Miracle-dz/UniFAR-FTUs huggingface dataset:
Marine Collagen/Apatite Composite Scaffolds Envisaging Hard Tissue Applications

The high prevalence of bone defects has become a worldwide problem. Despite the significant amount of research on the subject, the available therapeutic solutions lack efficiency. Autografts, the most commonly used approaches to treat bone defects, have limitations such as donor site morbidity, pain and lack of donor site. Marine resources emerge as an attractive alternative to extract bioactive compounds for further use in bone tissue-engineering approaches. On one hand they can be isolated from by-products, at low cost, creating value from products that are considered waste for the fish transformation industry. One the other hand, religious constraints will be avoided. We isolated two marine origin materials, collagen from shark skin (Prionace glauca) and calcium phosphates from the teeth of two different shark species (Prionace glauca and Isurus oxyrinchus), and further proposed to mix them to produce 3D composite structures for hard tissue applications. Two crosslinking agents, 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride/N-Hydroxysuccinimide (EDC/NHS) and hexamethylene diisocyanate (HMDI), were tested to enhance the scaffolds’ properties, with EDC/NHS resulting in better properties. The characterization of the structures showed that the developed composites could support attachment and proliferation of osteoblast-like cells. A promising scaffold for the engineering of bone tissue is thus proposed, based on a strategy of marine by-products valorisation.
A speed-adaptive intraspinal microstimulation controller to restore weight-bearing stepping in a spinal cord hemisection model

Objective. The goal of this study was to develop control strategies to produce alternating, weight-bearing stepping in a cat model of hemisection spinal cord injury (SCI) using intraspinal microstimulation (ISMS). Approach. Six cats were anesthetized and the functional consequences of a hemisection SCI were simulated by manually moving one hind-limb through the gait cycle over a moving treadmill belt. ISMS activated the muscles in the other leg by stimulating motor networks in the lumbosacral enlargement using low levels of current (<110 µA). The control strategy used signals from ground reaction forces and angular velocity from the manually-moved limb to anticipate states of the gait cycle, and controlled ISMS to move the other hind-limb into the opposite state. Adaptive control strategies were developed to ensure weight-bearing at different stepping speeds. The step period was predicted using generalizations obtained through four supervised machine learning algorithms and used to adapt the control strategy for faster steps. Main results. At a single speed, 100% of the steps had sufficient weight-bearing; at faster speeds without adaptation, 97.6% of steps were weight-bearing (significantly less than that for single speed; p = 0.002). By adapting the control strategy for faster steps using the predicted step period, weight-bearing was achieved in more than 99% of the steps in three of four methods (significantly more than without adaptation p < 0.04). Overall, a multivariate model tree increased the number of weight-bearing steps, restored step symmetry, and maintained alternation at faster stepping speeds. Significance. Through the adaptive control strategies guided by supervised machine learning, we were able to restore weight-bearing and maintain alternation and step symmetry at varying stepping speeds.
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions

Abstract We report a new class of artifacts in DNA methylation measurements from Illumina HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed hybridization to target DNA, often due to germline or somatic deletions and manifest as incorrectly reported intermediate methylation. The artifacts often survive existing preprocessing pipelines, masquerade as epigenetic alterations and can confound discoveries in epigenome-wide association studies and studies of methylation-quantitative trait loci. We implement a solution, P-value with out-of-band (OOB) array hybridization (pOOBAH), in the R package SeSAMe. Our method effectively masks deleted and hyperpolymorphic regions, reducing or eliminating spurious reports of epigenetic silencing at oft-deleted tumor suppressor genes such as CDKN2A and RB1 in cases with somatic deletions. Furthermore, our method substantially decreases technical variation whilst retaining biological variation, both within and across HM450 and EPIC platform measurements. SeSAMe provides a light-weight, modular DNA methylation data analysis suite, with a performant implementation suitable for efficient analysis of thousands of samples.
Maternal Immunity and the Natural History of Congenital Human Cytomegalovirus Infection

Congenital human cytomegalovirus (HCMV) is the most common viral infection of the developing fetus, and a significant cause of neurodevelopmental abnormalities in infants and children. Congenital HCMV infections account for an estimated 25% of all cases of hearing loss in the US. It has long been argued that maternal adaptive immune responses to HCMV can modify both the likelihood of intrauterine transmission of HCMV, and the severity of fetal infection and risk of long term sequelae in infected infants. Over the last two decades, multiple studies have challenged this paradigm, including findings that have demonstrated that the vast majority of infants with congenital HCMV infections in most populations are born to women with established immunity prior to conception. Furthermore, the incidence of clinically apparent congenital HCMV infection in infants born to immune and non-immune pregnant women appears to be similar. These findings from natural history studies have important implications for the design, development, and testing of prophylactic vaccines and biologics for this perinatal infection. This brief overview will provide a discussion of existing data from human natural history studies and animal models of congenital HCMV infections that have described the role of maternal immunity in the natural history of this perinatal infection.
Response Inhibition Deficits in Insomnia Disorder: An Event-Related Potential Study With the Stop-Signal Task

