Miracle-dz/UniFAR-FTUs huggingface dataset:
Timing, variability and cross-protection in bacteria – Insights from dynamic gene expression responses to antibiotics

Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature.
Adaptive Behavior Modeling in Logistic Systems with Agents and Dynamic Graphs

Inside a logistic system, actors of the logistics have to interact to manage a coherent flow of goods. They also must deal with the constraints of their environment. The article’s first goal is to study how macro properties (such as global performance) emerge from the dynamic and local behaviors of actors and the structure of the territory. The second goal is to understand which local parameters affect these macro properties. A multi-scale approach made of an agent-based model coupled with dynamic graphs describes the system’s components, including actors and the transportation network. Adaptive behaviors are implemented in this model (with data about the Seine axis) to highlight the system’s dynamics. Agent strategies are evolving according to traffic dynamics and disruptions. This logistic system simulator has the capacity to exhibit large-scale evolution of territorial behavior and efficiency face to various scenarios of local agent behaviors.
The amoeboid migration of monocytes in confining channels requires the local remodeling of the cortical actin cytoskeleton by cofilin-1

Within the bloodstream, monocytes must traverse the microvasculature to prevent leukostasis, which is the entrapment of monocytes within the confines of the microvasculature. Using the model cell line, THP-1, and VCAM-1 coated channels to simulate the microvasculature, we demonstrate that monocytes predominantly adopt an amoeboid phenotype, which is characterized by the formation of blebs. As opposed to cortical actin flow in leader blebs, cell movement is correlated with myosin contraction at the cell rear. Previously, we documented that cofilin-1 promotes cortical actin turnover at leader bleb necks in melanoma cells. In monocytes, our data suggest that cofilin-1 promotes the local upregulation of myosin contractility through actin cytoskeleton remodeling. In support of this concept, cofilin-1 is found to localize to a single cell edge. Moreover, the widespread upregulation of myosin contractility was found to inhibit migration. Thus, monocytes within the microvasculature may avoid entrapment by adopting an amoeboid mode of migration. Summary Statement In confining channels, monocytes largely adopt an amoeboid migrating phenotype, which is found to depend on the upregulation of myosin contractility at the cell rear and cortical actin remodeling by cofilin-1.
Automatic Design of Controllers for Modular Reconfigurable Robot Manipulators

Modular robotic systems offer the possibility to create different robots from arbitrary assembly of modules. These robots will have different kinematics and dynamics, and generating model-based controllers for all possible assemblies of modules a priori is impractical. This thesis addresses the control problem for this class of robots by designing centralized model-based controllers automatically, right after assembly of modules. The results show that the automatic generation of centralized model-based controllers is feasible and practical, even when compliant actuators are employed.
Variation of cardiac troponin I and T measured with sensitive assays in emergency department patients with noncardiac chest pain

BACKGROUND : New-generation high-sensitivity assays for cardiac troponin have lower detection limits and less imprecision than earlier assays. Reference 99th-percentile cutoff values for these new assays are also lower, leading to higher frequencies of positive test re-sults. When cardiac troponin concentrations are minimally increased, serial testing allows discrimination of myocardial infarction from other causes of increased cardiac troponin. We assessed various measures of short-term variation, including absolute concentration changes, reference change values (RCVs), and indices of individuality (II) for 2 cardiac troponin assays in emergency department (ED) patients. METHODS : We collected blood from patients presenting with cardiac chest pain upon arrival in the ED and 2, 6, and 12 h later. Cardiac troponin was measured with the high-sensitivity cardiac troponin T (hs-cTnT) assay (Roche Diagnostics) and a sensitive cTnI assay (Siemens Diagnostics). Cardiac troponin results from 67 patients without acute coronary syndrome or stable angina were used in calculating absolute changes in cardiac troponin, RCVs, and II. RESULTS : The 95th percentiles for absolute change in cardiac troponin were 8.3 ng/L for hs-cTnT and 28 ng/L for cTnI. Within-individual and total CVs were 11% and 14% for hs-cTnT and 18% and 21% for cTnI, respectively. RCVs were 38% (hs-cTnT) and 57% (cTnI). The corresponding log-normal RCVs were (cid:1) 46%/ (cid:2) 32% for hs-cTnT and (cid:1) 76%/ (cid:2) 43% for cTnI. II values were 0.31 (cTnI) and 0.12 (hs-cTnT). CONCLUSIONS : The short-term
EFFECTIVE UNIVERSITY TEACHING IN NIGERIA: A CORE COMPONENT OF INTERNAL QUALITY ASSURANCE MECHANISM

