to assist in lowering the postoperative hypoparathyroidism in thyroid surgery. The objective of the current review is to give an overview of the different fluorescence imaging techniques and applications in order demonstrate the value of fluorescence imaging in protecting parathyroid glands during thyroid surgery.
Additional file 1: of Use of integrated imaging and serum biomarker profiles to identify subclinical dysfunction in pediatric cancer patients treated with anthracyclines
Creators: name: Toro-Salazar, Olga
name: Lee, Ji
name: Zellars, Kia
name: Perreault, Paige
name: Mason, Kathryn
name: Wang, Zhu
name: Hor, Kan
name: Gillan, Eileen
name: Zeiss, Caroline
name: Gatti, Daniel
name: Davey, Brooke
name: Kutty, Shelby
name: Liang, Bruce
name: Spinale, Francis
Publisher: name: figshare
Year: 2018
Subjects: Biochemistry
Space Science
Medicine
Cell Biology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Developmental Biology
Cancer

description: Normal Control Cohort. (DOCX 22 kb)
Supplementary Material from Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification
Creators: name: Gaitán-Espitia, Juan Diego
name: Marshall, Dustin
name: Dupont, Sam
name: Bacigalupe, Leonardo
name: Bodrossy, Levente
name: Hobday, Alistair J.
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA.
Digital tools for medical education amidst the COVID-19 pandemic: challenges, solutions and the CHERRIES on top
Creators: name: Suppan, Mélanie
Publisher: name: Université de Genève
Year: 2024
Subjects: info:eu-repo/classification/ddc/617

description:
The COVID-19 pandemic has caused disruptions in many aspects of daily life. Healthcare workers and students were particularly affected since they had to face a yet-unknown lethal disease without being able to attend regular and continuous education sessions. This Privat-Docent thesis is based on five studies assessing the impact of innovative and highly interactive web-based or blended education interventions on knowledge and skill acquisition, and, when relevant, on infection prevention behavior. All these trials were designed according to the checklist for reporting results of internet e-surveys, better known as its acronym, CHERRIES. Since all but one of these trials were randomized, the eHealth extension of the consolidated standards of reporting trials was consistently used and methods and results reported accordingly. Several perspectives can be drawn from these five trials and are detailed at the end of this thesis, including the importance of a collaborative, interprofessional and trans-departmental approach.
MOESM1 of Enhancement of the catalytic activity of Isopentenyl diphosphate isomerase (IDI) from Saccharomyces cerevisiae through random and site-directed mutagenesis
Creators: name: Chen, Hailin
name: Li, Meijie
name: Liu, Changqing
name: Zhang, Haibo
name: Xian, Mo
name: Liu, Huizhou
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 1. Methods, Tables and Figures.
MOESM2 of Heterologous expression of Spathaspora passalidarum xylose reductase and xylitol dehydrogenase genes improved xylose fermentation ability of Aureobasidium pullulans
Creators: name: Guo, Jian
name: Huang, Siyao
name: Chen, Yefu
name: Guo, Xuewu
name: Xiao, Dongguang
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2: Figure S1. The sketch map for knock-in of XI gene by one-step homologous recombination-based method. Figure S2. PCR verification of the transformant with overexpressed XI gene. Figure S3. PCR verification of the transformant with overexpressed XYL1.1 (A), XYL1.2 (B), XYL2.1 (C) and XYL2.2 (D). Figure S4. PCR verification of the transformant with overexpressed XYL1.1 and XYL2.1 (A), XYL1.1 and XYL2.2 (B), XYL1.2 and XYL2.1 (C), XYL1.2 and XYL2.2 (D). Figure S5. Comparing the production of pullulan, heavy oil and melanin of the strains with single overexpressed XR gene or XDH gene with that of the parent strain.
Social inequalities in cancer risk factors, screening and beyond
Creators: name: Bico Rosa Gamero Sandoval, Jose Luis
Publisher: name: Université de Genève
Year: 2024
Subjects: info:eu-repo/classification/ddc/616

description:
Cancer is one of the leading causes of mortality and morbidity worldwide, but particularly in high-income countries. Nevertheless, medium and low-income countries have been undergoing an epidemiological transition, with falling mortality from transmissible diseases and increased mortality from non-communicable diseases, such as cancer.