Background: Response inhibition is a hallmark of executive function, which was detected impaired in various psychiatric disorders. However, whether insomnia disorder (ID) impairs response inhibition has caused great controversy. Methods: Using the auditory stop-signal paradigm coupled with event-related potentials (ERPs), we carried out this study to examine whether individuals with ID presented response inhibition deficits and further investigated the neural mechanism correlated to these deficits. Twelve individuals with ID and 13 matched good sleepers (GSs) had participated in this study, and then they performed an auditory stop-signal task (SST) in the laboratory setting with high density EEG recordings. Results: The behavioral results revealed that compared to GSs, patients with ID presented significantly longer stop-signal reaction time (SSRT), suggesting the impairment of motor inhibition among insomniacs. Their reaction time in go trials, however, showed no significant between-group difference. Considering the electrophysiological correlate underlying the longer SSRT, we found reduced P3 amplitude in patients with insomnia in the successful stop trials, which might reflect their poor efficiency of response inhibition. Finally, when we performed exploratory analyses in the failed stop and go trials, patients with ID presented reduced Pe and N1 amplitude in the failed sop trials and go trials respectively. Discussion: Taken together, these findings indicate that individuals with ID would present response inhibition deficits. Moreover, the electrophysiological correlate underlying these deficits mainly revolves around the successful stop P3 component. The present study is the first to investigate the electrophysiological correlate underlying the impaired response inhibition among insomniacs.
Fine-Grained, Multi-Domain Network Resource Abstraction as a Fundamental Primitive to Enable High-Performance, Collaborative Data Sciences

Multi-domain network resource reservation systems are being deployed, driven by the demand and substantial benefits of providing predictable network resources. However, a major lack of existing systems is their coarse granularity, due to the participating networks' concern of revealing sensitive information, which can result in substantial inefficiencies. This paper presents Mercator, a novel multi-domain network resource discovery system to provide fine-grained, global network resource information, for collaborative sciences. The foundation of Mercator is a resource abstraction through algebraic-expression enumeration (i.e., linear inequalities/equations), as a compact representation of the available bandwidth in multi-domain networks. In addition, we develop an obfuscating protocol, to address the privacy concerns by ensuring that no participant can associate the algebraic expressions with the corresponding member networks. We also introduce a super-set projection technique to increase Mercator's scalability. Finally, we implement Mercator and demonstrate both its efficiency and efficacy through extensive experiments using real topologies and traces.
Determinants of Successful Weight Loss in Low-Income African American Women: A Positive Deviance Analysis

Objective: We set out to investigate the behaviors of low-income African American women who successfully lost weight. Methods: From an urban, academic, family medicine practice, we used a mixed methods positive deviance approach to evaluate 35 low-income African American women who were obese and lost at least 10% of their maximum weight, and maintained this loss for 6 months, comparing them with 36 demographically similar control participants who had not lost weight. Survey outcomes included demographics and behaviors that were hypothesized to be related to successful weight loss. Interviews focused on motivations, barriers, and what made weight loss successful. Survey data were analyzed using t tests and linear regression for continuous outcomes and chi-square tests and logistic regression for categorical outcomes. Interviews were analyzed using a modified approach to grounded theory. Results: In adjusted analyses, women in the positive deviant group were more likely to be making diet changes compared with those women who did not lose at least 10% of their initial body weight. Major themes from qualitative analyses included (a) motivations (of health, appearance, quality of life, family, and epiphanies), (b) opportunity (including time and support), (c) adaptability. Conclusions: The findings of this study may be useful in developing motivational interviewing strategies for primary care providers working with similar high-risk populations.
Scalable Distributed-Computing IoT Applied Architecture with Semantic Interoperable Gateway

Interoperability and enormous data processing remain significant challenges for Internet of Things' Systems. High heterogeneity in protocols, Vendors, data formats and worldwide acceptable standards' scarcity increase Interoperability Challenge. Depending on a centralized cloud server for data processing increased data latency and turn brokered systems into a bottleneck. In this paper, we proposed generic IoT applied architecture based on scalable distributed computing model from sensor node passing by IoT gateway to Cloud Server to minimize data latency and mitigate data processing burden on a centralized server. Our architecture is also based on an interoperable gateway using semantic web technologies to provide Interoperability among heterogeneous IoT devices.
Modeling of Flank Wear Using ANFIS