This paper discussed the effectiveness of university teaching in Nigeria: a core component of the internal quality assurance mechanism. University education is/are to contribute to national development through high-level workforce training and to create the intellectual capability of individuals to realize and acknowledge their local and external environs, among others. University cannot effectively or nobly serve the nation until it fulfills these responsibilities to itself. As part of contributing to national development, University promotes the acquisition of knowledge, nourishes the latent potentials of the individuals and qualities for a gainful profession. Effective teaching requires lecturers to possess certain characteristics, such as empathy for students, knowledge of the subject, preparedness, openness to change, feedback and creativity among others. There are principles of effective teaching in University which include relationship building, engaging active learning, assessment and feedback from students and lecturers. Unless university teaching is effective and efficient, it will be difficult for the university to meet its primary responsibility of feeding the mind with desirable knowledge and liquidation of ignorance. It is therefore recommended that mechanisms should be put in place for continuous assessment of effective University teaching. Seminars should be organized on a regular basis for lecturers on the need for effective teaching in the university.
Wenn Mediendarbietungen Antwortleistung und Antwortdisposition gleichzeitig bestimmen

Medien-und werbepsychologischen Forschung übliche Analysemodelle untersuchen Effekte durch direkten Vergleich der Häufigkeiten oder Durchschnitte manifester Indikatorvariablen. Zentral für sogenannte True-Score-Analysen nach der klassischen Testtheorie (KTT) ist die Annahme, dass Schwankungen in den individuellen Ausprägungen der manifesten Indikatorvariable, die nicht auf Variationen der angenomme-nen Verursachungsgröße (wahrer ‚Prädiktor’) zurückgehen sondern durch Drittvariablen (‚Fehler’) verursacht werden, stochastisch unabhängig davon sind. Da diese Voraussetzung in der empirischen Praxis regelmäßig verletzt ist, kommen Kovarianz-, Interaktionseffekt-und Mehrebe-nenanalysen immer häufiger zum Einsatz. Die folgend diskutierte Re-Analyse von zwei medienpsychologischen Studien verweist theoretisch und empirisch auf eine Problematik, die in der Arbeit mit Häufigkeiten und Durchschnitten manifester Indikatorvariablen selbst bei Anwendung der
A Review of Chinese Sentiment Analysis: Subjects, Methods, and Trends

Sentiment analysis has emerged as a prominent research domain within the realm of natural language processing, garnering increasing attention and a growing body of literature. While numerous literature reviews have examined sentiment analysis techniques, methods, topics and applications, there remains a gap in the literature concerning thematic trends and research methodologies in sentiment analysis, particularly in the context of Chinese text. This study addresses this gap by presenting a comprehensive survey dedicated to the progression of research subjects, methods and trends in sentiment analysis of Chinese text. Employing a framework that combines keyword co-occurrence analysis with a sophisticated community detection algorithm, this survey offers a novel perspective on the landscape of Chinese sentiment analysis research. By tracing the interplay between research methodologies and emerging topics over the past two decades, our study not only facilitates a comparative analysis of their correlations but also illuminates evolving patterns, identifying significant hotspots and trends over time for Chinese language text analysis. This invaluable insight provides a roadmap for researchers seeking to navigate the intricate terrain of sentiment analysis within the context of Chinese language. Moreover, this paper extends beyond the academic realm, offering practical insights into sentiment analysis methodologies and themes while pinpointing avenues for future exploration, technical limitations, and directions for sentiment analysis of Chinese text.
Robbers, marshals, and guards: game theoretic and logical characterizations of hypertree width

