Miracle-dz/UniFAR-FTUs huggingface dataset:
Data-Enabled Sustainability: The Collective Work of Turning Data into Actions for Environmental Care

This one-day workshop invites discussions on the role of data and data-enabled practices in addressing challenges of environmental sustainability. Fostering acts of care for the environment is a complex endeavor entailing multi-lifespan relations to people and institutions, to the environment and other non-human actors, and to existing infrastructures and processes. The workshop addresses such challenges by exploring the role of data, and the work of making them actionable for the many actors involved in protecting the environment. It will bring together interdisciplinary scholars, representatives of public institutions, activists, environmental collectives, and IT practitioners interested in the design of more sustainable futures. The workshop will discuss analytical and design issues of data-enabled sustainability, along with the practical opportunities of using data to infrastructure acts of care for the environment. The workshop will accommodate up to twenty participants and will be mainly run on-site.
Inference of drug off-target effects on cellular signaling using Interactome-Based Deep Learning

Many diseases emerge from dysregulated cellular signaling, and drugs are often designed to target specific nodes in cellular networks e.g. signaling proteins, or transcription factors. However, off-target effects are common and may ultimately result in failed clinical trials. Computational modeling of the cell’s transcriptional response to drugs could improve our understanding of their mechanisms of action. Here we develop such an approach based on ensembles of artificial neural networks, that simultaneously infer drug-target interactions and their downstream effects on intracellular signaling. Applied to gene expression data from different cell lines, it outperforms basic machine learning approaches in predicting transcription factors’ activity, while recovering most known drug-target interactions and inferring many new, which we validate in an independent dataset. As a case study, we explore the inferred interactions of the drug Lestaurtinib and its effects on downstream signaling. Beyond its intended target FLT3 the model predicts an inhibition of CDK2 that enhances downregulation of the cell cycle-critical transcription factor FOXM1, corroborating literature findings. Our approach can therefore enhance our understanding of drug signaling for therapeutic design.
Time- and lineage-resolved transcriptional profiling uncovers gene expression programs and clonal relationships that underlie human T lineage specification

T cells develop from multi-potent hematopoietic progenitors in the thymus and provide adaptive protection against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors, and their subsequent specification to the T lineage, has been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process. Time-resolved single cell RNA sequencing revealed that cell-cycle exit, downregulation of the multipotent hematopoietic program, and upregulation of >90 lineage-associated transcription factors all occur within a highly co-ordinated and narrow developmental window. Computational gene-regulatory network inference elucidated the transcriptional logic of T lineage specification, uncovering an important role for YBX1. We mapped the differentiation cell fate hierarchy using transcribed lineage barcoding and mathematical trajectory inference and discovered that mast and myeloid potential bifurcate from each other early in haematopoiesis, upstream of T lineage restriction. Collectively, our analyses provide a quantitative, time-resolved model of human T cell specification with relevance for regenerative medicine and developmental immunology.
Intraspecific plant-soil feedbacks vary under field conditions among species in a tropical tree community

Premise Soil microbes can influence patterns of diversity in plant communities via plant-soil feedbacks. Intraspecific plant-soil feedbacks occur when plant genotype causes variation in soil microbial composition, resulting in differences in the performance of seedlings growing near their maternal plants versus seedlings growing near non-maternal conspecific plants. How commonly such intraspecific plant-soil feedbacks occur in natural plant communities is unclear, especially under variable field conditions. Methods We conducted an in situ experiment with four native tree species on Barro Colorado Island (BCI), Panama. Seedlings of each species were transplanted beneath their maternal tree or another conspecific tree in the BCI forest. Mortality and growth were assessed at the end of the wet season (∼4 months post-transplant) and at the end of the experiment (∼7 months post-transplant). Results Patterns of seedling performance varied among species and were inconsistent over time. Significant effects of field environment were detected for two of the four species: at the end of the wet season, Virola surinamensis seedlings had higher survival beneath their maternal tree than other conspecific trees, while the opposite pattern was found in Ormosia macrocalyx. However, these differences disappeared by the end of the experiment. Conclusions Our results suggest that intraspecific plant-soil feedbacks occur inconsistently under field conditions in tropical tree species and may have a limited role in determining seedling performance in tropical tree communities. Future studies are needed to elucidate the environmental and genetic factors that determine the incidence and direction of intraspecific plant-soil feedbacks in plant communities.
Multifunction Fluorescence Open-Source In Vivo/In Vitro Imaging System (openIVIS)

