Pyrimidine de novo synthesis inhibition selectively blocks effector but not memory T cell development.

Blocking pyrimidine de novo synthesis by inhibiting dihydroorotate dehydrogenase is used to treat autoimmunity and prevent expansion of rapidly dividing cell populations including activated T cells. Here we show memory T cell precursors are resistant to pyrimidine starvation. Although the treatment effectively blocked effector T cells, the number, function and transcriptional profile of memory T cells and their precursors were unaffected. This effect occurred in a narrow time window in the early T cell expansion phase when developing effector, but not memory precursor, T cells are vulnerable to pyrimidine starvation. This vulnerability stems from a higher proliferative rate of early effector T cells as well as lower pyrimidine synthesis capacity when compared with memory precursors. This differential sensitivity is a drug-targetable checkpoint that efficiently diminishes effector T cells without affecting the memory compartment. This cell fate checkpoint might therefore lead to new methods to safely manipulate effector T cell responses.

Graft-versus-host disease is locally maintained in target tissues by resident progenitor-like T cells.

In allogeneic hematopoietic stem cell transplantation, donor αß T cells attack recipient tissues, causing graft-versus-host disease (GVHD), a major cause of morbidity and mortality. A central question has been how GVHD is sustained despite T cell exhaustion from chronic antigen stimulation. The current model for GVHD holds that disease is maintained through the continued recruitment of alloreactive effectors from blood into affected tissues. Here, we show, using multiple approaches including parabiosis of mice with GVHD, that GVHD is instead primarily maintained locally within diseased tissues. By tracking 1,203 alloreactive T cell clones, we fitted a mathematical model predicting that within each tissue a small number of progenitor T cells maintain a larger effector pool. Consistent with this, we identified a tissue-resident TCF-1+ subpopulation that preferentially engrafted, expanded, and differentiated into effectors upon adoptive transfer. These results suggest that therapies targeting affected tissues and progenitor T cells within them would be effective.

Ions Speciation at the Water-Air Interface.

In typical aqueous systems, including naturally occurring sweet and salt water and tap water, multiple ion species are co-solvated. At the water-air interface, these ions are known to affect the chemical reactivity, aerosol formation, climate, and water odor. Yet, the composition of ions at the water interface has remained enigmatic. Here, using surface-specific heterodyne-detected sum-frequency generation spectroscopy, we quantify the relative surface activity of two co-solvated ions in solution. We find that more hydrophobic ions are speciated to the interface due to the hydrophilic ions. Quantitative analysis shows that the interfacial hydrophobic ion population increases with decreasing interfacial hydrophilic ion population at the interface. Simulations show that the solvation energy difference between the ions and the intrinsic surface propensity of ions determine the extent of an ion's speciation by other ions. This mechanism provides a unified view of the speciation of monatomic and polyatomic ions at electrolyte solution interfaces.

Acute hydrocephalus following post-traumatic peri-mesencephalic subarachnoid hemorrhage: an uncommon and potentially fatal event in children.

PURPOSE: In pediatric, head trauma acute hydrocephalus is an uncommon but possible complication. Association with a subarachnoid hemorrhage is poorly described. METHODS: We described a case of an 8-year-old girl with acute hydrocephalus secondary to peri-mesencephalic subarachnoid hemorrhage after mild head trauma resolved with external ventricular drainage. Furthermore, we have conducted a review of the literature about this complication in pediatric head trauma. DISCUSSION AND CONCLUSION: Acute hydrocephalus related to post-traumatic peri-mesencephalic subarachnoid hemorrhage (tSAH) is an unknown entity in pediatric head trauma. According to our experience, traumatic peri-mesencephalic SAH should be under close clinical monitoring to identify post-traumatic hydrocephalus (PTH), a potentially fatal complication in pediatric mild head trauma.

Researching the level of agreement among experts on terms used to describe wounds: An international study.

