Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal variation of human induced pluripotent stem cells for induction into the germ cell fate†

Abstract The mechanisms for human germ cell development have remained largely unknown, due to the difficulty in obtaining suitable experimental materials. The establishment of an in vitro system to reconstitute human germ cell development will thus provide a critical opportunity to understand its mechanisms at a molecular level. It has previously been shown that human induced pluripotent stem cells (hiPSCs) are first induced into incipient mesoderm-like cells (iMeLCs), which are in turn induced into primordial germ-cell like cells (PGCLCs) with gene expression properties similar to early migratory PGCs. Here, we report that the efficiency of PGCLC induction varies among hiPSC clones, and, interestingly, the clonal variations in PGCLC induction efficiency are reflected in the gene expression states of the iMeLCs. Remarkably, the expression levels of EOMES, MIXL1, or T in the iMeLCs are positively correlated with the efficiency of subsequent PGCLC generation, while the expressions of CDH1, SOX3, or FGF2 are negatively correlated. These results indicate that the expression changes of these genes occurring during iMeLC induction are key markers indicative of successful induction of PGCLCs, and furthermore, that hiPSC clones have different properties that influence their responsivity to the iMeLC induction. Our study thus provides important insights into the mechanism of hPGC specification as well as the development of a better strategy for inducing human germ cell fate from PSCs in vitro. Summary Sentence Gene expression responses to activin A/WNT signaling vary among clones of human induced pluripotent stem cells, and these differences greatly reflect the clonal variations in the induction efficiency into in vitro primordial germ cells.
Mechanistic and Evolutionary Insights from Comparative Enzymology of Phosphomonoesterases and Phosphodiesterases across the Alkaline Phosphatase Superfamily

Naively one might have expected an early division between phosphate monoesterases and diesterases of the alkaline phosphatase (AP) superfamily. On the contrary, prior results and our structural and biochemical analyses of phosphate monoesterase PafA, from Chryseobacterium meningosepticum, indicate similarities to a superfamily phosphate diesterase [Xanthomonas citri nucleotide pyrophosphatase/phosphodiesterase (NPP)] and distinct differences from the three metal ion AP superfamily monoesterase, from Escherichia coli AP (EcAP). We carried out a series of experiments to map out and learn from the differences and similarities between these enzymes. First, we asked why there would be independent instances of monoesterases in the AP superfamily? PafA has a much weaker product inhibition and slightly higher activity relative to EcAP, suggesting that different metabolic evolutionary pressures favored distinct active-site architectures. Next, we addressed the preferential phosphate monoester and diester catalysis of PafA and NPP, respectively. We asked whether the >80% sequence differences throughout these scaffolds provide functional specialization for each enzyme’s cognate reaction. In contrast to expectations from this model, PafA and NPP mutants with the common subset of active-site groups embedded in each native scaffold had the same monoesterase:diesterase specificities; thus, the >107-fold difference in native specificities appears to arise from distinct interactions at a single phosphoryl substituent. We also uncovered striking mechanistic similarities between the PafA and EcAP monoesterases, including evidence for ground-state destabilization and functional active-site networks that involve different active-site groups but may play analogous catalytic roles. Discovering common network functions may reveal active-site architectural connections that are critical for function, and identifying regions of functional modularity may facilitate the design of new enzymes from existing promiscuous templates. More generally, comparative enzymology and analysis of catalytic promiscuity can provide mechanistic and evolutionary insights.
Cardiac troponins: 25 years on the stage and still improving their clinical value