In a previous paper [10], the authors introduced the notion of hypertree decomposition and the corresponding concept of hypertree width and showed that the conjunctive queries whose hypergraphs have bounded hypertree-width can be evaluated in polynomial time. Bounded hypertree-width generalizes the notions of acyclicity and bounded treewidth and corresponds to larger classes of tractable queries. In the present paper, we provide natural characterizations of hypergraphs and queries having bounded hypertree-width in terms of game-theory and logic. First we define the Robber and Marshals game, and prove that a hypergraph H has hypertree-width at most k iff k marshals have a winning strategy on H, allowing them to trap a robber who moves along the hyperedges. This game is akin the well-known Robber and Cops game (which characterizes bounded treewidth), except that marshals are more powerful than cops: They can control entire hyperedges instead of just vertices. Kolaitis and Vardi [17] recently gave an elegant characterization of the conjunctive queries having treewidth < k in terms of the k-variable fragment of a certain logic L ( = existential-conjunctive fragment of positive FO). We use the Robber and Marshals game to derive a surprisingly simple and equally elegant characterization of the class HW[k] of queries of hypertree-width at most k in terms of guarded logic. In particular, we show that HW[k] = GFk (L), where GFk(L) denotes the k-guarded fragment of L. In this fragment, conjunctions of k atoms rather than just single atoms are allowed to act as guards. Note that, for the particular case k = 1, our results provide new characterizations of the class of acyclic queries. We extend the notion of bounded hypertreewidth to nonrecursive stratified datalog and show that the k-guarded fragment GFk(FO) of first order logic has the same expressive power as nonrecursive stratified datalog of hypertreewidth ⪇ k.
ADVANCES IN AGRICULTURAL AND FOOD RESEARCH JOURNAL

: Industrial machines and robots use actuators to facilitate repetitive tasks. Conventionally, stiff actuators are used to enable precise position control in a high-pace system. They are usually placed in human-free environments because of safety concerns as they do not comply in a collision. On the other hand, there has been a growing interest in human-robot interactions that require robots to be placed alongside humans. These applications need a soft actuator. An example of a soft actuator is a pneumatic muscle actuator (PMA) which produces a one-way motion and force as a result of the muscle’s contraction under air pressure. In this paper, the aim is to present a systematic review covering the main published solutions of soft actuators including PMA in agricultural applications. This paper provides a useful foundation on the soft actuators, their main applications in agriculture, their challenges and opportunities, as well as supporting new research works in the soft actuators' field.
Trust and Public Policy: Lessons from the Pandemic

This paper examines the importance of mutual con(cid:133)dence or trust be-tween a government and its citizens on the e⁄ectiveness of public policies. We develop a theoretical framework where the designing of government policies and the concomitant actions of the citizens are meditated by the degree of social trust. We introduce a short term aggregative health shock - a pandemic - which is novel: its charateristics are not fully known at the onset. This creates scope for government intervention in the form of framing of the policy announcement and its information content. We use this framework to examine the relationship between government communication, social trust and compliance. For any given level of trust, we analyse the equilibrium framing of the policy as well as the corresponding response and examine the degree of policy e⁄ectiveness as a function of the existing level of trust.
A rare case of calcaneal bone osteomyelitis resulting from local paracoccidioidomycosis in an immunosuppressed patient: a case report

Isolated bone involvement of paracoccidioidomycosis without any pulmonary focus is rare. This report documents the first case of calcaneal osteomyelitis, where bone infection was the only manifestation of the disease. A young 22-year-old male, mixed race, from a rural area in Brazil, was treated in the orthopedics emergency room. He reported a callus in the region of the Achilles tendon and developed intermittent claudication and, at times, inability to walk. In addition to having a low fever and sweating. He was hypertensive and on immunosuppressive medication due to a previous kidney transplant. An intracalcaneal collection was observed on magnetic resonance imaging, requiring surgical treatment for debridement and filling of the bone defect. After surgical intervention and administration of antifungal medication, the patient’s symptoms gradually improved. The epidemiological evaluation for differential diagnosis and the multidisciplinary clinical-orthopedic approach with effective diagnosis and treatment enabled the best clinical outcomes for the patient.
Genome-wide association study of lifetime cannabis use based on a large meta-analytic sample of 32 330 subjects from the International Cannabis Consortium

