Miracle-dz/UniFAR-FTUs huggingface dataset:
Capecitabine-associated enterocolitis: Narrative literature review of a rare adverse event and a case presentation

Abstract Capecitabine is an oral 5-fluorouracil prodrug with antimetabolite activity commonly used in advanced colorectal and breast cancer. It presents with a generally good toxicity profile and most of the adverse events can be managed effectively. Enterocolitis is a rare, under-reported, but potentially fatal adverse event associated with capecitabine use. To the best of our knowledge, there are 21 cases of capecitabine-related enterocolitis reported in the literature. We herein present a narrative literature review of enteritis/colitis cases associated with capecitabine use, with highlight to the most common clinical presentation, common imaging and microscopic findings and management approach. We furthermore present a case of severe capecitabine-related enteritis.
Downscaling hermit crab-gastropod network to demographic groups unveils recurrent patterns

We studied the hermit crab–shell interaction network of rocky shores in South Brazil using both community and populational (demographic groups) approaches which evaluated both inter and intraspecific perspectives. The community was composed of six hermit crab species and 33 gastropod shell species. We found a recurrent pattern in which the network structure was characterized by a modular and specialized pattern. The specialization at the species level varies in the community species and for ontogenetic groups. The configuration of the modules changed when switching from community to populational approaches, consisting of three and four modules, respectively. Resource partitioning must be a very important feature in these systems due to both the specific and demographic needs of each group. Our results reveal a pattern in which these types of interactions are modular and specialized, with those patterns being uncommon for non-mutualistic interactions in hermit crab-gastropod networks. The analyses showed difference in the network metrics when considering intra and interspecific perspectives. The mandatory nature of these interactions and the resource dynamics of the gastropod shells when occupied by hermit crabs may partially explain the patterns found for these unique interactions.
Making addicts: critical reflections on agency and responsibility from lawyers and decision makers

Various activities are increasingly characterised as ‘addictions’, including within the law, and raise important questions. Do ‘addicts’ have agency? Do addictions shape social problems such as family and sexual violence? And how do those involved in legal systems perceive addictions? This paper explores these questions. Drawing on qualitative interviews with lawyers and decision makers (N = 48), it explores addiction in law. Lawyers and decision makers see themselves as playing important roles in making addiction and ‘addicts’. Addiction is an effect principally of legal strategy, and other forces. Legal processes bring differing conceptions of agency and responsibility into being, problematising understandings of agency as an ‘effect’ of addiction, or as pre-existing legal processes. There are also important variations in approach regarding different addictions. Alcohol or other drug addiction is seen as ‘genuine’, and a major factor in family violence, while sex addiction lacks credibility. I explore some implications of these approaches.
Hypometabolism to survive the long polar night in the diatom Fragilariopsis cylindrus

Diatoms, the major eukaryotic phytoplankton in polar regions, are essential to sustain Arctic and Antarctic ecosystems. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their resilience to the long polar night. Here, we report an integrative approach revealing that in prolonged darkness, diatom cells enter a state of quiescence associated with reduced metabolic and transcriptional activity during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate, and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness. Our results further indicate that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis. Cell division resumed rates similar to those before darkness. Our study demonstrates the remarkable robustness of polar diatoms to prolonged darkness at low temperatures. Graphical abstract Teaser To survive the long winter, polar diatoms slow down metabolism and express genes to assure survival following return to light.
Cytoplasmic Aggregation of RPB1 Predicts Failure of Neoadjuvant Chemotherapy

We aimed to investigate the contribution of co-translational protein aggregation to the chemotherapy resistance of tumor cells. Increased co-translational protein aggregation reflects altered translation regulation that may have the potential to buffer transcription under genotoxic stress. As an indicator for such event, we followed cytoplasmic aggregation of RPB1, the aggregation prone largest subunit of RNA polymerase II, in biopsy samples taken from patients with invasive carcinoma of no special type. RPB1 frequently aggregates co-translationally in the absence of proper HSP90 chaperone function or in ribosome mutant cells as revealed formerly in yeast. We found that cytoplasmic foci of RPB1 occur in larger sizes in tumors that showed no regression after therapy. Based on these results, we propose that monitoring the cytoplasmic aggregation of RPB1 may be suitable for determining – from biopsy samples taken before treatment – the effectiveness of neoadjuvant chemotherapy.
Limit analysis of plates-a finite element formulation

A procedure for the computation of the load carrying capacity of perfectly plastic plates in bending is presented. The approach, based on the kinematic theorem of limit analysis, requires the evaluation of the minimum of a convex, but non-smooth, function under linear equality constraints. A systematic solution procedure is devised, which detects and eliminates the finite elements which are predicted as rigid in the collapse mechanism, thus reducing the problem to the search for the minimum of a smooth and essentially unconstrained function of nodal velocities. Both Kirchhoff and Mindlin plate models are considered. The effectiveness of the approach is illustrated by means of some examples.
DReAmocracy: A Method to Capitalize on Prior Drug Discovery Efforts to Highlight Candidate Drugs for Repurposing

