Miracle-dz/UniFAR-FTUs huggingface dataset:
Lef1-dependent Wnt/β-catenin signalling drives the proliferative engine that maintains tissue homeostasis during lateral line development

During tissue morphogenesis and differentiation, cells must self-renew while contemporaneously generating daughters that contribute to the growing tissue. How tissues achieve this precise balance between proliferation and differentiation is, in most instances, poorly understood. This is in part due to the difficulties in dissociating the mechanisms that underlie tissue patterning from those that regulate proliferation. In the migrating posterior lateral line primordium (PLLP), proliferation is predominantly localised to the leading zone. As cells emerge from this zone, they periodically organise into rosettes that subsequently dissociate from the primordium and differentiate as neuromasts. Despite this reiterative loss of cells, the primordium maintains its size through regenerative cell proliferation until it reaches the tail. In this study, we identify a null mutation in the Wnt-pathway transcription factor Lef1 and show that its activity is required to maintain proliferation in the progenitor pool of cells that sustains the PLLP as it undergoes migration, morphogenesis and differentiation. In absence of Lef1, the leading zone becomes depleted of cells during its migration leading to the collapse of the primordium into a couple of terminal neuromasts. We show that this behaviour resembles the process by which the PLLP normally ends its migration, suggesting that suppression of Wnt signalling is required for termination of neuromast production in the tail. Our data support a model in which Lef1 sustains proliferation of leading zone progenitors, maintaining the primordium size and defining neuromast deposition rate.
Online Community Detection by Using Nearest Hubs

Community and cluster detection is a popular field of social network analysis. Most algorithms focus on static graphs or series of snapshots. In this paper we present an algorithm, which detects communities in dynamic graphs. The method is based on shortest paths to high-connected nodes, so called hubs. Due to local message passing we can update the clustering results with low computational power. The presented algorithm is compared with other for some static social networks. The reached modularity is not as high as the Louvain method, but even higher then spectral clustering. For large-scale real-world datasets with given ground truth, we could reconstruct most of the given community structure. The advantage of the algorithm is the good performance in dynamic scenarios.
Arsenic and other water‐quality issues affecting groundwater, Indus alluvial plain, Pakistan

Groundwater beneath the alluvial plain of the Indus River, Pakistan, is reported to be widely polluted by arsenic (As) and to adversely affect human health. In 79 groundwaters reported here from the lower Indus River plain in southern Sindh Province, concentrations of As exceeded the WHO guideline value for drinking water of 10 μg/L in 38%, with 22% exceeding 50 μg/L, Pakistan's guideline value. The As pollution is caused by microbially‐mediated reductive dissolution of sedimentary iron oxyhydroxides in anoxic groundwaters; oxic groundwaters contain <10 μg/L of As. In the upper Indus River plain, in Punjab Province, localized As pollution of groundwater occurs by alkali desorption as a consequence of ion exchange in groundwater, possibly supplemented by the use for irrigation of groundwater that has suffered ion exchange in the aquifer and so has values >0 for residual sodium carbonate. In the field area in southern Sindh, concentrations of Mn in groundwater exceed 0.4 mg/L in 11% of groundwaters, with a maximum of 0.7 mg/L, as a result of reduction of sedimentary manganese oxides. Other trace elements pose little or no threat to human health. Salinities in groundwaters range from fresh to saline (electrical conductivity up to 6 mS/cm). High salinities result from local inputs of waste water from unsewered sanitation but mainly from evaporation/evapotranspiration of canal water and groundwater used for irrigation. The process does not concentrate As in the groundwater owing to sorption of As to soils. Ion exchange exerts a control on concentrations of Na, Ca, and B but not directly on As. High values of Cl/Br mass ratios (most ≫288, the marine value) reflect the pervasive influence on groundwater of sewage‐contaminated water from irrigation canals through seepage loss and deep percolation of irrigation water, with additional, well‐specific, contributions from unsewered sanitation.
Faithful Representation of Stimuli with a Population of Integrate-and-Fire Neurons