This paper presents the modeling of Flank Wear of machining hot work tool steel (AISI H11) with ceramic tools. This work determined the effect of various cutting parameters:cutting speed, feed rate, depth of cut and nose radius on Flank Wear. Two models have been proposed, the first model is Taguchi method and the second one is adaptive neuro-fuzzy inference system ANFIS. The results obtained by the two models are compared with the experimental results.
Sepsis-Like Systemic Inflammation Induced by Nano-Sized Extracellular Vesicles From Feces

Nano-sized extracellular vesicles (EVs), including exosomes, microvesicles, and other types of vesicles, are released by most mammalian cells and bacteria. We here ask whether feces contain EVs of mammalian and/or bacterial origin, and whether these EVs induce systemic inflammation. Fecal extracellular vesicles (fEVs) were isolated from mice and humans. The presence of EVs from Gram-negative and Gram-positive bacteria was detected by enzyme-linked immunosorbent assay using anti-lipid A and anti-lipoteichoic acid antibodies, whereas Western blot using anti-beta-actin antibody was employed to detect host-derived EVs in the fEVs. Further, fEVs were administered into mice by intraperitoneal injection, and inflammatory responses were investigated in the peritoneum, blood, and lungs. The role of TLR2 and TLR4 were studied using knockout mice. Significant quantities of EVs were present in feces from mice as well as humans, and derived from Gram-negative and Gram-positive bacteria, as well as the host. Bacteria-free fEVs introduced into the peritoneum induced local and systemic inflammation (including in the lungs), but fEVs from germ-free animals had weaker effects. This pronounced local and systemic inflammatory responses seemed to be induced by EVs from both Gram-negative and Gram-positive bacteria, and was attenuated in mice lacking TLR2 or TLR4. Our findings show that fEVs cause sepsis-like systemic inflammation, when introduced intraperitoneally, a process regulated by TLR2 and TLR4.
Formation of a Methylenedioxy Bridge in (+)-Epipinoresinol by CYP81Q3 Corroborates with Diastereomeric Specialization in Sesame Lignans

Plant specialized metabolites are often found as lineage-specific diastereomeric isomers. For example, Sesamum alatum accumulates the specialized metabolite (+)-2-episesalatin, a furofuran-type lignan with a characteristic diastereomeric configuration rarely found in other Sesamum spp. However, little is known regarding how diastereomeric specificity in lignan biosynthesis is implemented in planta. Here, we show that S. alatum CYP81Q3, a P450 orthologous to S. indicum CYP81Q1, specifically catalyzes methylenedioxy bridge (MDB) formation in (+)-epipinoresinol to produce (+)-pluviatilol. Both (+)-epipinoresinol and (+)-pluviatilol are putative intermediates of (+)-2-episesalatin based on their diastereomeric configurations. On the other hand, CYP81Q3 accepts neither (+)- nor (-)-pinoresinol as a substrate. This diastereomeric selectivity of CYP81Q3 is in clear contrast to that of CYP81Q1, which specifically converts (+)-pinoresinol to (+)-sesamin via (+)-piperitol by the sequential formation of two MDBs but does not accept (+)-epipinoresinol as a substrate. Moreover, (+)-pinoresinol does not interfere with the conversion of (+)-epipinoresinol to (+)-pluviatilol by CYP81Q3. Amino acid substitution and CO difference spectral analyses show that polymorphic residues between CYP81Q1 and CYP81Q3 proximal to their putative substrate pockets are crucial for the functional diversity and stability of these two enzymes. Our data provide clues to understanding how the lineage-specific functional differentiation of respective biosynthetic enzymes substantiates the stereoisomeric diversity of lignan structures.
Persuasive Events and User's Roles in Mobile-Based Interactive Solutions for Nature Discovery

The exploration and discovery of nature through walking, cycling, touring, trekking and hiking are targeted by this work, part of an on-going research on mobile-based persuasive user interaction. Considering HCI solutions dedicated to discover and explore nature, we uncover the concept of persuasive event and several classes of roles that users may endorse during a long-term usage of such interactive solutions. We claim the importance of these events and roles as, leveraging persuasion, they may contribute to improve nature discovery experience and to sustain motivation through user interaction. In this work we share these insights from our studies on the Mhikes platform, designed for such kind of nature-involved activities.
A Fine-grained and Transparent Congestion Control Enforcement Scheme

