Miracle-dz/UniFAR-FTUs huggingface dataset:
IGF signaling between blastema and wound epidermis is required for fin regeneration

In mammals, the loss of a limb is irreversible. By contrast, urodele amphibians and teleost fish are capable of nearly perfect regeneration of lost appendages. This ability depends on direct interaction between the wound epithelium and mesenchymal progenitor cells of the blastema. It has been known for decades that contact between the wound epithelium and the underlying blastema is essential for successful regeneration. However, the underlying mechanisms are poorly understood. Here, we show that upon amputation the blastema induces expression of the ligand Igf2b, which then activates IGF signaling specifically in cells of the adjacent apical epithelium. Inhibition of IGF signaling by either morpholino antisense technology, or by specific chemical inhibitors of Igf1 receptor function NVP-AEW541 and NVP-ADW742, impairs fin regeneration. At the cellular level, this block in regeneration is reflected by a lack of the distinctive basal epithelium, increased apoptosis in the wound epidermis and reduced proliferation of blastema cells. Furthermore, induction of the blastemal and wound epidermal markers cannot be supported in the absence of IGF signaling. These data provide evidence that Igf2b expressed in the blastema promotes the properties of the adjacent wound epidermis, which subsequently are necessary for blastema function. Thus, IGF signaling upregulated upon fin amputation represents a signal from the blastema to the wound epithelium, a crucial step in appendage regeneration.
EVIDENCE FOR RECYCLING OF SYNAPTIC VESICLE MEMBRANE DURING TRANSMITTER RELEASE AT THE FROG NEUROMUSCULAR JUNCTION

When the nerves of isolated frog sartorius muscles were stimulated at 10 Hz, synaptic vesicles in the motor nerve terminals became transiently depleted. This depletion apparently resulted from a redistribution rather than disappearance of synaptic vesicle membrane, since the total amount of membrane comprising these nerve terminals remained constant during stimulation. At 1 min of stimulation, the 30% depletion in synaptic vesicle membrane was nearly balanced by an increase in plasma membrane, suggesting that vesicle membrane rapidly moved to the surface as it might if vesicles released their content of transmitter by exocytosis. After 15 min of stimulation, the 60% depletion of synaptic vesicle membrane was largely balanced by the appearance of numerous irregular membrane-walled cisternae inside the terminals, suggesting that vesicle membrane was retrieved from the surface as cisternae. When muscles were rested after 15 min of stimulation, cisternae disappeared and synaptic vesicles reappeared, suggesting that cisternae divided to form new synaptic vesicles so that the original vesicle membrane was now recycled into new synaptic vesicles. When muscles were soaked in horseradish peroxidase (HRP), this tracerfirst entered the cisternae which formed during stimulation and then entered a large proportion of the synaptic vesicles which reappeared during rest, strengthening the idea that synaptic vesicle membrane added to the surface was retrieved as cisternae which subsequently divided to form new vesicles. When muscles containing HRP in synaptic vesicles were washed to remove extracellular HRP and restimulated, HRP disappeared from vesicles without appearing in the new cisternae formed during the second stimulation, confirming that a one-way recycling of synaptic membrane, from the surface through cisternae to new vesicles, was occurring. Coated vesicles apparently represented the actual mechanism for retrieval of synaptic vesicle membrane from the plasma membrane, because during nerve stimulation they proliferated at regions of the nerve terminals covered by Schwann processes, took up peroxidase, and appeared in various stages of coalescence with cisternae. In contrast, synaptic vesicles did not appear to return directly from the surface to form cisternae, and cisternae themselves never appeared directly connected to the surface. Thus, during stimulation the intracellular compartments of this synapse change shape and take up extracellular protein in a manner which indicates that synaptic vesicle membrane added to the surface during exocytosis is retrieved by coated vesicles and recycled into new synaptic vesicles by way of intermediate cisternae.
The Amino Acid Valine Is Secreted in Continuous-Flow Bacterial Biofilms