Abstract Twenty-five years ago, non-isotopic immunoassays for measuring the cardiac specific isoforms of troponin I (cTnI) and T (cTnT) were developed. Both biomarkers radically changed the diagnosis, prognosis, and therapy indication of acute coronary syndromes (ACS) and, particularly, of myocardial infarction (MI). However, cardiac troponins (cTn) rapidly demonstrated their usefulness in other cardiac and non-cardiac conditions, a part of the ischemic coronary diseases. Consequently, the number of patients to be tested for cTn and the number of tests requested to clinical laboratories sharply increased. Though the manufacturers continuously improved the analytical characteristics of the first cTn assays and produced different cTn assay “generations”, the universal definition of myocardial infarction required less-than-available analytical imprecision at the cTn concentration used to assess MI (i.e. the 99th reference percentile). To address the clinical requirements, manufacturers developed the high-sensitivity cTn (hs-cTn) assays that allow to measure the 99th reference percentile with adequate precision, to detect cTn in many healthy subjects and, hence, to calculate the hs-cTn biological variation and especially to observe in very short time intervals serial differences in hs-cTn attributable to cardiac ischemia. Since the number of patients attending the emergency departments (ED) for a suspected ACS or MI is increasing, the improved properties of hs-cTn assays, allowing faster and safer patient assessment, will help to alleviate the sometimes overcrowded EDs. However, there are many biological, analytical, and clinical factors that can influence the true hs-cTn values of a patient. Clinicians and laboratory professionals should know about them for the best interpretation of the otherwise largely useful hs-cTn measurements. In conclusion, 25 years after their introduction for clinical use, “cTn are still on the stage and improving their clinical value”.
Predicting Medical Emergency Team Calls, Cardiac Arrest Calls and Re-Admission after Intensive Care Discharge: Creation of a Tool to Identify At-Risk Patients

We aimed to develop a predictive model for intensive care unit (ICU)–discharged patients at risk of post-ICU deterioration. We performed a retrospective, single-centre cohort observational study by linking the hospital admission, patient pathology, ICU, and medical emergency team (MET) databases. All patients discharged from the Alfred Hospital ICU to wards between July 2012 and June 2014 were included. The primary outcome was a composite endpoint of any MET call, cardiac arrest call or ICU re-admission. Multivariable logistic regression analysis was used to identify predictors of outcome and develop a risk-stratification model. Four thousand, six hundred and thirty-two patients were included in the study. Of these, 878 (19%) patients had a MET call, 51 (1.1%) patients had cardiac arrest calls, 304 (6.5%) were re-admitted to ICU during the same hospital stay, and 964 (21%) had MET calls, cardiac arrest calls or ICU re-admission. A discriminatory predictive model was developed (area under the receiver operating characteristic curve 0.72 [95% confidence intervals {CI} 0.70 to 0.73]) which identified the following factors: increasing age (odds ratio [OR] 1.012 [95% CI 1.007 to 1.017] P <0.001), ICU admission with subarachnoid haemorrhage (OR 2.26 [95% CI 1.22 to 4.16] P=0.009), admission to ICU from a ward (OR 1.67 [95% CI 1.31 to 2.13] P <0.001), Acute Physiology and Chronic Health Evaluation (APACHE) III score without the age component (OR 1.005 [95% CI 1.001 to 1.010] P=0.025), tracheostomy on ICU discharge (OR 4.32 [95% CI 2.9 to 6.42] P <0.001) and discharge to cardiothoracic (OR 2.43 [95%CI 1.49 to 3.96] P <0.001) or oncology wards (OR 2.27 [95% CI 1.05 to 4.89] P=0.036). Over the two-year period, 361 patients were identified as having a greater than 50% chance of having post-ICU deterioration. Factors are identifiable to predict patients at risk of post-ICU deterioration. This knowledge could be used to guide patient follow-up after ICU discharge, optimise healthcare resources, and improve patient outcomes and service delivery.
H7N9 avian influenza A virus in China: a short report on its circulation, drug resistant mutants and novel antiviral drugs