In the area of drug research, several computational drug repurposing studies have highlighted candidate repurposed drugs, as well as drugs from clinical trial studies in different phases. To our knowledge, the aggregation of the proposed lists of drugs by previous studies has not been extensively exploited towards the generation of a dynamic reference matrix regarding the disease-related frequencies of drug features such as the modes of action, the initial indications and the targeted pathways. To fill this knowledge gap, we performed a weight-modulated majority voting of the modes of action, initial indications and targeted pathways of the drugs in a well-known repository, namely the Drug Repurposing Hub. Our method, DReAmocracy, exploits this pile of information and creates frequency tables and finally a disease suitability score for each drug. As a testbed, we applied this method to a group of neurodegenerative diseases (Alzheimer’s, Parkinson’s, Huntington’s and Multiple Sclerosis). A super-reference table with drug suitability scores has been created for all four neurodegenerative diseases and can be queried for any drug candidate against them. Top-scored drugs for Alzheimer’s disease include agomelatine and mirtazapine, for Parkinson’s disease apomorphine and pramipexole, for Huntington’s fluphezine and perphezine, and for Multiple Sclerosis zonisamide and disopyramide. Overall, DReAmocracy is a methodology that leverages the existing experimental and/or computational knowledge (1) to reveal trends in selected tracks of drug discovery research that includes modes of action, targeted pathways and initial indications for the investigated drugs and (2) to score new candidate drugs for repurposing against a selected disease.
Ex vivo tissue perturbations coupled to single cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis

Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivo cytokine and drug perturbations of human precision-cut lung slices (hPCLS) with scRNAseq and induced a multi-lineage circuit of fibrogenic cell states in hPCLS, which we show to be highly similar to the in vivo cell circuit in a multi-cohort lung cell atlas from pulmonary fibrosis patients. Using micro-CT staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the ex vivo hPCLS model provides evidence that the basaloid cell state was derived from alveolar type-2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in the hPCLS model and anti-fibrotic drug treatments showed highly cell type specific effects. Our work provides an experimental framework for perturbational single cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration and pathology. We further demonstrate that hPCLS offers novel avenues for scalable, high-resolution drug testing to accelerate anti-fibrotic drug development and translation.
Kinematic and neuromuscular characterization of cognitive involvement in gait control in healthy young adults

The signature of cognitive involvement in gait control has rarely been studied using both kinematic and neuromuscular features. The present study aimed to address this gap. Twenty-four healthy young adults walked on an instrumented treadmill in a virtual environment under two optic flow conditions: normal (NOF) and perturbed (POF, continuous mediolateral pseudo-random oscillations). Each condition was performed under single-task and dual-task conditions of increasing difficulty (1-, 2-, 3- back). Subjective mental workload (raw NASA-TLX), cognitive performance (mean reaction time and d-prime), kinematic (steadiness, variability and complexity in the mediolateral and anteroposterior directions) and neuromuscular (duration and variability of motor primitives) control of gait were assessed. The cognitive performance and the number and composition of motor modules were unaffected by simultaneous walking, regardless of the optic flow condition. Kinematic and neuromuscular variability was greater under POF compared to NOF conditions. Young adults sought to counteract POF by rapidly correcting task-relevant gait fluctuations. The depletion of cognitive resources through dual-tasking led to reduced kinematic and neuromuscular variability but this occurred to the same extent regardless of simultaneous WM load. Increasing WM load led to a prioritization of gait control in the ML direction over the AP direction. The impact of POF on kinematic variability (step velocity) was reduced when a cognitive task was performed simultaneously, but this phenomenon was no more pronounced with increasing WM load. Collectively, these findings highlight the kinematic and neuromuscular adjustments in gait control associated with the separate and joint effects of cognitive and visual constraints during treadmill walking. NEW & NOTEWORTHY The kinematic and neuromuscular signatures of cognitive involvement in gait control have rarely been studied jointly. We sought to address this issue using gait perturbation and dual-task paradigms. The protocol consisted of a fixed-speed treadmill walk to which visual and cognitive constraints were applied separately and together. The results revealed that young adults optimally regulated their gait to cope with these constraints by maintaining relatively stable muscle synergies and flexibly allocating attentional resources.
Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities cultured in vitro from human feces to uncover simple assembly rules and develop a predictive model of community composition upon addition of single nutrients from central carbon metabolism to a complex medium. Community membership was largely determined by the donor feces, whereas relative abundances were determined by the supplemental carbon source. The absolute abundance of most taxa was independent of the supplementing nutrient, due to the ability of fast-growing organisms to quickly exhaust their niche in the complex medium and then exploit and monopolize the supplemental carbon source. Relative abundances of dominant taxa could be predicted from the nutritional preferences and growth dynamics of species in isolation, and exceptions were consistent with strain-level variation in growth capabilities. Our study reveals that community assembly follows simple rules of nutrient utilization dynamics and provides a predictive framework for manipulating gut commensal communities through nutritional perturbations.
Global biogeography of the smallest plankton across ocean depths

Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography are partially understood. Comprehending whether these microorganisms are structured by niche vs. neutral processes is highly relevant in the context of global change. The ecological drivers structuring picoplankton communities differ between prokaryotes and minute eukaryotes (picoeukaryotes) in the global surface ocean: while prokaryotic communities are shaped by a balanced combination of dispersal, selection, and drift, picoeukaryotic communities are mainly shaped by dispersal limitation. Yet, whether or not the relative importance of these processes in structuring picoplankton varies as we dive into the deep ocean was unknown. Here we investigate the mechanisms structuring picoplanktonic communities inhabiting different ocean depths. We analyzed 451 samples from the tropical and subtropical global ocean and the Mediterranean Sea covering the epi- (0-200m), meso- (200- 1,000m), and bathypelagic (1,000-4,000m) depth zones. We found that selection decreased with depth possibly due to lower habitat heterogeneity. In turn, dispersal limitation increased with depth, possibly due to dispersal barriers such as water masses and bottom topography. Picoplankton β-diversity positively correlated with environmental heterogeneity and water mass variability in both the open-ocean and the Mediterranean Sea. However, this relationship tended to be weaker for picoeukaryotes than for prokaryotes. Community patterns were generally more pronounced in the Mediterranean Sea, probably because of its substantial cross-basin environmental heterogeneity and deep-water isolation. Altogether, we found that different combinations of ecological mechanisms shape the biogeography of the smallest members of the ocean microbiome across ocean depths.
Effect of three‐dimensionality on the lift and drag of nominally two‐dimensional cylinders

It has been known for some time that two‐dimensional numerical simulations of flow over nominally two‐dimensional bluff bodies at Reynolds numbers for which the flow is intrinsically three dimensional, lead to inaccurate prediction of the lift and drag forces. In particular, for flow past a normal flat plate (International Symposium on Nonsteady Fluid Dynamics, edited by J. A. Miller and D. P. Telionis, 1990, pp. 455–464) and circular cylinders [J. Wind Eng. Indus. Aerodyn. 35, 275 (1990)], it has been noted that the drag coefficient computed from two‐dimensional simulations is significantly higher than what is obtained from experiments. Furthermore, it has been found that three‐dimensional simulations of flows lead to accurate prediction of drag [J. Wind Eng. Indus. Aerodyn. 35, 275 (1990)]. The underlying cause for this discrepancy is that the surface pressure distribution obtained from two‐dimensional simulations does not match up with that obtained from experiments and three‐dimensional simulations an.
Magnetic resonance fingerprinting based thermometry (MRFT): application to ex vivo imaging near DBS leads

The purpose of this study is to demonstrate the first work of T 1-based magnetic resonance thermometry using magnetic resonance fingerprinting (dubbed MRFT). We compared temperature estimation of MRFT with proton resonance frequency shift (PRFS) thermometry on ex vivo bovine muscle. We demonstrated MRFT’s feasibility in predicting temperature on ex vivo bovine muscles with deep brain stimulation (DBS) lead. B 0 maps generated from MRFT were compared with gold standard B 0 maps near the DBS lead. MRFT and PRFS estimated temperatures were compared in the presence of motion. All experiments were performed on a 3 Tesla whole-body GE Premier system with a 21-channel receive head coil (GE Healthcare, Milwaukee, WI). Four fluoroptic probes were used to measure the temperature at the center of a cold muscle (probe 1), the room temperature water bottle (probe 2), and the center and periphery of the heated muscle (probes 3 and 4). We selected regions of interest (ROIs) around the location of the probes and used simple linear regression to generate the temperature sensitivity calibration equations that convert T 1 maps and Δs maps to temperature maps. We then repeated the same setup and compared MRFT and PRFS thermometry temperature estimation with gold standard probe measurements. For the MRFT experiment on DBS lead, we taped the probe to the tip of the DBS lead and used a turbo spin echo sequence to induce heating near the lead. We selected ROIs around the tip of the lead to compare MRFT temperature estimation with probe measurements and compared with PRFS temperature estimation. Vendor-supplied B 0 mapping sequence was acquired to compare with MRFT-generated B 0 maps. We found strong linear relationships (R 2 > 0.958) between T 1 and temperature and Δs and temperatures in our temperature sensitivity calibration experiment. MRFT and PRFS thermometry both accurately predict temperature (RMSE < 1.55 °C) compared to probe measurements. MRFT estimated temperature near DBS lead has a similar trend as the probe temperature. Both B 0 maps show inhomogeneities around the lead. MRFT estimated temperature is less sensitive to motion.
Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification

The transition between pluripotent and tissue-specific states is a key aspect of development. Understanding the pathways driving these transitions will facilitate the engineering of properly differentiated cells for experimental and therapeutic uses. Here, we showed that during mesoderm differentiation, the transcription factor Oct1 activated developmental lineage-appropriate genes that were silent in pluripotent cells. Using mouse embryonic stem cells (ESCs) with an inducible knockout of Oct1, we showed that Oct1 deficiency resulted in poor induction of mesoderm-specific genes, leading to impaired mesodermal and terminal muscle differentiation. Oct1-deficient cells exhibited poor temporal coordination of the induction of lineage-specific genes and showed inappropriate developmental lineage branching, resulting in poorly differentiated cell states retaining epithelial characteristics. In ESCs, Oct1 localized with the pluripotency factor Oct4 at mesoderm-associated genes and remained bound to those loci during differentiation after the dissociation of Oct4. Binding events for Oct1 overlapped with those for the histone lysine demethylase Utx, and an interaction between Oct1 and Utx suggested that these two proteins cooperate to activate gene expression. The specificity of the ubiquitous Oct1 for the induction of mesodermal genes could be partially explained by the frequent coexistence of Smad and Oct binding sites at mesoderm-specific genes and the cooperative stimulation of mesodermal gene transcription by Oct1 and Smad3. Together, these results identify Oct1 as a key mediator of mesoderm lineage–specific gene induction.
Two-Dimensional TE-Plane Wave Scattering by a Dielectric-Loaded Semicircular Trough in a Ground Plane

The Rayleigh method is applied to solving the boundary value problem (BVP) for an E-polarized plane wave scattering by a dielectric-loaded semicircular trough in a perfectly electrically conducting (PEC) plane. A Fredholm second kind matrix equation is obtained for the Fourier coefficients upon using an additional equation in contrast to the traditional method. The Fredholm equation obtained yields a numerical solution with guaranteed convergence to the mentioned BVP. Proposed method is applied to study the radar cross section (RCS) reduction problem and to a model investigation of backscattering from an iceberg compared to rough estimated low-angle sea-clutter.
Structure of the light-induced metastable state SII inNa2[Fe(CN)5NO]∙2H2O

The structure of the light-induced metastable state SII of Na{sub 2}[Fe(CN){sub 5}NO]{center_dot}2H{sub 2}O was investigated by single-crystal neutron diffraction. The population of SII of 16(3)% was determined by an in situ transmission measurement. The final structural refinement yields a side-on bonded configuration of NO in the metastable state SII with distances Fe-O, Fe-N, and N-O of 2.01(5) A, 1.96(5) A, and 1.11(8) A, respectively. The angle Fe-N-O is 77(4) deg. The population determined from the refinement is 12(2)%, in good agreement with the value of 16(3)% determined from the independent in situ transmission measurement.
A Low-resource Approach to SemTab 2022

Mapping tabular data to a Knowledge Graph is a common task that often involves the use of considerable resources in terms of disk space, system memory and processing power. This paper introduces a barebones system that needs only modest computer hardware and only relies on Python, yet still achieves 77.0% F1 and 84.6% F1 on the SemTab 2022 Round 1 CTA and CEA tasks respectively. In its current form, the system can only solve specific kinds of cases, but pointers are provided as to how it could be expanded to become more versatile. Our source code has been made available online.
JenTab: Do CTA Solutions Affect the Entire Scores?

Semantic Table Annotation remains a crucial task to exploit tabular data in knowledge-aware systems. However, in the process, annotation systems have to overcome various issues ranging from mere typos over inconsistent naming conventions to homonymy among values. The Semantic Web Challenge on Tabular Data to Knowledge Graph Matching (SemTab) continues to provide demanding datasets to evaluate annotation systems and drive their continued development. In this paper, we describe JenTab’s adaptations to the 2022 edition of SemTab: In particular, we added an additional preprocessing step to target Tough Tables (2T)’s excessive misspellings and a new pipeline to exploit meaningful header information. In addition, for each round, we execute two different settings of Column Type Annotation (CTA) creation. We report on the impact of these changes on JenTab’s results. In 2022, we highlight the effect of the CTA on the overall score per round. Our GitHub Repository: https://github.com/fusion-jena/JenTab