ABSTRACT Biofilms are structured communities characterized by distinctive gene expression patterns and profound physiological changes compared to those of planktonic cultures. Here, we show that many gram-negative bacterial biofilms secrete high levels of a small-molecular-weight compound, which inhibits the growth of only Escherichia coli K-12 and a rare few other natural isolates. We demonstrate both genetically and biochemically that this molecule is the amino acid valine, and we provide evidence that valine production within biofilms results from metabolic changes occurring within high-density biofilm communities when carbon sources are not limiting. This finding identifies a natural environment in which bacteria can encounter high amounts of valine, and we propose that in-biofilm valine secretion may be the long-sought reason for widespread but unexplained valine resistance found in most enterobacteria. Our results experimentally validate the postulated production of metabolites that is characteristic of the conditions associated with some biofilm environments. The identification of such molecules may lead to new approaches for biofilm monitoring and control.
Navigating Relationships and Boundaries: Concerns around ICT-uptake for Elderly People

Despite a proliferation of research in the use of ICTs to support active and healthy ageing, few have considered the privacy and security concerns particular to the elderly. We investigated the appropriation of tablet devices and a neighborhood portal as well as emerging privacy and security issues through ethnographic and action research in a long-term participatory design (PD) project with elderly participants. We discuss two major themes: a) the tensions related to perceived digital threats and the social pressures of online disclosure to the social environment; and b) the relation of these issues to the ICT appropriation process and the referring challenges we encountered. We argue that there is a need to understand the interleaving of physical and virtual habitats, the various ways resulting in discomfort and the senior citizens' actions -- which at first glance appear contradictory. We consider the implications of the issues observed for examining privacy and security concerns more broadly as well as discussing implications for the design of the portal and the shaping of social measures for appropriation support.
Chan-Vese based method to segment mouse brain MRI images: Application to cerebral malformation analysis in Trisomy 21

A semi automatic active contour method based on Chan-Vese model is proposed for the segmentation of mouse brain MR images. First, a 2 ½ D strategy is applied on the axial images to segment the 3D volume of interest. The method takes into account the special shape of the object to segment. Moreover, the user defines the limits where to search these contours and also provides an initial contour. This semi automatic method makes that human intervention is limited and the tedious manual handling is greatly reduced. Results have shown that the brain volumes estimated by the method are identical to expert manually estimated volumes. Last but not least, the new method was used in the analysis of the cerebral malformations linked to Trisomy 21: no significant difference of the brain volumes between Trisomy 21 mice and the control ones were found.
Choline Uptake in Agrobacterium tumefaciens by the High-Affinity ChoXWV Transporter

ABSTRACT Agrobacterium tumefaciens is a facultative phytopathogen that causes crown gall disease. For successful plant transformation A. tumefaciens requires the membrane lipid phosphatidylcholine (PC), which is produced via the methylation and the PC synthase (Pcs) pathways. The latter route is dependent on choline. Although choline uptake has been demonstrated in A. tumefaciens, the responsible transporter(s) remained elusive. In this study, we identified the first choline transport system in A. tumefaciens. The ABC-type choline transporter is encoded by the chromosomally located choXWV operon (ChoX, binding protein; ChoW, permease; and ChoV, ATPase). The Cho system is not critical for growth and PC synthesis. However, [14C]choline uptake is severely reduced in A. tumefaciens choX mutants. Recombinant ChoX is able to bind choline with high affinity (equilibrium dissociation constant [KD] of ≈2 μM). Since other quaternary amines are bound by ChoX with much lower affinities (acetylcholine, KD of ≈80 μM; betaine, KD of ≈470 μM), the ChoXWV system functions as a high-affinity transporter with a preference for choline. Two tryptophan residues (W40 and W87) located in the predicted ligand-binding pocket are essential for choline binding. The structural model of ChoX built on Sinorhizobium meliloti ChoX resembles the typical structure of substrate binding proteins with a so-called “Venus flytrap mechanism” of substrate binding.
Head pose and gaze direction tracking for detecting a drowsy driver

This paper proposes a system that uses gaze direction tracking and head pose estimation to detect drowsiness of a driver. Head pose is estimated by calculating optic flow of the facial features, which are acquired with a corner detection algorithm. Analysis of the driver's head behavior leads to three moving components: nodding, shaking, and tilting. To track the gaze direction of the driver, we trace the center point of the pupil using CDF analysis and estimate the frequency of eye-movement.
Human ileal bile acid transporter gene ASBT (SLC10A2) is transactivated by the glucocorticoid receptor

