Miracle-dz/UniFAR-FTUs huggingface dataset:
Giant gastric lipoma successfully removed by endoscopic submucosal dissection: case report and systematic review

Abstract Objectives: Gastric lipomas are rare adipose tumors that constitute less than 1% of gastric tumors. While lipomas generally do not need removal unless symptomatic, endoscopic resection has been proposed as safe for gastric lipomas smaller than 2 cm. Yet, there is no consensus on the optimal treatment method for larger lipomas. We report a case of a giant 7-cm gastric lipoma successfully removed by endoscopic submucosal dissection (ESD) and systematically review the literature for gastric lipomas removed by ESD. Methods: Systematic review was conducted by searching PubMed and Scopus databases, up to 15 February 2018, using combinations of relevant terms. Results: We report a 55-year-old male with known gastroesophageal reflux disease and asthma, who sought medical attention due to chronic heartburn and asthma exacerbations. These symptoms were attributed to a large 7 cm × 3 cm gastric lipoma that caused gastric outlet obstruction. The lipoma was safely removed by ESD, allowing quick recovery and alleviation of symptoms. In our review, we identified 20 gastric lipomas treated with ESD, with 15 (75%) being 2 cm or larger. The average size of the lipomas was 4 cm (range: 1.2–9 cm). All lipomas were limited to the submucosa, with 80% of the tumors located in the antrum. Three lipomas were removed by submucosal tunneling. All tumors were successfully removed en bloc and no major complications were reported. Conclusion: Our findings support the conclusion that ESD may be a safe alternative to conventional surgery for removal of large symptomatic gastric lipomas.
Morphological and ecological adaptation of limpet-shaped top shells (Gastropoda: Trochidae: Fossarininae) to wave-swept rock reef habitats

Flattening of coiled shells has occurred in several gastropod lineages, while the evolutionary process of shell flattening is little known. The subfamily Fossarininae of the top shell family (Trochidae) is unique, because it includes four genera at various stages of shell flattening. Broderipia and Roya, have zygomorphic shells that has lost coiling, while the sister genera, Fossarina and Synaptocochlea, have respectively turbiniform and auriform shells. Therefore, comparisons of biology, habitats and detailed morphology among these four genera may help us to detect selection pressure driving shell flattening and loss of coiling. Although Broderipia has recently been identified as living symbiotically in the pits of sea urchins, the habitats and biology of the other three Fossarininae species, especially Roya are poorly known. After an extensive search on rocky shores of the Japanese Archipelago, we found live Roya eximia snails on intertidal/subtidal rock surfaces exposed to strong waves. Roya snails crept on the bare rock surface to graze periphyton at low tide, and fled into vacant barnacle shells at high tide. Comparison of the morphology of soft bodies in Fossarininae revealed that the columellar muscle of flattened species has been drastically elongated and arranged in posterior semi-outer edge of the flattened shell as observed in true limpets. The flattering and loss of coiling of the shell in Roya caused acquisition of a zygomorphic flat body, retraction of coiled visceral mass, and expansion of the foot sole. All of these changes improved tolerance against strong waves and the ability to cling to rock surfaces, and thus enabled a lifestyle utilizing both wave-swept rock surfaces and the inside of vacant barnacle shells.
Participatory tensions in working with a vulnerable population

This note uncovers a design tension in participatory design practice in the context of two organizations in Nepal working on reducing sex-trafficking and helping survivors. The dilemma consists of contradictions between the public face that the organizations present to the world and the more complex underlying picture painted by survivors. In initial work, we created and deployed a value-elicitation game for survivors that gave us better access to their voices. However, the implications for ongoing participatory work remain to be unpacked. The veneer may constitute a necessary part of the staffs' successful interactions with external funders. The survivors rely on the resources that the organization gathers, yet the veneer may also obscure some aspects of the survivors' needs. The question raised is "how should our PD practice position itself with respect to the ideal of comprehensive democratic participation when potential harm may ensue to vulnerable people? "
Exploring app features with outcomes in mHealth studies involving chronic respiratory diseases, diabetes, and hypertension: a targeted exploration of the literature