The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study we designed and built a multifunction fluorescent open-source in-vivo/in-vitro imaging system (openIVIS) fluorescent imaging system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the various potential applications of our system, we tested its performance against a diverse set of experiments including laboratory type assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of a couple of weeks. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.
Diverse stimuli induce piloerection and yield varied autonomic responses in humans

This research provides an in-depth exploration into the triggers and corresponding autonomic responses of piloerection, a phenomenon prevalent across various species. In non-human species, piloerection occurs in reaction to a variety of environmental changes, including social interactions and temperature shifts. However, its understanding in humans has been confined to emotional contexts. This is problematic because it reflects solely upon subjective experience rather than an objective response to the environment, and because, given our shared evolutionary paths, piloerection should function similarly in humans and other animals. We observed 1,198 piloerection episodes from eight participants while simultaneously recording multiple autonomic and body temperature indices, finding that piloerection in humans can indeed be elicited by thermal, tactile, and audio-visual stimuli. The data also revealed variations in cardiac reactivity measures: audio-visual piloerection was associated with greater sympathetic arousal, while tactile piloerection was linked to greater parasympathetic arousal. Despite prevailing notions of piloerection as a vestigial response in humans, it does respond to decreases in skin temperature and induces a rise in skin temperature during episodes. This research underscores that piloerection in humans is not solely an affective response to emotional stimuli. Rather, it is best understood as a reflexive response to environmental changes, suggesting a shared functional similarity with other species.
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model

In molecular optimization, one popular way is R-groups decoration on molecular scaffolds, and many efforts have been put to generate R-groups based on deep generative models. However, these methods mostly use information of known binding ligands, without fully utilizing target structure information. In this study, we proposed a new method, DiffDec, to involve three-dimensional pocket constraints by a modified diffusion technique for optimizing molecules through molecular scaffold decoration. For an end-to-end generation of R-groups with different sizes, we designed a novel fake atom mechanism. DiffDec was shown able to generate structure-aware R-groups, and simultaneously generate multiple R-groups for one scaffold on different growth anchors. The growth anchors could be provided by users or automatically determined by our model. DiffDec achieved R-group recovery rates of 69.67% and 45.34% in the single and multiple R-group decoration tasks, respectively, and these values were significantly higher than competing methods (37.33% and 26.85%). According to the molecular docking study, our decorated molecules obtained better average binding affinity than baseline methods. The docking pose analysis revealed that DiffDec could decorate scaffolds with R-groups that exhibited improved binding affinities and more favourable interactions with the pocket. These results demonstrated the potential and applicability of DiffDec in real-world scaffold decoration for molecular optimization.
The Escherichia coli TolC efflux pump protein is immunogenic and elicits protective antibodies

Antimicrobial resistance is an increasing worldwide public health burden that threatens to make the existent antimicrobials obsolete. Among the mechanisms of antimicrobial resistance is the overexpression of efflux pumps, such as the AcrA–AcrB–TolC which extrude diverse compounds, reducing the intracellular concentration of antimicrobials. TolC is the outer membrane protein of this pump and has recently gained attention as a therapeutic target. However, little is known about the immune response generated against the TolC protein. Here we evaluated the cellular and humoral immune response against the TolC from Escherichia coli. An in silico epitope prediction of the E. coli TolC showed several residues could bind to human antibodies, and we showed that human plasma presented anti-TolC IgG and IgA antibodies. Gram-negative infected patients presented a slight increase in anti-TolC IgM amounts, compared to controls. Recombinant E. coli TolC protein stimulated macrophages in vitro to produce nitric oxide, as well as IL-6 and TNF-α, assessed by Griess assay and ELISA, respectively. Immunization of mice with TolC intraperitoneally and an in vitro re-stimulation of lymph node cells led to increased percentage of T cell proliferation and IFNγ production, evaluated by flow cytometry and ELISA, respectively. We observed that TolC mouse immunization stimulated anti-TolC IgM and IgG production, with a higher level of IgG1 and IgG2, amongst the IgG subclasses. Finally, TolC IgG from mouse immune serum could bind to live E. coli, increase bacterial uptake by macrophages in vitro. TolC immunized mice had a survival rate increased in 60% post infection with E. coli. Our results showed that TolC is immunogenic, activating macrophages, T and B cells, leading to the production of protective antibodies against E. coli.
Design and Control of Admittance-Type Telemanipulation Systems

