Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyborg islets: implanted flexible electronics reveal principles of human islet electrical maturation

Flexible electronics implanted during tissue formation enable chronic studies of tissue-wide electrophysiology. Here, we integrate tissue-like stretchable electronics during organogenesis of human stem cell-derived pancreatic islets, stably tracing single-cell extracellular spike bursting dynamics over months of functional maturation. Adapting spike sorting methods from neural studies reveals maturation-dependent electrical patterns of α and β-like (SC-α and β) cells, and their stimulus-coupled dynamics. We identified two major electrical states for both SC-α and β cells, distinguished by their glucose threshold for action potential firing. We find that improved hormone stimulation capacity during extended culture reflects increasing numbers of SC-α/β cells in low basal firing states, linked to energy and hormone metabolism gene upregulation. Continuous recording during further maturation by entrainment to daily feeding cycles reveals that circadian islet-level hormone secretion rhythms reflect sustained and coordinate oscillation of cell-level SC-α and β electrical activities. We find that this correlates with cell-cell communication and exocytic network induction, indicating a role for circadian rhythms in coordinating system-level stimulus-coupled responses. Cyborg islets thus reveal principles of electrical maturation that will be useful to build fully functional in vitro islets for research and therapeutic applications.
A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat

One of the most widely distributed bats in the New World, the big brown bat (Eptesicus fuscus) exhibits well‐documented geographic variation in morphology and life history traits, suggesting the potential for significant phylogeographic structure as well as adaptive differentiation among populations. In a pattern broadly consistent with morphologically defined subspecies, we found deeply divergent mitochondrial lineages restricted to different geographic regions. In contrast, sequence data from two nuclear loci suggest a general lack of regional genetic structure except for peripheral populations in the Caribbean and Mexico/South America. Coalescent analyses suggest that the striking difference in population structure between genomes cannot be attributed solely to different rates of lineage sorting, but is likely due to male‐mediated gene flow homogenizing nuclear genetic diversity across most of the continental range. Despite this ongoing gene flow, selection has apparently been effective in producing and maintaining adaptive differentiation among populations, while strong female site fidelity, maintained over the course of millions of years, has produced remarkably deep divergence among geographically isolated matrilines. Our results highlight the importance of evaluating multiple genetic markers for a more complete understanding of population structure and history.
Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce.
An Indicator of Probable Semicircular Canal Dehiscence

The n10 component of the ocular vestibular evoked myogenic potential (oVEMP) to sound and vibration stimuli is a crossed response that has enhanced amplitude and decreased threshold in patients with CT-verified superior semicircular canal dehiscence (SSCD). However, demonstrating enhanced VEMP amplitude and reduced VEMP thresholds requires multiple trials and can be very time consuming and tiring for patients, so a specific indicator of probable SCD that is fast and not tiring would be preferred. Here we report a 1-trial indicator: that the oVEMP n10 in response to a very high frequency stimulus (4000 Hz), either air-conducted sound (ACS) or bone conducted vibration (BCV), is such a fast indicator of probable SCD. In 22 healthy subjects, oVEMP n10 at 4000 Hz was not detectable; however, in all 22 CT-verified SSCD patients tested, oVEMP n10 responses were clearly present to 4000 Hz to either ACS or BCV stimuli.
The bidirectional role of GABAA and GABAB receptors during the differentiation process of neural precursor cells of the subventricular zone

The intricate process of neuronal differentiation integrates multiple signals to induce transcriptional, morphological, and electrophysiological changes that reshape the properties of neural precursor cells during their maturation and migration process. An increasing number of neurotransmitters and biomolecules have been identified that serve as molecular signals that trigger and guide this process. In this sense, taurine, a sulfur-containing, non-essential amino acid widely expressed in the mammal brain, modulates the neuronal differentiation process. In this study, we describe the effect of taurine acting via the ionotropic GABAA receptor and the metabotropic GABAB receptor on the neuronal differentiation and electrophysiological properties of precursor cells derived from the subventricular zone of the mouse brain. Taurine stimulates the number of neurites and favors the dendritic complexity of the neural precursor cells, accompanied by changes in the somatic input resistance and the strength of inward and outward membranal currents. At the pharmacological level, the blockade of GABAA receptors inhibits these effects, whereas the stimulation of GABAB receptors has no positive effects on the taurine-mediated differentiation process. Strikingly, the blockade of the GABAB receptor with CGP533737 stimulates neurite outgrowth, dendritic complexity, and membranal current kinetics of neural precursor cells. The effects of taurine on the differentiation process involve Ca2+ mobilization and the activation of intracellular signaling cascades since chelation of intracellular calcium with BAPTA-AM, and inhibition of the CaMKII, ERK1/2, and Src kinase inhibits the neurite outgrowth of neural precursor cells of the subventricular zone.
Color-tuned neurons are spatially clustered according to color preference within alert macaque posterior inferior temporal cortex