ABSTRACT Introduction: The first human H7N9 avian influenza virus case was reported in Shanghai in 2013. Shortly thereafter, this virus spread to other regions in China. Molecular analysis indicated that the H7N9 virus is a reassortant virus containing internal genes from the H9N2 virus and previously described mammalian adaption markers, which could allow the virus to adapt efficiently to a mammalian host. Fortunately, there is no evidence of sustained person-to-person spread. Most of the human H7N9 cases have a history of exposure to live poultry markets (LPMs). The circulating H7N9 were low pathogenic viruses, however highly pathogenic H7N9 viruses were recently identified in human cases. Areas covered: In the present article, the circulation of H7N9 in LPMs of China, the five waves of H7N9 infection in humans, recently identified drug resistant mutants and potential antiviral drugs against H7N9 are discussed; this may provide further understanding of the evolution and pandemic potential of the H7N9 influenza viruses. Expert commentary: All the data reveal that the major source of H7N9 viruses are LPMs and the H7N9 virus is still circulating widely in China. It is concerning that the recent emergence of highly pathogenic H7N9 viruses may result in highly transmissible viruses in mammalian species.
Development of a two-phase flow model for the investigation of collisions between heavy gasoil doplets and catalytic particles in Fluid Catalytic Cracking Reactors

The goal of this work is to study computationally the flow induced by the collision between a single gasoil droplet and a spherical catalytic particle under realistic Fluid Catalytic Cracking (FCC) conditions. FCC reactors are found in the fossil fuel refineries and are used to upgrade heavy fuel (gas oil) to lighter products (gasoline or LPG), which are industrially more important. Gasoil is injected in the reactor and atomizes; the produced droplets vaporize intensely and come in contact with the hot fluidized solid catalysts. The “cracking” reactions accommodated at the particle porous surface (ex. zeolite) result in the decomposition of gasoil to lighter products. The two-phase flow model developed solves the incompressible Navier-Stokes equations for mass and momentum, along with the energy conservation equation. The VOF methodology is used to track the liquid-gas interface, while a dynamic local grid refinement technique is adopted, so that high accuracy is achieved with a relative low computational cost. A local evaporation model coupled with the additional solution of the species transport equation is utilized to consider phase change. Cracking surface reactions are taken into account via a simplified 2-lump scheme. The model is successfully validated in fundamental droplet dynamics flow conditions, such as droplet acceleration, droplet impingement onto flat and solid surfaces under isothermal conditions and droplet evaporation. Insights into these phenomena provide important information that are missing from experimental measurements. The numerical novelties of the current work include the implementation of a new Wetting Force Model to simulate drop-solid interaction, as well as the proposition of a sharpening scheme for the volume fraction field, to suppress diffusion. Concerning FCC collisions, the numerical model is able to reproduce both the hydrodynamics (drop deformation, spreading, breakup), as well as the chemical products (gasoil converted to gasoline). It is found that droplets of similar size to the catalytic particles tend to be levitated more easily by hot catalysts, thus resulting in higher cracking reaction rates/cracking product yield, and limited possibility for liquid pore blocking. For larger sized droplets, solid-liquid contact increases. The main ambition of the current Thesis, which is to combine the droplet hydrodynamics with the chemical reactions acts as a novel step towards the understanding of such micro-scale physical phenomena that are difficult to capture/measure in experimental apparatus. This fundamental numerical tool can provide insight to the spray system strategy of an FCC reactor for a wide range of operating conditions.
Propensity score–based comparison of the graft failure risk between kidney transplant recipients of standard and expanded criteria donor grafts: Toward increasing the pool of marginal donors

From a prospective and multicentric French cohort, we proposed an external validation study for the expanded criteria donor (ECD), based on 4833 kidney recipients transplanted for the first time between 2000 and 2014. We estimated the subject‐specific effect from a multivariable Cox model. We confirmed a 1.75‐fold (95% confidence interval [CI] 1.53‐2.00, P < .0001) increase in graft failure risk if a given patient received an ECD graft compared to a graft from a donor with standard criteria (standard criteria donor [SCD]). Complementarily, we estimated the population‐average effect using propensity scores. We estimated a 1.34‐fold (95% CI 1.09‐1.64, P = .0049) increase in graft failure risk among ECD patients receiving an ECD graft compared to receiving a SCD graft. With a 10‐year follow‐up, it corresponded to a decrease of 8 months of the mean time to graft failure due to ECD transplantation (95% CI 2‐14 months). The population‐average relative risk due to ECD transplantation and the corresponding absolute effect seem finally not so high. Regarding the increase of quality of life in transplantation, our study constitutes an argument to extend the definition of marginality by considering more grafts at high risk and thereby enlarging the pool of kidney grafts.
MR Acquisition-Invariant Representation Learning