Background: Patients with Crohn’s disease suffer from intestinal bile acid malabsorption. Intestinal bile acid absorption is mediated by the apical sodium dependent bile acid transporter ASBT/IBAT (SLC10A2). In rats, ASBT is induced by glucocorticoids. Aims: To study whether human ASBT is activated by glucocorticoids and to elucidate the mechanism of regulation. Patients and methods: ASBT expression in ileal biopsies from patients with Crohn’s disease and from healthy subjects was quantified by western blot. ASBT promoter function was studied in luciferase assays and by electrophoretic mobility shift assay. Results: In 16 patients with Crohn’s disease, ASBT expression was reduced to 69 (7.5)% compared with healthy controls (mean (SEM); p = 0.01). In 10 healthy male volunteers, ASBT protein expression was increased 1.34 (0.11)-fold (mean (SEM); p<0.05) after 21 days’ intake of budesonide (9 mg/day) whereas expression of the peptide transporter 1 was unaffected. Reporter constructs of the human ASBT promoter were activated 15–20-fold by coexpression of the glucocorticoid receptor (GR) and exposure to the GR ligands dexamethasone or budesonide. Two glucocorticoid response elements in the ASBT promoter, arranged as inverted hexanucleotide repeats (IR3 elements), conferred inducibility by GR and dexamethasone in a heterologous promoter context and were shown to bind GR in mobility shift assays. Conclusions: Human ASBT is induced by glucocorticoids in vitro and in vivo. Induction of ASBT by glucocorticoids could be beneficial in patients with Crohn’s disease who exhibit reduced ASBT expression. This study identifies ASBT as a novel target of glucocorticoid controlled gene regulation in the human intestine.
Multiscale Biomaterials for Cell and Tissue Engineering

ii Dedication . v Acknowledgements . vi VITA . viii Statement of Contributions . xii List of Figures . xix List of Tables . xxii Chapter 1: Introduction to multiscale biomaterials for cell and tissue engineering . 1 1.1. Overview of tissue engineering and its challenges . 1 1.2. Sources of cells . 2 1.3. Native tissue microenvironment . 3 1.4. Current techniques for culturing cells (2D vs. 3D culture system) . 4 1.5. Biomaterials for 3D cell culture . 8 1.5. 1. Types of biomaterials being used for tissue engineering . 8 1.5. 2. Properties of Ideal biomaterials . 12 1.5. 3. Manufacturing technology . 13 1.6. Cell encapsulation in micro-hydrogels for tissue engineering . 14 1.6. 1. Core-shell microcapsules for cell encapsulation and its advantages. 15 1.7. Cell encapsulation via droplet microfluidics . 16 1.8. Modular tissue engineering for fabricating complex tissues . 21 1.9. Scope of the thesis and organization . 23 Chapter 2: Microfluidic generation of core-shell microcapsules for miniaturized culture of mouse embryonic stem cells . 25 2.
Comparison of Electroacupuncture and Moxibustion for Relieving Visceral Hypersensitivity in Rats with Constipation-Predominant Irritable Bowel Syndrome

Aim. To compare whether there is different effect between electroacupuncture (EA) and moxibustion (Mox) on visceral hypersensitivity (their analgesic effects) in constipation-predominant irritable bowel syndrome (C-IBS). Methods. EA at 1 mA and 3 mA and Mox at 43°C and 46°C were applied to the Shangjuxu (ST37, bilateral) acupoint in rats with C-IBS and normal rats. An abdominal withdrawal reflex (AWR) score was used to assess visceral hypersensitivity. Toluidine blue staining was used to assess mast cell (MC) activity in colon of rats. Immunochemistry was used to measure 5-HT and 5-HT4 receptor expression in the colon. Results. AWR scores in all EA (1 mA and 3 mA) and Mox (43°C and 46°C) treatment groups after colorectal distention (CRD) stimulation pressure of 20, 40, 60, and 80 mmHg were significantly lower than those of the model (MC) group (P all < 0.01). The MC counts and degranulation rates in the colon of all EA and Mox treatment groups and the MC group were significantly higher than those of the NC group (P all < 0.01). MC degranulation rates in the colon of all EA and Mox treatment groups were lower than those of the MC group (P all < 0.05). 5-HT expression in colon of all EA and Mox treatment groups was significantly lower than that of the MC group (P all < 0.01), and 5-HT4R expression in colon of both EA groups was significantly higher than that of the MC group (P both < 0.01). Conclusion. EA and Mox treatments may both ameliorate visceral hypersensitivity at different degree in rats with C-IBS, and EA treatment was better than Mox.
SYMPATRIC CONVERGENCE AND ENVIRONMENTAL CORRELATION BETWEEN TWO LAND‐SNAIL SPECIES