This thesis summarizes guidelines for the design and control of a highly integrated, multi-modal, and intuitive teleoperation system that can be used to perform a variety of different manipulation tasks requiring bimanual and multi-fingered interactions as well as the collaboration of multiple operators. Hereby, exclusively teleoperation systems using admittance-type devices are investigated. Bimanual 6 DOF manipulations with high interaction forces are realized by newly developed admittance-type haptic interfaces, which are mounted on a mobile platform and thus also allow performance of manipulations in large remote environments. Taking into account a large number of mechatronic requirements, a novel, enhanced, and highly integrated teleoperation system consisting of redundant haptic interfaces and telemanipulators as well as a stereo-vision-system is developed. Dextrous fine manipulations are realized by a multi-fingered telemanipulation system, whereby efficient position and force mapping algorithms are used to map human hand motions to gripper motions and to provide a realistic force feedback. The usage of admittance-type devices instead of classical impedance-type devices poses new challenges on the control concepts. Different types of bilateral control algorithms suitable for admittance-type devices are proposed and robust stability of them is analyzed by using the parameter space approach. Further improvements are achieved by incorporating human factors in the development process. Effects of varied human movement control on task performance and feeling of telepresence are analyzed by means of experimental evaluation and new design guidelines for a user-friendly teleoperation system are derived. Finally, different types of collaborative teleoperation architectures are proposed, application scenarios are described, and challenges on the control of these systems are formulated. In particular, robust stability of a bimanual, a multi-user, and a cooperative teleoperation system is investigated in detail. A variety of laboratory experiments, characterized particularly by their very high complexity, serve for the evaluation and validation of all proposed software and hardware developments.
The Probabilistic Active Shape Model: From Model Construction to Flexible Medical Image Segmentation

Automatic processing of three-dimensional image data acquired with computed tomography or magnetic resonance imaging plays an increasingly important role in medicine. For example, the automatic segmentation of anatomical structures in tomographic images allows to generate three-dimensional visualizations of a patient’s anatomy and thereby supports surgeons during planning of various kinds of surgeries. Because organs in medical images often exhibit a low contrast to adjacent structures, and because the image quality may be hampered by noise or other image acquisition artifacts, the development of segmentation algorithms that are both robust and accurate is very challenging. In order to increase the robustness, the use of model-based algorithms is mandatory, as for example algorithms that incorporate prior knowledge about an organ’s shape into the segmentation process. Recent research has proven that Statistical Shape Models are especially appropriate for robust medical image segmentation. In these models, the typical shape of an organ is learned from a set of training examples. However, Statistical Shape Models have two major disadvantages: The construction of the models is relatively difficult, and the models are often used too restrictively, such that the resulting segmentation does not delineate the organ exactly. This thesis addresses both problems: The first part of the thesis introduces new methods for establishing correspondence between training shapes, which is a necessary prerequisite for shape model learning. The developed methods include consistent parameterization algorithms for organs with spherical and genus 1 topology, as well as a nonrigid mesh registration algorithm for shapes with arbitrary topology. The second part of the thesis presents a new shape model-based segmentation algorithm that allows for an accurate delineation of organs. In contrast to existing approaches, it is possible to integrate not only linear shape models into the algorithm, but also nonlinear shape models, which allow for a more specific description of an organ’s shape variation. The proposed segmentation algorithm is evaluated in three applications to medical image data: Liver and vertebra segmentation in contrast-enhanced computed tomography scans, and prostate segmentation in magnetic resonance images.
Acoustic anisotropy of synthetics with controlled crack geometries

The knowledge of crack distributions is of vital importance for the withdrawal of fluids from reservoirs in which cracks exist as penetrating fractures, serving as primary channels for fluid flow. The presence rif cracks affects the acoustic wave velocities giving rise to anisotropy. It is to be able to predict theoretically whether the observed anisotropy is caused by a large number of small, isolated microcracks, or by a few similarly oriented, larger and possibly connected fractures. Several theoretical models for the acoustic behaviour in cracked and jointed media exist (Hudson, 1981, Thomsen, 1986), yet none of them have been confirmed in a controlled experiment, one in which sizes, shapes, amounts and orientational distributions of cracks are known. In geomaterials these are generally unknown parameters. Hence we have undertaken the task of producing a synthetic material in which the above crack parameters are known.
Fast Neutron Induced Nuclear Counter Effect in Hamamatsu Silicon PIN Diodes and APDs