We consider a formal model of stimulus encoding with a circuit consisting of a bank of filters and an ensemble of integrate-and-fire neurons. Such models arise in olfactory systems, vision, and hearing. We demonstrate that bandlimited stimuli can be faithfully represented with spike trains generated by the ensemble of neurons. We provide a stimulus reconstruction scheme based on the spike times of the ensemble of neurons and derive conditions for perfect recovery. The key result calls for the spike density of the neural population to be above the Nyquist rate. We also show that recovery is perfect if the number of neurons in the population is larger than a threshold value. Increasing the number of neurons to achieve a faithful representation of the sensory world is consistent with basic neurobiological thought. Finally we demonstrate that in general, the problem of faithful recovery of stimuli from the spike train of single neurons is ill posed. The stimulus can be recovered, however, from the information contained in the spike train of a population of neurons.
ATYPICAL PRESENTATIONS OF GALL BLADDER CARCINOMA

The incidence of gallbladder carcinoma is 1.2 cases per 100,000/ year and increases with age, particularly after the sixth decade of life. Ethnic background and geographical location are important factors in the incidence of this cancer. It is more common in Central and South America, Japan and North India. Risk factors include cholelithiasis, calcified gallbladder wall, adenomatous gallbladder polyps, choledochal cyst and anomalous pancreatobiliary junction.
Antibacterial and Cytotoxic Efficacy of Extracellular Silver Nanoparticles Biofabricated from Chromium Reducing Novel OS4 Strain of Stenotrophomonas maltophilia

Biofabricated metal nanoparticles are generally biocompatible, inexpensive, and ecofriendly, therefore, are used preferably in industries, medical and material science research. Considering the importance of biofabricated materials, we isolated, characterized and identified a novel bacterial strain OS4 of Stenotrophomonas maltophilia (GenBank: JN247637.1). At neutral pH, this Gram negative bacterial strain significantly reduced hexavalent chromium, an important heavy metal contaminant found in the tannery effluents and minings. Subsequently, even at room temperature the supernatant of log phase grown culture of strain OS4 also reduced silver nitrate (AgNO3) to generate nanoparticles (AgNPs). These AgNPs were further characterized by UV–visible, Nanophox particle size analyzer, XRD, SEM and FTIR. As evident from the FTIR data, plausibly the protein components of supernatant caused the reduction of AgNO3. The cuboid and homogenous AgNPs showed a characteristic UV-visible peak at 428 nm with average size of ∼93 nm. The XRD spectra exhibited the characteristic Bragg peaks of 111, 200, 220 and 311 facets of the face centred cubic symmetry of nanoparticles suggesting that these nanoparticles were crystalline in nature. From the nanoparticle release kinetics data, the rapid release of AgNPs was correlated with the particle size and increasing surface area of the nanoparticles. A highly significant antimicrobial activity against medically important bacteria by the biofabricated AgNPs was also revealed as decline in growth of Staphylococcus aureus (91%), Escherichia coli (69%) and Serratia marcescens (66%) substantially. Additionally, different cytotoxic assays showed no toxicity of AgNPs to liver function, RBCs, splenocytes and HeLa cells, hence these particles were safe to use. Therefore, this novel bacterial strain OS4 is likely to provide broad spectrum benefits for curing chromium polluted sites, for biofabrication of AgNPs and ultimately in the nanoparticle based drug formulation for the treatment of infectious diseases.
Biodiversity and Urban Gardens: Medicinal and Aromatic Plants That Can Used In Erzurum (Turkey) Urban Gardens