In the southern Appalachian region of North America, the phylogenetically convergent shells of the polygyrid snails Triodopsinae Neohelix major (Binney) and Polygyrinae Mesodon normalis (Pilsbry) are even more convergent in size and shape in sympatry (7 sites) than in allopatry (23 and 10 sites). Environmental correlations account for 34% and 30% of size and shape variations in N. major (larger, taller, and more loosely coiled at northern, high‐altitude, sheltered sites), but for only 14% and 9% in M. normalis (larger, flatter, and more loosely coiled at south‐facing, exposed sites). The statistical significance of the sympatric convergence dropped out when these correlations were removed. This phenomenon helps account for the many cases in eastern North America of nearly identical land‐snail shells in sympatry and questions the importance of competitive character displacement in the evolution of land‐snail shell morphology. This apparently nonmimetic case of sympatric convergence provides an unusually precise and well‐delimited, naturally replicated experiment in evolutionary morphology, which is analyzed for controlling factors in a follow‐up paper.
Adhesional Friction Law and Adhesive Wear Law of Micromechanical Surface Contact

The paper describes the investigation on adhesional friction law and adhesive wear law of micromechanical surface contact. Adhesion theory of loading force and friction force is incorporated in multiasperity contact to find out static coefficient of friction which supports Amontons's law of friction. New adhesive wear law is developed from almost linear relationship of dimensionless real area of contact and dimensionless adhesive wear volume, and it is compared with existing Archard's adhesive wear law.
The simBorg Approach to Modeling a Dynamic Decision-making Task

Understanding decision-making processes within dynamic task environments via embodied computational cognitive models proves to be a challenge for the modeling community (see Gonzalez, Lerch, & Lebiere, 2003 for an example). Decisions made by an agent may be the result of explicit, strategic moves, or result from implicit, costbenefit tradeoffs occurring at the level of 1/3 of a second. Understanding and properly modeling decisions occurring at these different levels is a challenge for the modeler. This paper proposes a novel incremental modeling approach (see Byrne, 2001 and Gonzalez et al., 2003 for examples of other incremental approaches) that promises to inform decision theory as well as limitations within the chosen modeling architecture. The simulated cyborg (or, simBorg) approach blends computational embodied-cognitive models of interactive behavior with artificial intelligence based components in a simulated task environment (Gray, Schoelles, & Veksler, 2004). simBorgs combine human and machine components. This combination of high fidelity cognitive modeling (human) and AI (machine) facilitates the development of families of models that allow the modeler to hold components (memory, vision, etc) at different levels of expertise without concern for cognitive plausibility. For example, rather than modeling human problem solving, the modeler can rely on various black-box techniques (i.e., cognitively implausible AI), thereby focusing on predicting how subtle differences in costs and benefits in interactive methods affect performance and errors. The current modeling endeavor adopts the simBorg approach in order to build a family of interactive decisionmaking agents. The following section will present the task of interest followed by a fraction of the family of simBorgs under development. Finally, we conclude with future directions we plan to lead the family of simBorgs.
Unified Power Format (UPF) methodology in a vendor independent flow

To provide designers with an efficient low power design flow, several methodologies have been proposed such as the Unified Power Format (UPF). The main issue faced by designers is the non-interoperability of those methods across different Computer Aided Design (CAD) tools. Although the UPF standard was originally created with interoperability in mind, few of its constructs are actually supported by all CAD vendors. In this paper, we aim at providing a UPF 2.0 methodology that is compatible with different tools. The proposed case study is a circuit with three power domains and a cross-vendor UPF specification. This paper demonstrates a full low power design flow, with formal power checking, power aware simulation, synthesis and back-end.
Effect of thickness of the porous material on the peristaltic pumping when the tube wall is provided with non-erodible porous lining