Neutron induced nuclear counter effect in Hamamatsu silicon PIN diodes and APDs was measured by irradiating fast neutrons from a pair of 252Cf sources directly to these devices. It was found that the entire kinetic energy of these neutrons may be converted into electron signals in these devices, leading to anomalous signals of up to a few million electrons in a single isolated calorimeter readout channel. Signals of such amplitude represent equivalent energy of several hundred GeV and a few GeV for PWO and LSO/LYSO crystals respectively assuming the corresponding light yields of 4 and 800 p.e. /MeV. The overall rate of the neutron induced nuclear counter effect in APDs is found to be more than an order of magnitude less than that in PIN diodes. Increasing the APD gain was also found to reduce the neutron induced nuclear counter effect. An intelligent front-end chip capable of selecting un-contaminated signal is proposed to eliminate completely the nuclear counter effect without significant cost increase.
North African savanna fires and atmospheric carbon dioxide

The effect of north African savanna fires on atmospheric CO2 is investigated using a tracer transport model. The model uses winds from operational numerical weather prediction analyses and provides CO2 concentrations as a function of space and time. After a spin-up period of several years, biomass-burning sources are added, and model experiments are run for an additional year, utilizing various estimates of CO2 sources. The various model experiments show that biomass burning in the north African savannas significantly affects CO2 concentrations in South America. The effect is more pronounced during the period from January through March, when biomass burning in South America is almost nonexistent. During this period, atmospheric CO2 concentrations in parts of South America typically may increase by 0.5 to 0.75 ppm at 970 mbar, the average pressure of the lowest model layer. These figures are above the probable uncertainty level, as model runs with biomass-burning sources estimated from independent studies using distinct data sets and techniques indicate. From May through September, when severe biomass burning occurs in South America, the effect of north African savanna fires over South America has become generally small at 970 mbar, but north of the equator it may be of the same magnitude or larger than the effect of South American fires. The CO2 concentration increase in the extreme northern and southern portions of South America, however, is mostly due to southern African fires, whose effect may be 2–3 times larger than the effect of South American fires at 970 mbar. Even in the central part of the continent, where local biomass-burning emissions are maximum, southern African fires contribute to at least 15% of the CO2 concentration increase at 970 mbar. At higher levels in the atmosphere, less CO2 emitted by north African savanna fires reaches South America, and at 100 mbar no significant amount of CO2 is transported across the Atlantic Ocean. The vertical structure of the CO2 concentration increase due to biomass burning differs substantially, depending on whether sources are local or remote. A prominent maximum of CO2 concentration increase in the lower layers characterizes the effect of local sources, whereas a more homogenous profile of CO2 concentration increase characterizes the effect of remote sources. The results demonstrate the strong remote effects of African biomass burning which, owing to the general circulation of the atmosphere, are felt as far away as South America.
Satellite Geodesy: Foundations, Methods, and Applications

Completely revised and updated edition. The book covers the entire field of satellite geodesy (status spring/\break summer 2002). Basic chapters on reference systems, time, signal propagation, and satellite orbits are updated. All currently important observation methods are included and also all newly launched satellites of interest to geodesy. Particular emphasis is given to the current status of the Global Positioning System (GPS), which covers now about one third of the book. A new chapter on Differential GPS and active GPS reference networks is included. The GPS modernization plans, GLONASS, the forthcoming European system GALILEO, modern developments in GPS data analysis, error modelling, precise real time methods and ambiguity resolution are dealt with in detail. New satellite laser ranging missions, new altimetry missions (e.g. TOPEX/Poseidon, ERS-1/2, GFO, JASON), and new and forthcoming gravity field missions (CHAMP, GRACE, GOCE) are also considered. The book serves as a textbook for advanced undergraduate and graduate students, as well as a reference for professionals and scientists in the field of engineering and geosciences such as geodesy, surveying, geo-information, navigation, geophysics and oceanography.