Large islands of extrastriate cortex that are enriched for color-tuned neurons have recently been described in alert macaque using a combination of functional magnetic resonance imaging (fMRI) and single-unit recording. These millimeter-sized islands, dubbed “globs,” are scattered throughout the posterior inferior temporal cortex (PIT), a swath of brain anterior to area V3, including areas V4, PITd, and posterior TEO. We investigated the micro-organization of neurons within the globs. We used fMRI to identify the globs and then used MRI-guided microelectrodes to test the color properties of single glob cells. We used color stimuli that sample the CIELUV perceptual color space at regular intervals to test the color tuning of single units, and make two observations. First, color-tuned neurons of various color preferences were found within single globs. Second, adjacent glob cells tended to have the same color tuning, demonstrating that glob cells are clustered by color preference and suggesting that they are arranged in color columns. Neurons separated by 50 μm, measured parallel to the cortical sheet, had more similar color tuning than neurons separated by 100 μm, suggesting that the scale of the color columns is <100 μm. These results show that color-tuned neurons in PIT are organized by color preference on a finer scale than the scale of single globs. Moreover, the color preferences of neurons recorded sequentially along a given electrode penetration shifted gradually in many penetrations, suggesting that the color columns are arranged according to a chromotopic map reflecting perceptual color space.
Nanotechnology and the Treatment of HIV Infection

Suboptimal adherence, toxicity, drug resistance and viral reservoirs make the lifelong treatment of HIV infection challenging. The emerging field of nanotechnology may play an important role in addressing these challenges by creating drugs that possess pharmacological advantages arising out of unique phenomena that occur at the “nano” scale. At these dimensions, particles have physicochemical properties that are distinct from those of bulk materials or single molecules or atoms. In this review, basic concepts and terms in nanotechnology are defined, and examples are provided of how nanopharmaceuticals such as nanocrystals, nanocapsules, nanoparticles, solid lipid nanoparticles, nanocarriers, micelles, liposomes and dendrimers have been investigated as potential anti-HIV therapies. Such drugs may, for example, be used to optimize the pharmacological characteristics of known antiretrovirals, deliver anti-HIV nucleic acids into infected cells or achieve targeted delivery of antivirals to the immune system, brain or latent reservoirs. Also, nanopharmaceuticals themselves may possess anti-HIV activity. However several hurdles remain, including toxicity, unwanted biological interactions and the difficulty and cost of large-scale synthesis of nanopharmaceuticals.
Decentralised intermittent control

Intermittent control uses open-loop control punctuated with feedback at times determined by error-driven events. The open-loop trajectories are based on an underlying closed-loop strategy and are generated by a system-matched hold. The single-loop event-driven intermittent control method is extended to the multi-loop decentralised control situation. This decentralised intermittent controller is based on an underlying continuous-time decentralised design which is suitable for systems with both input and state interactions. This extension is achieved by using local models of the remote interacting subsystems. These models are used for control signal generation and they are only updated with remote information at discrete event-driven sample times thus reducing information flow. The approach is illustrated using a simulation of a five-pool irrigation channel model previously examined in the literature.
A fast approach for traffic panel detection from natural scene images

Traffic panels contain rich text and symbolic information for transportation and scene understanding. Fast detection of traffic panels facilitates text information extraction but has been paid little attention by the community. In this paper, we propose a fast and robust approach for rectangular traffic panel detection from traffic scene images. Considering the rectangular shape of traffic panels, we first extract candidate line segments in gray-level image using a fast line segment detector, and panel proposals are formed from the line segments. The proposals are then filtered using a multi-stage classifier with multiple features. The surviving proposals undergo a post-processing refinement procedure using geometric constraints to give the bounding boxes of detected panels. Experimental results on real images from Baidu Street View demonstrate the effectiveness of the proposed method.
Time trend in access to the waiting list and renal transplantation: a comparison of four European countries.