Abstract Turkey is a rich country in biodiversity due to its characteristics like topographic and geomorphological structures it shelters, being an extended peninsula and climatic features. Europe and Middle East countries with the richest biodiversity distribution showing the number of plant species in Turkey is close to the number of plant species in the whole of the European continent. According to data of TUBIVES 2017 (official plant database), Turkey owns more than 12000 plant taxa 3000 of which are endemic. Erzurum province shelters 264 of endemic plants growing in East Anatolia, some of which have medicinal and aromatic effects East Anatolia Region of Turkey is the second richest region in the country following the Mediterranean for the number of endemic plant species. The method of research consists of survey, data collection, analysis and synthesis. As a result of this study; among the medicinal and aromatic plants grown naturally in and around Erzurum city, fruit, flowers, calligraphic features, seasonal colour change, plants which can be used as ornamental plants were determined and their usage areas in landscape architecture were determined. _________________________________________________________________________________ Biyocesitlilik ve Kentsel Bahceler: Erzurum (Turkiye) Kentsel Bahcelerinde Kullanilan Tibbi ve Aromatik Bitkiler Oz Turkiye, sahip oldugu topografik, jeomorfolojik yapi, uc tarafinin denizlerle cevrili olmasi, iklim ozellikleri gibi faktorlerden dolayi biyocesitlilik yonunden oldukca zengin bir ulkedir. Avrupa ve Orta Dogunun en zengin biyolojik cesitlilige sahip ulkesi olan Turkiye’de yayilis gosteren bitki turlerinin sayisi Avrupa kitasinin tumundeki bitki turlerinin sayisina yakindir. Yani, bu haliyle Turkiye Florasi bir kita florasi niteligine sahiptir. TUBIVES 2017 verilerine gore; Turkiye, 3000 ’i askin endemik olmak uzere, 12000’e yakin bitki taksonuna sahiptir. Dogu Anadolu Bolgesi’nin sahip oldugu endemik bitkilerin 264 ’u Erzurum kentine aittir. Bu bitkilerin bir kismi tibbi ve aromatik etkiye sahiptir. Dogu Anadolu Bolgesi, endemik bitki sayisi yonunden Akdeniz Bolgesi’nden sonra ikinci sirada yer alir. Arastirmanin yontemini etut, veri toplama, analiz ve sentez olusturmaktadir. Bu calismanin sonucunda; Erzurum kenti ve cevresinde dogal olarak yetisen, tibbi, aromatik yonden kullanilan bitkiler arasindan meyve, cicek, kaligrafik ozellik, mevsimsel renk degisimi bakimindan etkili olan ayni zamanda sus bitkisi olarak kullanilabilecek bitkiler belirlenip peyzaj mimarligindaki kullanim alanlari tespit edilmistir. Anahtar Kelimeler: Biyocesitlilik, tibbi ve aromatik bitkiler, peyzaj mimarligi, Erzurum, Turkiye
Buildings in Urban Regeneration

The number of people living in urban areas worldwide is constantly rising. This puts significant pressure on resources in general—leading to an urgent need for the radical improvement of local infrastructure, especially housing, food, water and waste. Managing urban areas is therefore one of the most important development challenges of the twenty-first century. The built environment is a key element in urban living. Significant investments in infrastructure and further development must be made to accommodate the increasing number of people moving to cities, thereby increasing the pressure on available resources and waste generated. Cities also face a huge energetic refurbishment task. These transformations of cities at the same time offer new opportunities: energetic refurbishment could bring multiple benefits to the citizens, and smart material loops can make the circular economy a reality. The design of and the material used for buildings also have a bearing on other important aspects of sustainability and urban life. They affect factors such as health, thermal comfort, acoustic performance and fire resilience. By taking a holistic approach, buildings have the potential to be a part of the solution of today’s and tomorrow’s challenges through the creation of sustainable cities. Cities have the power to act and make changes happen within their boundaries.
Dimensionality Reduction Based Similarity Visualization for Neural Gas

Two commonly used neural networks for vector quantization based analysis of high-dimensional large datasets are the self-organizing map (SOM) and neural gas (NG). Owing to their rigid grid structure, SOMs are widely used for data visualization, whereas NG based visualization has been limited, despite the fact that NG can achieve better quantization than SOMs in terms of quantization error. As a visualization tool for NG, we propose to use a recent projection technique t-SNE (which depends on stochastic neighbor embedding using student t-distribution). T-SNE projection of NG will construct a low-dimensional space where local similarities of high-dimensional data space are preserved to a great extent. In addition, this enables the use of Connives (a topology-based visualization for SOMs) to represent the data space similarities on the low-dimensional projection space. Experiments on the synthetic and real datasets show that the proposed NG visualization based on t-SNE and enhanced with Connives is helpful for interactive analysis of high-dimensional large datasets.
Glutamate‐dependent astrocyte modulation of synaptic transmission between cultured hippocampal neurons