Objectives Limited data are available on the correlation of mHealth features and statistically significant outcomes. We sought to identify and analyze: types and categories of features; frequency and number of features; and relationship of statistically significant outcomes by type, frequency, and number of features. Materials and Methods This search included primary articles focused on app-based interventions in managing chronic respiratory diseases, diabetes, and hypertension. The initial search yielded 3622 studies with 70 studies meeting the inclusion criteria. We used thematic analysis to identify 9 features within the studies. Results Employing existing terminology, we classified the 9 features as passive or interactive. Passive features included: 1) one-way communication; 2) mobile diary; 3) Bluetooth technology; and 4) reminders. Interactive features included: 1) interactive prompts; 2) upload of biometric measurements; 3) action treatment plan/personalized health goals; 4) 2-way communication; and 5) clinical decision support system. Discussion Each feature was included in only one-third of the studies with a mean of 2.6 mHealth features per study. Studies with statistically significant outcomes used a higher combination of passive and interactive features (69%). In contrast, studies without statistically significant outcomes exclusively used a higher frequency of passive features (46%). Inclusion of behavior change features (ie, plan/goals and mobile diary) were correlated with a higher incident of statistically significant outcomes (100%, 77%). Conclusion This exploration is the first step in identifying how types and categories of features impact outcomes. While the findings are inconclusive due to lack of homogeneity, this provides a foundation for future feature analysis.
A prediction and scheduling framework in centralized cognitive radio network for energy efficient non‐real time communication

Advent of Internet of Things led to an exponential rise in battery‐operated sensors transmitting small non‐real time (NRT) data regularly. To this end, this work proposes a framework for centralized cognitive radio network (CRN) that facilitates better spectrum utilization and low‐cost opportunistic NRT data transfer with high energy efficiency. The novelty of this framework is to incorporate Hidden Markov Model–based prediction within the traditional cognitive radio sensing‐transmission cycle. To minimize the prediction time, we design a Hardware‐based Hidden Markov Model engine (H2M2) to be used by the cognitive base station (CBS). CBS exploits the H2M2 engine over high primary user (PU) activity channels to minimize the collisions between PUs and NRT secondary users, thereby reducing the SU energy consumption. However, this is at the cost of reduced throughput. Taking this into account, we propose an Intersensing‐Prediction Time Optimization algorithm that identifies the predictable PU activity channels and maximizes the throughput within a PU interference threshold. Furthermore, to minimize the total battery consumption of all the SUs within CRN, a Battery Consumption Minimizing Scheduler is designed at the CBS that efficiently allocates the predictable PU channels to the NRT SUs. By exploiting the unutilized high PU activity channels, the proposed Centralized Scheduling, Sensing and Prediction (CSSP) framework improves the spectral efficiency of the CRN. Exhaustive performance studies show that CSSP outperforms traditional nonpredictive sensing techniques in terms of energy efficiency and interference management. Finally, through a proof of concept, we validate the ability of CSSP framework in enabling NRT communication.
Invisible Pixels Are Dead, Long Live Invisible Pixels!

Privacy has deteriorated in the world wide web ever since the 1990s. The tracking of browsing habits by different third-parties has been at the center of this deterioration. Web cookies and so-called web beacons have been the classical ways to implement third-party tracking. Due to the introduction of more sophisticated technical tracking solutions and other fundamental transformations, the use of classical image-based web beacons might be expected to have lost their appeal. According to a sample of over thirty thousand images collected from popular websites, this paper shows that such an assumption is a fallacy: classical 1 x 1 images are still commonly used for third-party tracking in the contemporary world wide web. While it seems that ad-blockers are unable to fully block these classical image-based tracking beacons, the paper further demonstrates that even limited information can be used to accurately classify the third-party 1 x 1 images from other images. An average classification accuracy of 0.956 is reached in the empirical experiment. With these results the paper contributes to the ongoing attempts to better understand the lack of privacy in the world wide web, and the means by which the situation might be eventually improved.
Deep Association Learning for Unsupervised Video Person Re-identification