BACKGROUND To examine the time trend and international differences in access to the waiting list and renal transplantation of patients with end-stage kidney disease. METHODS We included all patients (n = 30 961) from Austria, Norway, the Netherlands and Scotland who started renal replacement therapy (RRT) between 1995 and 2003 with their kidney transplant waiting list data (until 31 December 2005) and follow-up data on RRT and mortality (until 31 December 2007). The outcome measure was access to the waiting list within 2 years and to a first renal transplant within 4 years from the start of RRT, expressed as incidence per million age-related population (p.m.a.r.p.) per year. To estimate trends over time, mean percentage annual change (MPAC) and 95% confidence interval (CI) were calculated. RESULTS In each country, the number of patients starting RRT > 65 years increased significantly over time, whereas the number of renal transplants did not increase to the same extent. Only in Norway were almost all patients on the waiting list transplanted within 4 years of RRT start if they were < 65 years. In patients who started RRT > 65 years, the access to renal transplantation was high in Norway (49 p.m.a.r.p.) and low in Austria ( < 26 p.m.a.r.p.), the Netherlands and Scotland (both < 10 p.m.a.r.p.) but increased significantly in Austria (MPAC = 9.8%; 95% CI = 3.9-16.9) and the Netherlands (MPAC = 9.0%; 95% CI = 3.2-15.0). CONCLUSION Only in Norway, virtually all patients on the waiting list < 65 years received a transplant within 4 years after the start of RRT and, remarkably, also most of those > 65 years of age.
Pathwidth vs cocircumference

The circumference of a graph G with at least one cycle is the length of a longest cycle in G . A classic result of Birmelé (2003) states that the treewidth of G is at most its circumference minus 1 . In case G is 2 -connected, this upper bound also holds for the pathwidth of G ; in fact, even the treedepth of G is upper bounded by its circumference (Briański, Joret, Majewski, Micek, Seweryn, Sharma; 2023). In this paper, we study whether similar bounds hold when replacing the circumference of G by its cocircumference , defined as the largest size of a bond in G , an inclusion-wise minimal set of edges F such that G ´ F has more components than G . In matroidal terms, the cocircumference of G is the circumference of the bond matroid of G . Our first result is the following ‘dual’ version of Birmelé’s theorem: The treewidth of a graph G is at most its cocircumference. Our second and main result is an upper bound of 3 k ´ 2 on the pathwidth of a 2 -connected graph G with cocircumference k . Contrary to circumference, no such bound holds for the treedepth of G . Our two upper bounds are best possible up to a constant factor.
Logica: Declarative Data Science for Mere Mortals

Logica (=Logic+aggregation) is a freely available, open-source, feature-enhanced version of Datalog that automatically compiles logic rules to several SQL platforms, i.e., a lightweight, serverless SQLite engine, a multi-user client-server PostgreSQL system, and a highly scalable, parallel BigQuery instance. Logica combines the beginner-friendly declarative features of Datalog (intuitive, pattern-based queries in the style of QBE), with advanced analytical features needed by data science practitioners when processing large, real-world datasets. The system has been used for data science applications and training in industry, and in graduate-level courses in academia. Logica allows beginners to seamlessly progress from traditional (toy) examples to intermediate and advanced use cases.
TASHEEH: Repairing Row-Structure in Raw CSV Files

Comma-separated value (CSV) files follow a useful and wide-spread format for data exchange due to their flexible standard. However, due to this flexibility and plain text format, such files often have structural issues, such as unescaped quote characters within quoted fields, columns containing different value formats, rows with different numbers of cells, etc. We refer to rows that contain such structural inconsistencies as ill-formed . Consequently, ingesting them into a host system, such as a database or an analytics platform, often requires prior data preparation steps.
Characterizing the Gilbert-Elliott Parameter Space under LDPC Decoding

There has been much recent interest in analyzing the performance of LDPC codes in channels with memory. Density evolution (DE) may be used to analyze estimation-decoding algorithms employing the Sum-Product Algorithm for LDPC codes in Gilbert-Elliott (GE) channels. In this paper, we provide theoretical results which mitigate the complexity of characterizing the 4-dimensional GE parameter space using DE. For each point in the parameter space which is shown by DE to converge to Pe → 0, we show that a region of convergence is induced, within which all points also converge to Pe → 0. Conversely, for points found not to converge, we show that a region of non-convergence is induced. Using these results, the GE parameter space is partitioned into a region of convergence, a region of nonconvergence, and an uncertain region, which guides the selection of new points to test using DE.
Fast wideband near-field imaging with URAs applied to urban sensing