As such, improving cancer-related outcomes is paramount to improving the world population life expectancy and quality of life. While scientific and technological breakthroughs have allowed substantive improvements in cancer-related outcomes, marked inequalities exist between countries. Furthermore, inequalities in cancer-related outcomes are also observed within countries or populations. While unfortunately inevitable, inequalities are unfair, and it has been acknowledged that tackling them is essential to achieve equity and improve society's overall health outcomes.

Cancer incidence and its related outcomes are shaped by the interplay between several factors in the cancer continuum. Inequalities exist at all stages of the cancer care continuum, from prevention to survivorship and palliative care. While public interventions have been devised to improve cancer-related outcomes, how they impact inequalities is often understudied.

This thesis includes a collection of research articles that evaluate the equity impact of measures to reduce tobacco smoking and alcohol consumption and improve mammography uptake in Geneva, Switzerland. In addition, one study is presented on how a key feature of the Swiss health care system (different health insurance deductibles) is associated with forgoing health care.

Together, these research works aim to inform decision-makers, medical professionals, researchers, patients and the general public of the current equity gaps in some cancer-related outcomes and how public health interventions impact them.
Detection, monitoring, and management of early dental caries: The future of individualized dental care
Creators: name: Abdelaziz, Marwa
Publisher: name: Université de Genève
Year: 2024
Subjects: info:eu-repo/classification/ddc/617.6

description: Dental caries remains a significant global health issue. It was highlighted by the World Health Organization’s 2022 reports that despite the efforts and scientific advancements in caries detection and management, the situation has only marginally improved over the past three decades. The persistence of this problem may be linked to outdated concepts developed almost a century ago but are still guiding dentists’ approach to caries management today. There is a need to reconsider professional strategies for preventing and managing the disease. Contemporary dentistry could benefit from embracing new concepts and technologies for caries detection and management. Dentists should explore, among others, alternative methods for caries detection such as optical-based caries detection. These tools have been established for over a decade and they align with current disease understanding and international recommendations, emphasizing early detection and minimally invasive management. This narrative review presents the current state of knowledge and recent trends in caries detection, diagnosis, monitoring, and management, offering insights into future perspectives for clinical applications and research topics.
MOESM1 of Comparative analysis of human sperm glycocalyx from different freezability ejaculates by lectin microarray and identification of ABA as sperm freezability biomarker
Creators: name: Xin, Ai-jie
name: Wu, Yan-cheng
name: Lu, Hui
name: Cheng, Li
name: Gu, Yi-hua
name: Diao, Hua
name: Chen, Guo-wu
name: Wu, Bin
name: Li, Zheng
name: Tao, Sheng-ce
name: Sun, Xiao-xi
name: Shi, Hui-juan
Publisher: name: figshare
Year: 2018
Subjects: subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 1. The characteristics of the sixty samples with different recovery rates.
Improving the treatment of localized rectal cancer, impact of the immunotherapy and new avenues of research
Creators: name: Kossler, Thibaud
Publisher: name: Université de Genève
Year: 2024
Subjects: info:eu-repo/classification/ddc/616
Rectal cancer, Immunotherapy, radiotherapy