Deep learning methods have started to dominate the research progress of video-based person re-identification (re-id). However, existing methods mostly consider supervised learning, which requires exhaustive manual efforts for labelling cross-view pairwise data. Therefore, they severely lack scalability and practicality in real-world video surveillance applications. In this work, to address the video person re-id task, we formulate a novel Deep Association Learning (DAL) scheme, the first end-to-end deep learning method using none of the identity labels in model initialisation and training. DAL learns a deep re-id matching model by jointly optimising two margin-based association losses in an end-to-end manner, which effectively constrains the association of each frame to the best-matched intra-camera representation and cross-camera representation. Existing standard CNNs can be readily employed within our DAL scheme. Experiment results demonstrate that our proposed DAL significantly outperforms current state-of-the-art unsupervised video person re-id methods on three benchmarks: PRID 2011, iLIDS-VID and MARS.
Cross Subspace Alignment and the Asymptotic Capacity of $X$ -Secure $T$ -Private Information Retrieval

<inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula>-secure and <inline-formula> <tex-math notation="LaTeX">$T$ </tex-math></inline-formula>-private information retrieval (XSTPIR) is a form of private information retrieval where data security is guaranteed against collusion among up to <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula> servers and the user’s privacy is guaranteed against collusion among up to <inline-formula> <tex-math notation="LaTeX">$T$ </tex-math></inline-formula> servers. The capacity of XSTPIR is characterized for an arbitrary number of servers <inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula> and arbitrary security and privacy thresholds <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$T$ </tex-math></inline-formula>, in the limit as the number of messages <inline-formula> <tex-math notation="LaTeX">$K\rightarrow \infty $ </tex-math></inline-formula>. Capacity is also characterized for any number of messages if either <inline-formula> <tex-math notation="LaTeX">$N=3, X=T=1$ </tex-math></inline-formula> or if <inline-formula> <tex-math notation="LaTeX">$N\leq X+T$ </tex-math></inline-formula>. Insights are drawn from these results, about aligning versus decoding noise, dependence of PIR rate on field size, and robustness to symmetric security constraints. In particular, the idea of cross subspace alignment, i.e., introducing a subspace dependence between Reed–Solomon code parameters, emerges as the optimal way to align undesired terms while keeping desired terms resolvable.
Status of Agents Targeting the HGF/c-Met Axis in Lung Cancer

Hepatocyte growth factor (HGF) is the ligand for the tyrosine kinase receptor c-Met (Mesenchymal Epithelial Transition Factor also known as Hepatocyte Growth Factor Receptor, HGFR), a receptor with expression throughout epithelial and endothelial cell types. Activation of c-Met enhances cell proliferation, invasion, survival, angiogenesis, and motility. The c-Met pathway also stimulates tissue repair in normal cells. A body of past research shows that increased levels of HGF and/or overexpression of c-Met are associated with poor prognosis in several solid tumors, including lung cancer, as well as cancers of the head and neck, gastro-intestinal tract, breast, ovary and cervix. The HGF/c-Met signaling network is complex; both ligand-dependent and ligand-independent signaling occur. This article will provide an update on signaling through the HGF/c-Met axis, the mechanism of action of HGF/c-Met inhibitors, the lung cancer patient populations most likely to benefit, and possible mechanisms of resistance to these inhibitors. Although c-Met as a target in non-small cell lung cancer (NSCLC) showed promise based on preclinical data, clinical responses in NSCLC patients have been disappointing in the absence of MET mutation or MET gene amplification. New therapeutics that selectively target c-Met or HGF, or that target c-Met and a wider spectrum of interacting tyrosine kinases, will be discussed.
Smooth Muscle-Specific BCL6+/− Knockout Abrogates Sex Bias in Chronic Hypoxia-Induced Pulmonary Arterial Hypertension in Mice