Establishing a common language that allows univocal and objective communication in describing wounds and their healing is of utmost importance in defining the diagnostic hypothesis and proper wound management. To measure the level of agreement on the description of wounds, an international study was performed among experts of different professional backgrounds on several common terms used to describe ulcerative lesions. A panel of 27 wound care experts anonymously completed a multiple-choice questionnaire on 100 images of 50 ulcerative lesions. The participants were asked to describe each image using a set of pre-defined terms. An expert data analyst interpreted the questionnaires to map the level of agreement on the used terminology. Our findings show a very low level of agreement among experts in using the proposed terminology to describe the wound bed, the wound edge, and the surrounding skin conditions. Efforts should be planned to find a consensus on the correct use of terminology for wound description. To this aim, partnership, consensus, and agreement with educators in medicine and nursing are necessary.

High-Performance Humidity Sensing in π-Conjugated Molecular Assemblies through the Engineering of Electron/Proton Transport and Device Interfaces.

The development of systems capable of responding to environmental changes, such as humidity, requires the design and assembly of highly sensitive and efficiently transducing elements. Such a challenge can be mastered only by disentangling the role played by each component of the responsive system, thus ultimately achieving high performance by optimizing the synergistic contribution of all functional elements. Here, we designed and synthesized a novel [1]benzothieno[3,2-b][1]benzothiophene derivative equipped with hydrophilic oligoethylene glycol lateral chains (OEG-BTBT) that can electrically transduce subtle changes in ambient humidity with high current ratios (>104) at low voltages (2 V), reaching state-of-the-art performance. Multiscale structural, spectroscopical, and electrical characterizations were employed to elucidate the role of each device constituent, viz., the active material's BTBT core and OEG side chains, and the device interfaces. While the BTBT molecular core promotes the self-assembly of (semi)conducting crystalline films, its OEG side chains are prone to adsorb ambient moisture. These chains act as hotspots for hydrogen bonding with atmospheric water molecules that locally dissociate when a bias voltage is applied, resulting in a mixed electronic/protonic long-range conduction throughout the film. Due to the OEG-BTBT molecules' orientation with respect to the surface and structural defects within the film, water molecules can access the humidity-sensitive sites of the SiO2 substrate surface, whose hydrophilicity can be tuned for an improved device response. The synergistic chemical engineering of materials and interfaces is thus key for designing highly sensitive humidity-responsive electrical devices whose mechanism relies on the interplay of electron and proton transport.

Combining Integrated Informative System and Historical Digital Twin for Maintenance and Preservation of Artistic Assets.

The protection of artistic and cultural heritage is a major challenge due to its peculiarities and its exposure to significant natural hazards. Several methodologies exist to assess the condition of artistic heritage and to protect it from exceptional actions. Moreover, novel digital technologies offer many solutions able to deliver a digital replica of artifacts of interest, so that a reduction in the uncertainties in the analysis models can be achieved. A rational approach to the preservation and protection of artistic heritage is based on traditional approaches supported and integrated by novel technologies, so that qualitative and quantitative indicators of the current condition of artistic heritage can be defined and validated in an interdisciplinary framework. The present paper reports the results of an approach to the maintenance and preservation of art objects housed in a museum complex based on a comprehensive digital path towards a Historical Digital Twin (HDT). A workflow aimed at estimating the stress regime and the dynamic properties of two sculptures, based on the detailed three-dimensional model resulting from a laser scanner survey, is illustrated and discussed. The results highlight the great advantages resulting from the integration of traditional and novel procedures in the field of conservation of artistic assets.

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.

DNA methylation has been associated with transcriptional repression and detection of differential methylation is important in understanding the underlying causes of differential gene expression. Bisulfite-converted genomic DNA sequencing is the current gold standard in the field for building genome-wide maps at a base pair resolution of DNA methylation. Here we systematically investigate the underlying features of detecting differential DNA methylation in CpG and non-CpG contexts, considering both the case of mammalian systems and plants. In particular, we introduce DMRcaller, a highly efficient R/Bioconductor package, which implements several methods to detect differentially methylated regions (DMRs) between two samples. Most importantly, we show that different algorithms are required to compute DMRs and the most appropriate algorithm in each case depends on the sequence context and levels of methylation. Furthermore, we show that DMRcaller outperforms other available packages and we propose a new method to select the parameters for this tool and for other available tools. DMRcaller is a comprehensive tool for differential methylation analysis which displays high sensitivity and specificity for the detection of DMRs and performs entire genome wide analysis within a few hours.

Improving the quality of clinical research on chronic wound infection treatment: expert-based recommendations.