description: Despite the fact that colon and rectal cancer are frequently treated as one entity, we show that there are subtle biological differences between the two. We argue that for this reason, in this age of targeted treatment the two cancers should be dealt with separately. Rectal cancer is the 7th most common cancer in the word. Localized disease is treated with surgery. When at risk of local or distant relapse patients receive a neo-adjuvant chemoradiotherapy (CRT) or short course radiotherapy (SCRT). Recently, total neo-adjuvant treatment (TNT, combining induction or consolidation chemotherapy with CRT or SCRT) has been shown to improve clinical outcomes. One of the major issues during the management of rectal cancer is the reduction of treatment-related side effects (e.g fecal incontinence due to sphincter removal or damage secondary to surgery or the low anterior syndrome following radiotherapy, particularly in patients who derive little or no benefit from them). Currently there is no routine test capable of predicting the benefit of neoadjuvant treatments; this is part of one of our lines of inquiry. Recently, a dozen patients with localized rectal cancer and harboring a MSI-H tumor have been treated with an anti-PD1 immunotherapy. After a short follow-up, all showed clinical complete response without the need for neo-adjuvant therapy or surgery, allowing the preservation of the organ and its function with a minimum of toxicity. These results suggest that we should select patients molecularly in order to use targeted therapies such as immunotherapy’. In rectal cancer, unlike in colon cancer, MSI-H and POLE mutated tumors are rare, accounting for 1-5% of patients. Although transcriptomic signatures such as CMS point towards a larger subgroup sensitive to immunotherapy, this remains to be clinically confirmed. For MSS rectal cancer patients, a combination of immunotherapy with neo-adjuvant treatments (CRT or TNT but not SCRT) has been tested in six trials. Although the results of the combination with TNT have been disappointing, with pCR ranging from 32% to 46%, the trials reporting on the combination with CRT seem more promising, with pCR ranging from 30% to 33%. Based on some preclinical data, we believe that immunotherapy could be more effective if associated with SCRT. To test this theory, we have designed a trial PEMREC NCT: NCT04109755, which is currently running. Our translation investigations on the effect of neo adjuvant treatment on the tumor microenvironment have led us to believe that this treatment segment, in addition to being clinically beneficial for some patients, can also be used as a molecular target enhancer. Indeed, early results show that immune content change following neoadjuvant treatment in the case of, for example CRT treated patients exhibited lower stromal T helper, T reg, and T cytotoxic
Genetics of the Eye and Anterior Segment Dysgenesis
Creators: name: Abouzeid, Hana
Publisher: name: Université de Genève
Year: 2024
Subjects: subject: info:eu-repo/classification/ddc/616.8
subject: Cataract
subject: Glaucoma
subject: Anterior segment dysgenesis
subject: Genetics
subject: FOS: Biological sciences
subject: Eye genetics

description:
This thesis aims to present some of the research we have performed on the genetics of the eye and of anterior segment dysgenesis. Our goal was to better understand the genetics of the eye development consecutive to genetic disorders. The presented studies were performed at a time when exome/genome sequencing for the purposes of molecular diagnosis was not widely performed and in which the advances in molecular analyses were not those we have today. Genetic counseling played a crucial role in assisting families, despite challenges posed by issues like incomplete penetrance and germinal mosaicism. The study of asymptomatic family members revealed previously undiagnosed mild phenotypes, further highlighting the complexity of these disorders. The identification of novel phenotypes and genotypes emphasized the ongoing need for comprehensive knowledge to better understand eye malformations.

The studies focused on various pathologies, with a significant number of families with anophthalmia/microphthalmia (A/M) being collected and studied. Other malformations, including anterior segment eye malformations (such as iris coloboma, congenital cataract, and congenital glaucoma), were also observed, often with or without associated systemic syndromes. These investigations led to the identification of new phenotypes and genotypes, contributing to the understanding of these malformations and their etiology. In conclusion, this thesis provides valuable insights into the genetics of eye development and anterior segment dysgenesis. The findings contribute to the understanding of phenotypes, genotypes, and the complex interplay of genetic and environmental factors in these disorders. The knowledge gained from these studies has the potential to enhance molecular diagnostics, refine genetic counseling, and improve medical management for affected individuals in the future.