Voxelwise classification approaches are popular and effective methods for tissue quantification in brain magnetic resonance imaging (MRI) scans. However, generalization of these approaches is hampered by large differences between sets of MRI scans such as differences in field strength, vendor or acquisition protocols. Due to this acquisition related variation, classifiers trained on data from a specific scanner fail or under-perform when applied to data that was acquired differently. In order to address this lack of generalization, we propose a Siamese neural network (MRAI-net) to learn a representation that minimizes the between-scanner variation, while maintaining the contrast between brain tissues necessary for brain tissue quantification. The proposed MRAI-net was evaluated on both simulated and real MRI data. After learning the MR acquisition invariant representation, any supervised classification model that uses feature vectors can be applied. In this paper, we provide a proof of principle, which shows that a linear classifier applied on the MRAI representation is able to outperform supervised convolutional neural network classifiers for tissue classification when little target training data is available.
Real‐time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context

Prevention and early detection are well recognized as the best strategies for minimizing the risks posed by nonindigenous species (NIS) that have the potential to become marine pests. Central to this is the ability to rapidly and accurately identify the presence of NIS, often from complex environmental samples like biofouling and ballast water. Molecular tools have been increasingly applied to assist with the identification of NIS and can prove particularly useful for taxonomically difficult groups like ascidians. In this study, we have developed real‐time PCR assays suited to the specific identification of the ascidians Didemnum perlucidum and Didemnum vexillum. Despite being recognized as important global pests, this is the first time specific molecular detection methods have been developed that can support the early identification and detection of these species from a broad range of environmental sample types. These fast, robust and high‐throughput assays represent powerful tools for routine marine biosecurity surveillance, as detection and confirmation of the early presence of species could assist in the timely establishment of emergency responses and control strategies. This study applied the developed assays to confirm the ability to detect Didemnid eDNA in water samples. While previous work has focused on detection of marine larvae from water samples, the development of real‐time PCR assays specifically aimed at detecting eDNA of sessile invertebrate species in the marine environment represents a world first and a significant step forwards in applied marine biosecurity surveillance. Demonstrated success in the detection of D. perlucidum eDNA from water samples at sites where it could not be visually identified suggests value in incorporating such assays into biosecurity survey designs targeting Didemnid species.
Discovery of Novel Potent Muscarinic M3 Receptor Antagonists with Proper Plasma Stability by Structural Recombination of Marketed M3 Antagonists

The marketed long‐acting M3 antagonists for treatment of chronic obstructive pulmonary disease have inappropriate plasma stability (either overstable or excessively unstable), which causes substantial systemic exposure or poor patient compliance. To discover novel M3 antagonists with proper plasma stability, we synthesized and biologically evaluated a series of chiral quaternary ammonium salts of pyrrolidinol esters, which were designed by structural recombination of the marketed M3 antagonists. As a result, two novel potent M3 antagonists, (R/S)‐3‐[2‐hydroxy‐2,2‐di(thiophen‐2‐yl)acetoxy]‐1,1‐dimethylpyrrolidinium bromides (1 a: Ki=0.16 nm, IC50=0.38 nm, t1/2=9.34 min; 1 b: Ki=0.32 nm, IC50=1.01 nm, t1/2=19.2 min) with proper plasma stability were identified, which (particularly 1 a) hold great promise as clinical drug candidates to overcome the drawbacks caused by the inappropriate stability of the currently marketed M3 antagonists. In addition, structure–activity relationship studies revealed that the R configuration of the pyrrolidinyl C3 atom was clearly better than the S configuration.
Novel insights into the composition and function of the Toxoplasma IMC sutures