The idea that astrocytes merely provide structural and trophic support for neurons has been challenged by the demonstration that astrocytes can regulate neuronal calcium levels. However, the physiological consequences of astrocyte–neuron signalling are unknown. Using mixed cultures of rat hippocampal astrocytes and neurons we have determined functional consequences of elevating astrocyte calcium levels on co‐cultured neurons. Electrical or mechanical stimulation of astrocytes to increase their calcium level caused a glutamate‐dependent slow inward current (SIC) in associated neurons. Microinjection of 1,2‐bis(2‐aminophenoxy)ethane‐N,N,N′,N′‐tetraacetic acid (BAPTA) into astrocytes to prevent the stimulus‐dependent increase in astrocyte calcium level, blocks the appearance of the neuronal SIC. Pharmacological manipulations indicate that this astrocyte‐dependent SIC is mediated by extracellular glutamate acting on N‐methyl‐d‐aspartate (NMDA) and non‐NMDA glutamate receptors. Additionally, stimulation of astrocytes reduced the magnitude of action potential‐evoked excitatory and inhibitory postsynaptic currents through the activation of metabotropic glutamate receptors. The demonstration that astrocytes modulate neuronal currents and synaptic transmission raises the possibility that astrocytes play a neuromodulatory role by controlling the extracellular level of glutamate.
Usher Syndrome: Genes, Proteins, Models, Molecular Mechanisms, and Therapies

Usher syndrome (USH) is an autosomal recessive genetic disease, characterized by both deafness and blindness. It was first described by Albrecht von Grafe, a German ophthalmologist, in 1858 (von Graefe, 1858) and then named after Charles Usher, a British ophthalmologist, who reported the inheritance of this disease on the basis of 69 cases in 1914 (Usher, 1914). USH is clinically heterogeneous and is categorized into three types, according to the severity of its hearing and vestibular symptoms (Smith et al., 1994; Petit, 2001). Type I (USH1) patients have congenital severe to profound deafness as well as vestibular dysfunction; Patients with USH2 exhibit congenital moderate degree of hearing loss and normal vestibular function; and those with USH3 display progressive hearing impairment and occasional vestibular dysfunction. The vision problem of all three types is manifested as retinitis pigmentosa (Hartong et al., 2006; Sadeghi et al., 2006; Fishman et al., 2007; Sandberg et al., 2008; Malm et al., 2011), showing early night and peripheral vision loss and eventual central vision loss.
Infliximab-related seizures: a first case study

Seizures following infliximab treatment are very rare and, to date, there is no detailed description of EEG abnormalities with cerebral radiological findings reported in cases with infliximab-related seizures. We describe a patient who acutely developed seizures temporally related to infliximab treatment, which disappeared after drug withdrawal. MRI showed encephalopathy involving mainly cortical regions and EEGs showed focal paroxysmal activity which completely disappeared a few days after infliximab withdrawal. No other plausible cause of the seizures was identified. The clear temporal association between seizure onset and infliximab treatment as well as the clinical improvement and disappearance of focal epileptiform activity after drug withdrawal indicated an evident correlation between seizures and infliximab therapy. The coexistence of pathological findings on MRI suggested that seizures were secondary to the encephalopathy. Further studies are required to evaluate whether infliximab per se has an epileptogenic effect or whether the seizures are caused by encephalopathy involving cortico-subcortical regions.
Simple Modification of Oja Rule Limits L1-Norm of Weight Vector and Leads to Sparse Connectivity

This letter describes a simple modification of the Oja learning rule, which asymptotically constrains the L1-norm of an input weight vector instead of the L2-norm as in the original rule. This constraining is local as opposed to commonly used instant normalizations, which require the knowledge of all input weights of a neuron to update each one of them individually. The proposed rule converges to a weight vector that is sparser (has more zero weights) than the vector learned by the original Oja rule with or without the zero bound, which could explain the developmental synaptic pruning.
WSN15-1: Resource Allocation in Wireless Relay Networks