OBJECTIVE:: To produce recommendations for the design of reliable and informative clinical investigations in chronic wound infection. METHOD:: A multidisciplinary panel of international experts from four countries (Italy, UK, Ireland and the US) were involved in a detailed, semi-structured discussion on how to better select and describe a target population, interventions and outcomes, and which infection-related criteria to apply in order to achieve a high-quality trial. Consent among the experts was measured using the Delphi method and GRADE Working Group suggestions. The project was fully supported by AISLeC 2016 (Italian Nursing Society for Wound Care Study). RESULTS:: In total, 37 recommendations achieved substantial agreement among the experts; 10 concerned the most appropriate description and selection of a target population, four related to interventions and 15 to outcomes. A further eight statements about critical methodological points were approved. CONCLUSION:: Developing recommendations in a systematic manner through a representative group of experts could generate tools for improving the design of clinical trials in this challenging area.

Towards Digital Twin Implementation for Assessing Production Line Performance and Balancing.

The optimization of production processes has always been one of the cornerstones for manufacturing companies, aimed to increase their productivity, minimizing the related costs. In the Industry 4.0 era, some innovative technologies, perceived as far away until a few years ago, have become reachable by everyone. The massive introduction of these technologies directly in the factories allows interconnecting the resources (machines and humans) and the entire production chain to be kept under control, thanks to the collection and the analyses of real production data, supporting the decision making process. This article aims to propose a methodological framework that, thanks to the use of Industrial Internet of Things-IoT devices, in particular the wearable sensors, and simulation tools, supports the analyses of production line performance parameters, by considering both experimental and numerical data, allowing a continuous monitoring of the line balancing and performance at varying of the production demand. A case study, regarding a manual task of a real manufacturing production line, is presented to demonstrate the applicability and the effectiveness of the proposed procedure.

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization.

Matrix factorization (MF) is an established paradigm for large-scale biological data analysis with tremendous potential in computational biology. Here, we challenge MF in depicting the molecular bases of epidemiologically described disease-disease (DD) relationships. As a use case, we focus on the inverse comorbidity association between Alzheimer's disease (AD) and lung cancer (LC), described as a lower than expected probability of developing LC in AD patients. To this day, the molecular mechanisms underlying DD relationships remain poorly explained and their better characterization might offer unprecedented clinical opportunities. To this goal, we extend our previously designed MF-based framework for the molecular characterization of DD relationships. Considering AD-LC inverse comorbidity as a case study, we highlight multiple molecular mechanisms, among which we confirm the involvement of processes related to the immune system and mitochondrial metabolism. We then distinguish mechanisms specific to LC from those shared with other cancers through a pan-cancer analysis. Additionally, new candidate molecular players, such as estrogen receptor (ER), cadherin 1 (CDH1) and histone deacetylase (HDAC), are pinpointed as factors that might underlie the inverse relationship, opening the way to new investigations. Finally, some lung cancer subtype-specific factors are also detected, also suggesting the existence of heterogeneity across patients in the context of inverse comorbidity.

Determining the optimal number of independent components for reproducible transcriptomic data analysis.

BACKGROUND: Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data. RESULTS: Here we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets. CONCLUSIONS: We suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.

Kinetics of liquid-liquid phase separation in protein solutions exhibiting LCST phase behavior studied by time-resolved USAXS and VSANS.

We study the kinetics of the liquid-liquid phase separation (LLPS) and its arrest in protein solutions exhibiting a lower critical solution temperature (LCST) phase behavior using the combination of ultra-small angle X-ray scattering (USAXS) and very-small angle neutron scattering (VSANS). We employ a previously established model system consisting of bovine serum albumin (BSA) solutions with YCl3. We follow the phase transition from sub-second to 104 s upon an off-critical temperature jump. After a temperature jump, the USAXS profiles exhibit a peak that grows in intensity and shifts to lower q values with time. Below 45 °C, the characteristic length scale (ξ) obtained from this scattering peak increases with time with a power of about 1/3 for different sample compositions. This is in good agreement with the theoretical prediction for the intermediate stage of spinodal decomposition where the growth is driven by interface tension. Above 45 °C, ξ follows initially the 1/3 power law growth, then undergoes a significant slowdown, and an arrested state is reached below the denaturation temperature of the protein. This growth kinetics may indicate that the final composition of the protein-rich phase is located close to the high density branch of the LLPS binodal when a kinetically arrested state is reached.