Cannabis is the most widely produced and consumed illicit psychoactive substance worldwide. Occasional cannabis use can progress to frequent use, abuse and dependence with all known adverse physical, psychological and social consequences. Individual differences in cannabis initiation are heritable (40 – 48%). The International Cannabis Consortium was established with the aim to identify genetic risk variants of cannabis use. We conducted a meta-analysis of genome-wide association data of 13 cohorts ( N =32 330) and four replication samples ( N =5627). In addition, we performed a gene-based test of association, estimated single-nucleotide polymorphism (SNP)-based heritability and explored the genetic correlation between lifetime cannabis use and cigarette use using LD score regression. No individual SNPs reached genome-wide signi ﬁ cance. Nonetheless, gene-based tests identi ﬁ ed four genes signi ﬁ cantly associated with lifetime cannabis use: NCAM1 , CADM2 , SCOC and KCNT2 . Previous studies reported associations of NCAM1 with cigarette smoking and other substance use, and those of CADM2 with body mass index, processing speed and autism disorders, which are phenotypes previously reported to be associated with cannabis use.
BIOINFORMATICS ORIGINAL

Motivation: Identifying piwi-interacting RNAs (piRNAs) of non-model organisms is a difﬁcult and unsolved problem because piRNAs lack conservative secondary structure motifs and sequence homology in different species. Results: In this article, a k -mer scheme is proposed to identify piRNA sequences, relying on the training sets from non-piRNA and piRNA sequences of ﬁve model species sequenced: rat, mouse, human, fruit ﬂy and nematode. Compared with the existing ‘static’ scheme based on the position-speciﬁc base usage, our novel ‘dynamic’ algorithm performs much better with a precision of over 90% and a sensitivity of over 60%, and the precision is veriﬁed by 5-fold cross-validation in these species. To test its validity, we use the algorithm to identify piRNAs of the migratory locust based on 603607 deep-sequenced small RNA sequences. Totally, 87536 piRNAs of the locust are predicted, and 4426 of them matched with existing locust transposons. The transcriptional difference between solitary and gregarious locusts was described. We also revisit the position-speciﬁc base usage of piRNAs and ﬁnd the conservation in the end of piRNAs. Therefore, the method we developed can be used to identify piRNAs of non-model organisms without
Substrate model extraction using ﬁnite differences and parallel multigrid

Substrate noise in integrated circuits is one of the most important problems in high-frequency mixed-signal designs, such as communication, biomedical and analog signal processing circuits and systems. Fast-switching digital blocks inject noise into the common substrate, hindering the performance of high-precision sensible analog circuitry. Miniaturization trends require increasing the accuracy in substrate coupling simulation environments. However, model extraction and evaluation times should not increase, which demands for fast and still accurate substrate model extraction tools. In this work, a three-dimensional ﬁnite difference extraction methodology is presented. The resulting three-dimensional mesh is efﬁciently reduced to a circuit-level contact-based model by means of a fast multigrid-based algorithm. Moreover, this contact-based model extraction is shown to be efﬁciently computed in a parallel environment, resulting in extremely useful extraction speedups. Extraction results prove the proposed method to be very efﬁcient, providing linear time and space complexity, and a constant number of iterations, outperforming competing algorithms.
Investigation of the Residual in Column-Integrated Atmospheric Energy Balance Using Cloud Objects

AbstractObservationally based atmospheric energy balance is analyzed using Clouds and the Earth’s Radiant Energy System (CERES)-derived TOA and surface irradiance, Global Precipitation Climatology Project (GPCP)-derived precipitation, dry static and kinetic energy tendency and divergence estimated from ERA-Interim, and surface sensible heat flux from SeaFlux. The residual tends to be negative over the tropics and positive over midlatitudes. A negative residual implies that the precipitation rate is too small, divergence is too large, or radiative cooling is too large. The residual of atmospheric energy is spatially and temporally correlated with cloud objects to identify cloud types associated with the residual. Spatially, shallow cumulus, cirrostratus, and deep convective cloud-object occurrence are positively correlated with the absolute value of the residual. The temporal correlation coefficient between the number of deep convective cloud objects and individual energy components, net atmospheric irradi.
Generalization of 𝑏 2 -metric spaces and some fixed point theorems

Highlights  Introduce the concept of extended 𝒃 𝟐 metric space.  Establish some fixed-point theorems for self-mapping define on such spaces.  As an application of our results, we will use fixed-point theorem to show that there is a unique solution to some integral equations.