The “estrogen paradox” in pulmonary arterial hypertension (PAH) refers to observations that while there is a higher incidence of idiopathic PAH in women, rodent models of PAH show male dominance and estrogens are protective. To explain these differences, we previously proposed the neuroendocrine-STAT5-BCL6 hypothesis anchored in the sex-biased and species-specific patterns of growth hormone (GH) secretion by the pituitary, the targeting of the hypothalamus by estrogens to feminize GH secretion patterns, and the role of the transcription factors STAT5a/b and BCL6 as downstream mediators of this patterned GH-driven sex bias. As a test of this hypothesis, we previously reported that vascular smooth muscle cell- (SMC-) specific deletion of the STAT5a/b locus abrogated the male-dominant sex bias in the chronic hypoxia model of PAH in mice. In the present study, we confirmed reduced BCL6 expression in pulmonary arterial (PA) segments in both male and female SMC:STAT5a/b−/− mice. In order to test the proposed contribution of BCL6 to sex bias in PAH, we developed mice with SMC-specific deletion of BCL6+/− by crossing SM22α-Cre mice with BCL6-floxed mice and investigated sex bias in these mutant mice in the chronic hypoxia model of PAH. We observed that the male-bias observed in wild-type- (wt-) SM22α-Cre-positive mice was abrogated in the SMC:BCL6+/− knockouts—both males and females showed equivalent enhancement of indices of PAH. The new data confirm BCL6 as a contributor to the sex-bias phenotype observed in hypoxic PAH in mice and support the neuroendocrine-STAT5-BCL6 hypothesis of sex bias in this experimental model of vascular disease.
Structure-Function Correlative Microscopy of Peritubular and Intertubular Dentine

Peritubular dentine (PTD) and intertubular dentine (ITD) were investigated by 3D correlative Focused Ion Beam (FIB)-Scanning Electron Microscopy (SEM)-Energy Dispersive Spectroscopy (EDS) tomography, tapping mode Atomic Force Microscopy (AFM) and scattering-type Scanning Near-Field Optical Microscopy (s-SNOM) mapping. The brighter appearance of PTD in 3D SEM-Backscattered-Electron (BSE) imaging mode and the corresponding higher grey value indicate a greater mineral concentration in PTD (~160) compared to ITD (~152). However, the 3D FIB-SEM-EDS reconstruction and high resolution, quantitative 2D map of the Ca/P ratio (~1.8) fail to distinguish between PTD and ITD. This has been further confirmed using nanoscale 2D AFM map, which clearly visualised biopolymers and hydroxyapatite (HAp) crystallites with larger mean crystallite size in ITD (32 ± 8 nm) than that in PTD (22 ± 3 nm). Correlative microscopy reveals that the principal difference between PTD and ITD arises primarily from the nanoscale packing density of the crystallites bonded together by thin biopolymer, with moderate contribution from the chemical composition difference. The structural difference results in the mechanical properties variation that is described by the parabolic stiffness-volume fraction correlation function introduced here. The obtained results benefit a microstructure-based mechano-chemical model to simulate the chemical etching process that can occur in human dental caries and some of its treatments.
A minimal physiologically based pharmacokinetic model to investigate FcRn-mediated monoclonal antibody salvage: Effects of Kon, Koff, endosome trafficking, and animal species