Minimally invasive plate osteosynthesis in proximal humeral fractures: one-year results of a prospective multicenter study.

PURPOSE: The aim of this multicentric study was to evaluate results of minimally invasive plate osteosynthesis (MIPO) for proximal humeral fractures in terms of postoperative shoulder function, radiological outcome and number of complications. METHODS: A consecutive series of 76 patients with proximal humeral fractures were treated with locking plate using a minimally invasive antero-lateral approach in two orthopaedic departments. Functional results with Constant score and radiographic evaluation were available for 74 patients at one-year follow up. RESULTS: The patients achieved a mean Constant score of 71 (range 28-100). Each functional result was evaluated also for both centres without significant differences. Significant statistical differences were only found for younger patients with better results (p < 0.05). Twenty patients (27%) developed complications. Subacromial impingement occurred in 16.2% of cases for varus malreduction (6.7%) and for too proximal plate positioning (9.5%). Primary screws perforation (2.7%), secondary perforation due to cut-out (1.4%), avascular necrosis (AVN) of humeral head (1.4%), partial resorption of greater tuberosity (2.7%), secondary dislocation of the greater tuberosity (2.7%) and stiffness (2.7%) were the other complications observed. CONCLUSIONS: The MIPO technique for proximal humeral fractures was safe and reproducible for most common patterns of fracture. Major complication rate was apparently low due to a soft tissue sparing, deltoid muscle and circumflex vessels, with easy access of the bar area to correct positioning of the plate.

Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge.

Due to the ambiguity related to the lack of phase information, determining the physical parameters of multilayer thin films from measured neutron and X-ray reflectivity curves is, on a fundamental level, an underdetermined inverse problem. This ambiguity poses limitations on standard neural networks, constraining the range and number of considered parameters in previous machine learning solutions. To overcome this challenge, a novel training procedure has been designed which incorporates dynamic prior boundaries for each physical parameter as additional inputs to the neural network. In this manner, the neural network can be trained simultaneously on all well-posed subintervals of a larger parameter space in which the inverse problem is underdetermined. During inference, users can flexibly input their own prior knowledge about the physical system to constrain the neural network prediction to distinct target subintervals in the parameter space. The effectiveness of the method is demonstrated in various scenarios, including multilayer structures with a box model parameterization and a physics-inspired special parameterization of the scattering length density profile for a multilayer structure. In contrast to previous methods, this approach scales favourably when increasing the complexity of the inverse problem, working properly even for a five-layer multilayer model and a periodic multilayer model with up to 17 open parameters.

Discovery of 1,3,4-Oxadiazole Derivatives as Broad-Spectrum Antiparasitic Agents.

Vector-borne parasitic diseases (VBPDs) pose a significant threat to public health on a global scale. Collectively, Human African Trypanosomiasis (HAT), Leishmaniasis, and Malaria threaten millions of people, particularly in developing countries. Climate change might alter the transmission and spread of VBPDs, leading to a global burden of these diseases. Thus, novel agents are urgently needed to expand therapeutic options and limit the spread of drug-resistant parasites. Herein, we report the development of broad-spectrum antiparasitic agents by screening a known library of antileishmanial and antimalarial compounds toward Trypanosoma brucei (T. brucei) and identifying a 1,3,4-oxadiazole derivative (19) as anti-T. brucei hit with predicted blood-brain barrier permeability. Subsequently, extensive structure-activity-relationship studies around the lipophilic tail of 19 led to a potent antitrypanosomal and antimalarial compound (27), with moderate potency also toward Leishmania infantum (L. infantum) and Leishmania tropica. In addition, we discovered a pan-active antiparasitic molecule (24), showing low-micromolar IC50s toward T. brucei and Leishmania spp. promastigotes and amastigotes, and nanomolar IC50 against Plasmodium falciparum, together with high selectivity for the parasites over mammalian cells (THP-1). Early ADME-toxicity assays were used to assess the safety profile of the compounds. Overall, we characterized 24 and 27, bearing the 1,3,4-oxadiazole privileged scaffold, as broad-spectrum low-toxicity agents for the treatment of VBPDs. An alkyne-substituted chemical probe (30) was synthesized and will be utilized in proteomics experiments aimed at deconvoluting the mechanism of action in the T. brucei parasite.