The Toxoplasma inner membrane complex (IMC) is a specialized organelle underlying the parasite's plasma membrane that consists of flattened rectangular membrane sacs that are sutured together and positioned atop a supportive cytoskeleton. We have previously identified a novel class of proteins localizing to the transverse and longitudinal sutures of the IMC, which we named IMC sutures components (ISCs). Here, we have used proximity‐dependent biotin identification at the sutures to better define the composition of this IMC subcompartment. Using ISC4 as bait, we demonstrate biotin‐dependent labeling of the sutures and have uncovered two new ISCs. We also identified five new proteins that exclusively localize to the transverse sutures that we named transverse sutures components (TSCs), demonstrating that components of the IMC sutures consist of two groups: those that localize to the transverse and longitudinal sutures (ISCs) and those residing only in the transverse sutures (TSCs). In addition, we functionally analyze the ISC protein ISC3 and demonstrate that ISC3‐null parasites have morphological defects and reduced fitness in vitro. Most importantly, Δisc3 parasites exhibit a complete loss of virulence in vivo. These studies expand the known composition of the IMC sutures and highlight the contribution of ISCs to the ability of the parasite to proliferate and cause disease.
Importance of Asphalt Binder Properties on Rut Resistance of Asphalt Mixture

Permanent deformation in asphalt mixture, also known as “rutting”, is one of the most important distresses observed in asphalt pavements. Rutting in the asphalt mixture layer is the permanent deformation of the asphaltic layer near the surface. As the binder phase is responsible for the viscoelastic behavior of a mixture, it plays a dominant part in determining many of the aspects of pavement performance, such as resistance to permanent deformation. This phenomenon is more critical during the warm season of the earlier period of pavement life due to the asphalt binder lower stiffness. To strengthen asphalt pavements against damage, modifiers are added to the asphalt binder. The polymers that are used for binder modification can be divided into two broad categories, namely plastomers and elastomers. Plastomers increase the binder’s stiffness and toughness, while elastomers are known to increase the stiffness and elastic response. Elastic and viscous response of binders are important aspects in the behavior of polymer modified binders and are believed to have an important role in rut resistance of asphalt mixture, although the exact nature of their effect is not well understood. In this study, finite element simulation and image analysis were used to simulate the behavior of asphalt mixture and study the effect of elastic and viscous component of binder behavior on performance of asphalt mixture in rutting. Finite element method provides data that cannot be directly obtained from experiments and are not readily accessible, such as information regarding local stress and strain distribution of the components in the aggregate structure. A multi-scale approach was developed and used to investigate the performance of asphalt mixture across a number of scales. Binder viscoelastic properties used in the analysis were derived from analysis of rheological data derived using a Dynamic Shear Rheometer (DSR), and were consequently used to determine the viscoelastic
A Serious Game Engine for Interview Simulation: Application to the Development of Doctor-Patient Communication Skills

In this paper we present the architecture of a conversation engine aimed to simulate an interview process between a human and a computer player. This component is a central element of many serious games where educational goal is to develop player communication skills. We demonstrate the use of our engine in AgileDoctor, a serious game project for training medical students and general practitioners to communicate with their patients, so as to improve their long-term relationship and provide a higher quality health care. Our proposed conversation engine uses a generic method to combine the game scenario and the educational objectives. The game scenario is described by an instance of a model that formalizes the general doctor-patient interview process and the skills to develop. The conversation engine is able to use this model to engage a challenging dialogue with a human player where missing skills are focused. The proposed design methodology is not bound to the health domain and is transferable to a large range of educational usages.
Technical characterization of an 8 or 16 channel recording system to acquire electrocorticograms of mice

Abstract When performing electrocorticography, reliable recordings of bioelectrical signals are essential for signal processing and analysis. The acquisition of cellular electrical activity from the brain surface of mice requires a system that is able to record small signals within a low frequency range. This work presents a recording system with self-developed software and shows the result of a technical characterization in combination with self-developed electrode arrays to measure electrocorticograms of mice.