ABSTRACT Manipulation of binding affinity between monoclonal antibodies (mAbs) and the neonatal Fc receptor (FcRn) has been leveraged to extend mAb half-life; however, the steps required for success remain ambiguous and experimental observations are inconsistent. Recent models have considered the time course of endosomal transit a major contributor to the relationship between FcRn affinity and antibody half-life. Our objective was to develop a minimal physiologically based pharmacokinetic model to explain how changes in IgG-FcRn association rate constant (Kon), dissociation rate constant (Koff), and endosomal transit time [T(w)] translate to improved IgG clearance across mice, monkeys and humans. By simulating mAb clearance across physiological values of Kon, Koff, and T(w), we found that lowering Koff improves clearance only until the dissociation half-life reaches endosomal transit time. In contrast, Kon influenced clearance independently of T(w). The model was then applied to fit 66 mAb plasma profiles across species digitized from the literature, and clearance of mAb (CLIgG) and vascular fluid-phase endocytosis rate (CLup) were estimated. We found that CLIgG scaled well with body weight (allometric exponent of 0.90). After accounting for mAbs with significant FcRn binding at physiological pH, CLup was allometrically scalable (exponent 0.72). For the antibodies surveyed, Kon was more highly correlated with CLIgG across all species. The relationship between Koff and KD with CLIgG was largely inconsistent. Taken together, this model provides a parsimonious approach to evaluate endosomal transit kinetics using only mAb plasma concentrations. These findings reinforce the idea that endosomal transit kinetics should be considered when modeling FcRn salvage.
IGF-1-Overexpressing Mesenchymal Stem/Stromal Cells Promote Immunomodulatory and Proregenerative Effects in Chronic Experimental Chagas Disease

Mesenchymal stem/stromal cells (MSCs) have been investigated for the treatment of diseases that affect the cardiovascular system, including Chagas disease. MSCs are able to promote their beneficial actions through the secretion of proregenerative and immunomodulatory factors, including insulin-like growth factor-1 (IGF-1), which has proregenerative actions in the heart and skeletal muscle. Here, we evaluated the therapeutic potential of IGF-1-overexpressing MSCs (MSC_IGF-1) in a mouse model of chronic Chagas disease. C57BL/6 mice were infected with Colombian strain Trypanosoma cruzi and treated with MSCs, MSC_IGF-1, or vehicle (saline) six months after infection. RT-qPCR analysis confirmed the presence of transplanted cells in both the heart and skeletal muscle tissues. Transplantation of either MSCs or MSC_IGF-1 reduced the number of inflammatory cells in the heart when compared to saline controls. Moreover, treatment with MSCs or MSC_IGF-1 significantly reduced TNF-α, but only MSC treatment reduced IFN-γ production compared to the saline group. Skeletal muscle sections of both MSC- and MSC_IGF-1-treated mice showed a reduction in fibrosis compared to saline controls. Importantly, the myofiber area was reduced in T. cruzi-infected mice, and this was recovered after treatment with MSC_IGF-1. Gene expression analysis in the skeletal muscle showed a higher expression of pro- and anti-inflammatory molecules in MSC_IGF-1-treated mice compared to MSCs alone, which significantly reduced the expression of TNF-α and IL-1β. In conclusion, our results indicate the therapeutic potential of MSC_IGF-1, with combined immunomodulatory and proregenerative actions to the cardiac and skeletal muscles.
The Effect of Digestion and Digestibility on Allergenicity of Food

Food allergy prevalence numbers are still on the rise. Apart from environmental influences, dietary habits, food availability and life-style factors, medication could also play a role. For immune tolerance of food, several contributing factors ensure that dietary compounds are immunologically ignored and serve only as source for energy and nutrient supply. Functional digestion along the gastrointestinal tract is essential for the molecular breakdown and a prerequisite for appropriate uptake in the intestine. Digestion and digestibility of carbohydrates and proteins thus critically affect the risk of food allergy development. In this review, we highlight the influence of amylases, gastric acid- and trypsin-inhibitors, as well as of food processing in the context of food allergenicity.
Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length. Beyond long repeats, the P19E3 assembly was further complicated by a shufflon region. Its complex genome could not be de novo assembled with long reads produced by Pacific Biosciences’ technology, but required very long reads from the Oxford Nanopore Technology. Another important factor for a full genomic resolution was the choice of assembly algorithm. Importantly, a repeat analysis indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this dark matter for de novo genome assembly of prokaryotes. Several of these dark matter genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assemblers capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.