Time-Driven Activity-Based Costing for Capturing the Complexity of Healthcare Processes: The Case of Deep Vein Thrombosis and Leg Ulcers.

Time-driven activity-based costing (TDABC) is suggested to assess costs within the value-based healthcare approach, but there is a paucity of applications in chronic diseases such as deep vein thrombosis (DVT) and leg ulcers. In this context, we applied TDABC in a cost-effectiveness analysis comparing venous stenting to compression ± anticoagulation (standard of care-SOC) from both hospital and societal perspectives in Italy. TDABC was applied to both treatments to assess costs that were included in a cost-effectiveness model. Clinical inputs were retrieved from the literature and integrated with real-world data. The Incremental Cost Utility Ratio (ICUR) of stenting compared to SOC was EUR 10,270/QALY and EUR 8962/QALY for hospital and societal perspectives, respectively. The mean cost per patient for venous stenting of EUR 5082 was higher than the Diagnosis-Related Group (DRG) reimbursement (EUR 4742). For SOC, an ulcer healing in 3 months costs EUR 1892, of which EUR 302 (16%) is borne by the patient versus a reimbursement of EUR 1132. TDABC showed that venous stenting may be cost-effective compared with SOC but that reimbursement rates may not completely cover the real costs, which are partially sustained by the patients. A more efficient policy for covering the real costs may be beneficial for both clinical centers and patients.

Machine learning for scattering data: strategies, perspectives and applications to surface scattering.

Machine learning (ML) has received enormous attention in science and beyond. Discussed here are the status, opportunities, challenges and limitations of ML as applied to X-ray and neutron scattering techniques, with an emphasis on surface scattering. Typical strategies are outlined, as well as possible pitfalls. Applications to reflectometry and grazing-incidence scattering are critically discussed. Comment is also given on the availability of training and test data for ML applications, such as neural networks, and a large reflectivity data set is provided as reference data for the community.

Memory Effect by Melt Crystallization Observed in Polymorphs of a Benzothieno-Benzothiophene Derivative.

This work provides a comprehensive illustration of a crystalline melt memory effect recorded for three solvates of the 2,7-bis(2-(2-methoxyethoxy)ethoxy)benzo[b]benzo[4,5] thieno[2,3-d]thiophene (OEG-BTBT) molecule with dichloromethane (DCM) molecules. Combined optical microscopy and X-ray diffraction measurements at different temperatures are used to get an overview of the structural and morphological properties like melting points, isotropic transition temperatures, induction times, and crystallization kinetics of the three forms. An outstanding observation is made upon annealing the three polymorphs at temperatures well above their respective melting points as well as above the optical clearance temperature. After cooling back to room temperature, recrystallization results in the formation of the initial phase present before the annealing process. This melt memory effect is observed for all three solvates. These observations can be correlated to the strong interaction between the DCM molecules and the oligoethylene glycol side chains, even in the molten state. This conclusion rationalizes the experimental observation made upon solvent vapor annealing of the crystalline sample with DCM, which unambiguously transformed the system into a disordered state.

Flt3- and Tie2-Cre tracing identifies regeneration in sepsis from multipotent progenitors but not hematopoietic stem cells.

In response to infections and stress, hematopoiesis rapidly enhances blood and immune cell production. The stage within the hematopoietic hierarchy that accounts for this regeneration is unclear under natural conditions in vivo. We analyzed by differentiation tracing, using inducible Tie2- or Flt3-driven Cre recombinase, the roles of mouse hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs). During polymicrobial sepsis, HSCs responded transcriptionally and increased their proliferation and cell death, yet HSC differentiation rates remained at steady-state levels. HSC differentiation was also independent from the ablation of various cellular compartments-bleeding, the antibody-mediated ablation of granulocytes or B lymphocytes, and genetic lymphocyte deficiency. By marked contrast, the fate mapping of MPPs in polymicrobial sepsis identified these cells as a major source for accelerated myeloid cell production. The regulation of blood and immune cell homeostasis by progenitors rather than stem cells may ensure a rapid response while preserving the integrity of the HSC population.