In this paper, a resource allocation scheme is proposed for wireless relay networks to achieve maximum system throughput in terms of achievable average mutual information with low computational complexity. A relay network, which has single source node, multiple relay nodes and single destination node, is analyzed from the information theory point of view. Both sufficient and necessary conditions are derived for the best relay node selection, and a close-form of optimal power allocation between the source and the relay nodes is obtained. Application of the proposed resource allocation schemes in practical relay networks with incomplete channel state information is also studied. Simulation results are presented to demonstrate the effectiveness of the proposed resource allocation schemes in wireless relay networks.
An efficient RMS admission control and its application to multiprocessor scheduling

A real-time system must execute functionally correct computations in a timely manner. In order to guarantee that all tasks accepted in the system will meet their timing requirements, an admission control algorithm must be used to only accept tasks whose requirements can be satisfied. Rate-monotonic scheduling (RMS) is arguably the best known scheduling policy for periodic real-time tasks on uniprocessors. We propose a new and efficient admission control for rate-monotonic scheduling on a uniprocessor and analyze its performance. This admission control is then modified to provide an admission control mechanism for multiprocessor systems. Experimental results indicate that this new admission control for multiprocessor systems achieves a processor utilization of up to 96% for a large number of tasks and has a low computational complexity. The proposed admission control is also used to derive a new and better multiprocessor schedulability bound for RMS with provisions for periodic servers and for RMS with tolerance to transient faults.
Vitamin D and Neurological Diseases: An Endocrine View

Vitamin D system comprises hormone precursors, active metabolites, carriers, enzymes, and receptors involved in genomic and non-genomic effects. In addition to classical bone-related effects, this system has also been shown to activate multiple molecular mediators and elicit many physiological functions. In vitro and in vivo studies have, in fact, increasingly focused on the “non-calcemic” actions of vitamin D, which are associated with the maintenance of glucose homeostasis, cardiovascular morbidity, autoimmunity, inflammation, and cancer. In parallel, growing evidence has recognized that a multimodal association links vitamin D system to brain development, functions and diseases. With vitamin D deficiency reaching epidemic proportions worldwide, there is now concern that optimal levels of vitamin D in the bloodstream are also necessary to preserve the neurological development and protect the adult brain. The aim of this review is to highlight the relationship between vitamin D and neurological diseases.
Arginine decarboxylase from Escherichia coli. II. Dissociation and reassociation of subunits.

Abstract The inducible arginine decarboxylase of Escherichia coli B has a sedimentation coefficient, s°20, ω of 23.3 S and a molecular weight of 850,000. It dissociates to five subunits of identical size which have a sedimentation coefficient of 8.0 S and a molecular weight of 165,000. Dissociation occurs when the buffer cations are monovalent, the pH is greater than 6.5, and the concentration of monovalent cations is less than 0.05 m. It proceeds more rapidly at elevated temperatures and low protein concentrations. The characteristics of this dissociation suggest that it is caused by the creation of a new electrostatic repulsion, possibly by ionization of the carboxyl groups of glutamic or aspartic acid. The dissociated species can be reassociated fully with an activity loss of less than 10% by dialysis against a buffer containing divalent cations or a high concentration of monovalent cations at a pH less than 6. If the dissociated species is exposed to an inhibitory substrate analogue such as α-chloroδ-guanidovaleric acid, as many as five species can be observed in the ultracentrifuge. Two of these correspond to the 8 S and 23 S species; the other three have sedimentation coefficients of approximately 12.1 S, 16.4 S, and 19.5 S. The five sedimentation coefficients are consistent with a molecular weight ratio of 5:4:3:2:1, providing excellent support for the conclusion that the 23 S species is composed of five 8 S subunits. Preliminary experiments indicate that the 8 S subunit is itself a dimer; this is consistent with the observation of 10 pyridoxal-P binding sites per (associated) molecule. Measurements of decarboxylase activity indicate that the 23 S species is almost certainly active, whereas the 8 S species is either less active or inactive.