In practice, a single TCP congestion control is often used to handle all TCP connections on a Web server, e.g., Cubic for Linux by default. Considering complex and ever-changing networking environment, the default congestion control algorithm may not always be the most suitable one. Adjusting congestion control usually to meet different networking scenarios requires modification of servers' TCP stacks. This is difficult, if not impossible, due to various operating systems and different configurations on the servers. In this paper, we propose Mystique, a light-weight and flexible scheme that allows administrators (or operators) to deploy any congestion control schemes transparently without changing existing TCP stacks on servers. We have implemented Mystique in Open vSwitch (OVS) and conducted extensive testbed experiments in public cloud environments. We have extensively evaluated Mystique and the results have demonstrated that it is able to effectively adapt to varying network conditions, and can always employ the most suitable congestion control for each TCP connection. Mystique can significantly reduce latency by up to 37.8% in comparison with other congestion controls.
Mutations in the gene PDE6C encoding the catalytic subunit of the cone photoreceptor phosphodiesterase in patients with achromatopsia

Biallelic PDE6C mutations are a known cause for rod monochromacy, better known as autosomal recessive achromatopsia (ACHM), and early‐onset cone photoreceptor dysfunction. PDE6C encodes the catalytic α′‐subunit of the cone photoreceptor phosphodiesterase, thereby constituting an essential part of the phototransduction cascade. Here, we present the results of a study comprising 176 genetically preselected patients who remained unsolved after Sanger sequencing of the most frequent genes accounting for ACHM, and were subsequently screened for exonic and splice site variants in PDE6C applying a targeted next generation sequencing approach. We were able to identify potentially pathogenic biallelic variants in 15 index cases. The mutation spectrum comprises 18 different alleles, 15 of which are novel. Our study significantly contributes to the mutation spectrum of PDE6C and allows for a realistic estimate of the prevalence of PDE6C mutations in ACHM since our entire ACHM cohort comprises 1,074 independent families.
The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation

ABSTRACT The initiation of macroautophagy/autophagy is tightly regulated by the upstream ULK1 kinase complex, which affects many downstream factors including the PtdIns3K complex. The phosphorylation of the right position at the right time on downstream molecules is governed by proper complex formation. One component of the ULK1 complex, ATG101, known as an accessory protein, is a stabilizer of ATG13 in cells. The WF finger region of ATG101 plays an important role in the recruitment of WIPI1 (WD repeat domain, phosphoinositide interacting protein 1) and ZFYVE1 (zinc finger FYVE-type containing 1). Here, we report that the C-terminal region identified in the structure of the human ATG101-ATG13HORMA complex is responsible for the binding of the PtdIns3K complex. This region adopts a β-strand conformation in free ATG101, but either an α-helix or random coil in our ATG101-ATG13HORMA complex, which protrudes from the core and interacts with other molecules. The C-terminal deletion of ATG101 shows a significant defect in the interaction with PtdIns3K components and subsequently impairs autophagosome formation. This result clearly presents an additional role of ATG101 for bridging the ULK1 and PtdIns3K complexes in the mammalian autophagy process. Abbreviations: ATG: autophagy related; BECN1: beclin 1; GFP: green fluorescent protein; HORMA: Hop1p/Rev7p/MAD2; HsATG13HORMA: HORMA domain of ATG13 from Homo sapiens; KO: knockout; MAD2: mitotic arrest deficient 2 like 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K: phosphatidylinositol 3-kinase; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SAXS: small-angle X-ray scattering; ScAtg13HORMA: HORMA domain of Atg13 from Sccharomyces cerevisiae; SEC-SAXS: size-exclusion chromatography with small-angle X-ray scattering; SpAtg13HORMA: HORMA domain of Atg13 from Schizosaccharomyces pombe; SQSTM1/p62: sequestosome 1; ULK1: unc51-like autophagy activating kinase 1; UVRAG: UV radiation resistance associated; WIPI1: WD repeat domain: phosphoinositide interacting 1; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1
Data-driven Approaches to Edge Caching

Content caching at network edge is a promising solution for serving emerging high-throughput low-delay applications, such as virtual reality, augmented reality and Internet-of-Things. The traditional caching algorithms need to adapt to the edge networking environment since old traffic assumptions may no longer hold. Meanwhile, user/group content interest as a new important element should be considered to improve the caching performance. In this work, we propose two novel caching strategies that mine user/group interests to improve caching performance at network edge. The static user-group interest patterns are handled by the Matrix Factorization method and the temporal content request patterns are handled by the Least-Recently-Used or Nearest-Neighbor algorithms. Through empirical experiments with a large-scale real IPTV user traces, we demonstrate that the proposed caching algorithms outperform the existing caching algorithms and approach the caching performance upper bound in the large cache size regime. Leveraging on offline computation, we can limit the online computation cost and achieve good caching performance in realtime.