High resolution wideband near-field imaging requires wideband signals and large array apertures. Hence, a large amount of data needs to be processed in the image formation step. The computational load of the standard delay and sum beamformer stems from the calculation of the focus delays and the evaluation of the sums over the measurements. We propose an approach tackling the problem of calculating the focus delays. Provided a uniform rectangular array (URA) is used, the image can be evaluated on a well tailored discrete grid such that most focus delays are redundant. Now by calculating only the non-redundant values we can reduce the numerical complexity significantly. The above approach is combined with fast beamforming based on the non-equispaced fast Fourier transform (NFFT). We demonstrate the good performance with experimental results from a through-the-wall radar imaging system.
A Method for Deciding Node Density in Non-Uniform Deployment of Wireless Sensor Networks

In a sensor network, if the sensors are deployed uniformly across the network, they experience different traffic intensities and energy depletion rates depending on their locations. Usually, the sensors near the sink tend to deplete their energy sooner; when enough of them exhaust their energy, they leave holes in the network, causing the remaining nodes to be disconnected from the sink. One of the solutions to this energyhole problem is to deploy the sensors non-uniformly. This paper describes a method for deciding the sensor deployment densities so as to equalize the energy consumption rates of all nodes. The method can be generalized to other similar objectives.
2009 Pandemic influenza A virus subtype H1N1 in Morocco, 2009-2010: epidemiology, transmissibility, and factors associated with fatal cases.

BACKGROUND Following the emergence of 2009 pandemic influenza A virus subtype H1N1 (A[H1N1]pdm09) in the United States and Mexico in April 2009, A(H1N1)pdm09 spread rapidly all over the world. There is a dearth of information about the epidemiology of A(H1N1)pdm09 in Africa, including Morocco. We describe the epidemiologic characteristics of the A(H1N1)pdm09 epidemic in Morocco during 2009-2010, including transmissibility and risk factors associated with fatal disease. METHODS We implemented influenza surveillance for patients presenting with influenza-like illness (ILI) at 136 private and public clinics for patients with severe acute respiratory illness (SARI) at 16 regional public hospitals from June 2009 through February 2010. Respiratory samples and structured questionnaires were collected from all enrolled patients, and samples were tested by real-time reverse-transcription polymerase chain reaction for influenza viruses. We estimated the risk factors associated with fatal disease as well as the basic reproduction number (R(0)) and the serial interval of the pandemic virus. RESULTS From June 2009 through February 2010, we obtained 3937 specimens, of which 1452 tested positive for influenza virus. Of these, 1398 (96%) were A(H1N1)pdm09. Forty percent of specimens from ILI cases (1056 of 2646) and 27% from SARI cases (342 of 1291) were positive for A(H1N1)pdm09. Sixty-four deaths occurred among laboratory-confirmed A(H1N1)pdm09 SARI cases. Among these cases, those who had hypertension (age-adjusted odd ratio [aOR], 28.2; 95% confidence interval [CI], 2.0-398.7), had neurological disorders (aOR, 7.5; 95% CI, 1.5-36.4), or were obese (aOR, 7.1; 95% CI, 1.6-31.1), as well as women of gestational age who were pregnant (aOR, 2.5; 95% CI, 1.1-5.6), were at increased risk of death. Across the country, elevated numbers of locally acquired infections were detected 4 months after the detection of the first laboratory-confirmed case and coincided with the expected influenza season (October-January) in Morocco. We obtained an R(0) estimate of 1.44 (95% CI, 1.32-1.56) and a mean serial interval (±SD) of 2.3 ± 1.4 days (95% CI, 1.6-3.0). CONCLUSION Widespread but delayed community transmission of A(H1N1)pdm09 occurred in Morocco in 2009, and A(H1N1)pdm09 became the dominant influenza virus subtype during the 2009-2010 influenza season. The transmissibility characteristics were similar to those observed in other countries.
Stomach development, stem cells and disease

The stomach, an organ derived from foregut endoderm, secretes acid and enzymes and plays a key role in digestion. During development, mesenchymal-epithelial interactions drive stomach specification, patterning, differentiation and growth through selected signaling pathways and transcription factors. After birth, the gastric epithelium is maintained by the activity of stem cells. Developmental signals are aberrantly activated and stem cell functions are disrupted in gastric cancer and other disorders. Therefore, a better understanding of stomach development and stem cells can inform approaches to treating these conditions. This Review highlights the molecular mechanisms of stomach development and discusses recent findings regarding stomach stem cells and organoid cultures, and their roles in investigating disease mechanisms. Summary: This Review highlights the molecular mechanisms of stomach development and discusses recent findings regarding stomach stem cells and organoid cultures, and their roles in investigating stomach diseases.