We investigate the effect of thickness of the porous material on the peristaltic pumping when the tube wall is provided with non-erodible porous lining . The motion is caused by the movement of peristaltic waves on the flexible walls of the tube. The effects of yield stress and permeability on the pumping characteristics are studied in detail.
n‐Type Doping Induced by Electron Transport Layer in Organic Photovoltaic Devices

Doping in an organic photovoltaic (OPV) device can largely impact its performance. In this work, it is discovered that n‐type electrical doping in the poly(3‐hexylthiophene):[6,6]‐phenyl‐C61‐butyric acid methyl ester active layer can be induced by a certain electron transport layer (ETL), particularly branched polyethylenimine (PEI). Consequently, OPV devices with different ETLs exhibit dramatically different current density–voltage behaviors and external quantum efficiency (EQE) spectra. Using drift‐diffusion modeling, Hall effect, and capacitance–voltage measurements, it is shown that the difference in EQE spectra originates from the different background carrier type and concentration in the OPV active layer, dictated by the specific properties of ETL. Factors that influence electrical doping and device behaviors, such as difference between PEI and another polymeric ETL, polyethylenimine ethoxylated, and the active layer thickness and energy of negative integer charge‐transfer state are elucidated. These findings provide insight into material selection and device design for organic electronic devices.
Percutaneous Cryoablation vs Partial Nephrectomy: Cost Comparison of T1a Tumors.

PURPOSE To compare cost of percutaneous cryoablation vs open and robot-assisted partial nephrectomy of T1a renal masses from the hospital perspective. MATERIALS AND METHODS We retrospectively compared cost, clinical and tumor data of 37 percutaneous cryoablations to 26 open and 102 robot-assisted partial nephrectomies. Total cost was the sum of direct and indirect cost of procedural and periprocedural variables. Clinical data included demographics, Charlson Comorbidity Index (CCI), hospitalization time, complication rate, ICU admission rate, and 30-day readmission rates. Tumor data included size, RENAL nephrometry score, and malignancy rate. Student's t-test was used for continuous variables and Fisher's exact or chi-square tests for categorical data. RESULTS Mean total cost was lower for percutaneous cryoablation than open or robot-assisted partial nephrectomy: $6067 vs $11392 or $11830 (p<0.0001) with lower cost of procedure room: $1516 vs $3272 or $3254 (p<0.0001), room and board: $95 vs $1907 or $1106 (p<0.0001), anesthesia: $684 vs $1223 or $1468 (p<0.0001), and laboratory/pathology fees: $205 vs $804 or $720 (p<0.0001). Supply and device cost was higher than open: $2596 vs $1352 (p<0.0001), but lower than robot-assisted partial nephrectomy: $3207 (p=0.002). Mean hospitalization times were lower for percutaneous cryoablation (p<0.0001), while age and CCI were higher (p<0.0001). No differences in tumor size, nephrometry score, malignancy rate complication, ICU, or 30-day readmission rates were observed. CONCLUSION Percutaneous cryoablation can be performed at significantly lower cost than open and robotic partial nephrectomies for similar masses.
Tetherway: a framework for tethering camouflage

The rapidly increasing data usage and overload in mobile broadband networks has driven mobile network providers to actively detect and bill customers who tether tablets and laptops to their mobile phone for mobile Internet access. However, users may not be willing to pay additional fees only because they use their bandwidth dierently, and may consider tethering detection as violation of their privacy. Furthermore, accurate tethering detection is becoming harder for providers as many modern smartphones are under full control of the user, running customized, complex software and applications similar to desktop systems. In this work, we analyze the network characteristics available to network providers to detect tethering customers. We present and categorize possible detection mechanisms and derive cost factors based on how well the approach scales with large customer bases. For those characteristics that appear most reasonable and practical to deploy by large providers, we present elimination or obfuscation mechanisms and substantiate our design with a prototype Android App.