Miracle-dz/UniFAR-FTUs huggingface dataset:
Using active colloids as machines to weave and braid on the micrometer scale

Significance Designing and building custom-made structures at the microscopic scale is a fundamental goal in nanotechnology. Many self-assembly approaches have the advantage of being autonomous in that no external input is required during the assembly process. We present a paradigm for the autonomous, out-of-equilibrium assembly of braids and weaves at the microscopic scale, using active particles. This approach, which involves controlling the precise motion of self-propelled colloids, not only provides a path for assembling complex structures but also demonstrates how active particles can be harnessed and used as a functional microscopic machine. Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles.
Comparative Molecular Dynamics Simulation of Hepatitis C Virus NS3/4A Protease (Genotypes 1b, 3a and 4a) Predicts Conformational Instability of the Catalytic Triad in Drug Resistant Strains

The protease domain of the Hepatitis C Virus (HCV) nonstructural protein 3 (NS3) has been targeted for inhibition by several direct-acting antiviral drugs. This approach has had marked success to treat infections caused by HCV genotype 1 predominant in the USA, Europe, and Japan. However, genotypes 3 and 4, dominant in developing countries, are resistant to a number of these drugs and little progress has been made towards understanding the structural basis of their drug resistivity. We have previously developed a 4D computational methodology, based on 3D structure modeling and molecular dynamics simulation, to analyze the active sites of the NS3 proteases of HCV-1b and 4a in relation to their catalytic activity and drug susceptibility. Here, we improved the methodology, extended the analysis to include genotype 3a (predominant in South Asia including Pakistan), and compared the results of the three genotypes (1b, 3a and 4a). The 4D analyses of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) indicate conformational instability of the catalytic site in HCV-3a and 4a compared to that of HCV-1b NS3 protease. The divergence is gradual and genotype-dependent, with HCV-1b being the most stable, HCV-4a being the most unstable and HCV-3a representing an intermediate state. These results suggest that the structural dynamics behavior, more than the rigid structure, could be related to the altered catalytic activity and drug susceptibility seen in NS3 proteases of HCV-3a and 4a.
Synthesis and Characterization of a Smart Super Absorbent Hydrogel

This research work aims to give an overview of the synthesis of a smart super absorbent semi interpenetrating hydrogel and their characterizations. The main objective is to mix polyacrylamide with Tamarind gum and to check how the parameters are varying to create a good strength sustained delivery system. We tried to optimize the process parameters of polyacrylamide and tamarind gum semi interpenetrating hydrogel. Swelling measurements were done and mechanical properties were investigated. Cyclic compression, creep & stress relaxation properties are observed. XRD and FTIR studies were analyzed, Biocompatibility is checked and cross linking density is calculated. Tamarind gum converted the polyacrylamide into a super absorbent. With the increasing concentration of tamarind gum, cross-link density increases. Addition of Tamarind gum increased the swelling capability of polyacrylamide gel and increased its pH sensitivity. From the mechanical test data, we can conclude that with increasing concentration of tamarind gum viscoelastic property is increased. From the XRD pattern, it is seen that the composite is highly amorphous. From the FTIR analysis, we can say that all the components used for making the composite are present. With the increasing concentration of tamarind gum, biocompatibility of the hydrogel increases
Respiratory rate detection using a camera as contactless sensor

Aim of this study is to extract near-continuously respiratory rate by a contactless method. An industrial camera was used to record subjects face. Video data were processed offline to derive the video-photoplethysmographic (videoPPG) signal. Three features were extracted from videoPPG and finger PPG signal: pulse rate variability (PRV), pulse amplitude variability (PAV) and pulse width variability (PWV). A combination of these methods has been exploited to estimate the respiratory rate for each time window of 5 second. The results showed relative error with median around 0.5% and interquartile range of 5% both for finger PPG and videoPPG system.
Deep Learning Nuclei Detection in Digitized Histology Images by Superpixels

Background: Advances in image analysis and computational techniques have facilitated automatic detection of critical features in histopathology images. Detection of nuclei is critical for squamous epithelium cervical intraepithelial neoplasia (CIN) classification into normal, CIN1, CIN2, and CIN3 grades. Methods: In this study, a deep learning (DL)-based nuclei segmentation approach is investigated based on gathering localized information through the generation of superpixels using a simple linear iterative clustering algorithm and training with a convolutional neural network. Results: The proposed approach was evaluated on a dataset of 133 digitized histology images and achieved an overall nuclei detection (object-based) accuracy of 95.97%, with demonstrated improvement over imaging-based and clustering-based benchmark techniques. Conclusions: The proposed DL-based nuclei segmentation Method with superpixel analysis has shown improved segmentation results in comparison to state-of-the-art methods.
Association of Pre-Transplant Dialysis Modality and Post-Transplant Outcomes: A Meta-Analysis

♦ Background: It remains unclear whether post-transplant outcomes differ according to the pre-transplant dialysis modality (peritoneal dialysis [PD] versus hemodialysis [HD]). We performed a meta-analysis of studies that assessed either post-transplant mortality, graft survival, or delayed graft function (DGF) in both PD and HD patients. ♦ Methods: Two independent authors searched English-language literature from January 1, 1980, through August 31, 2014, national conference proceedings, and reference lists. We used combinations of terms related to dialysis (hemodialysis, peritoneal dialysis, or renal replacement therapy), kidney transplant, and outcomes. Studies were included if they measured any of the 3 post-transplant study outcomes in both pre-transplant HD and PD. ♦ Results: A total of 16 studies were included in the final analysis. Of these, 6 studies reported adjusted hazard ratio for mortality, pooled adjusted risk ratio: 0.89 (95% confidence interval [CI] 0.82 – 0.97) in favor of PD (p = 0.006). The same 6 studies reported adjusted hazard ratio for graft survival, pooled adjusted risk ratio: 0.97 (95% CI 0.92 – 1.01, p = 0.16). A total of 13 studies reported unadjusted DGF. Pooled odds ratio: 0.5 (95% CI 0.41 – 0.63) in favor of PD (p < 0.005). Significant heterogeneity observed for all outcomes: I2 = 72.7%, I2 = 59.9%, and I2 = 66.8%, respectively. ♦ Conclusions: Based on these results, pre-transplant PD is associated with better post-transplant survival than HD. Pre-transplant PD was also associated with decreased risk for DGF compared with HD, although these results were unadjusted. There was no significant difference in graft survival between pre-transplant HD and PD. These results suggest that PD may be the preferred dialysis modality for patients expected to receive a transplant.
Therapeutics in Osteoarthritis Based on an Understanding of Its Molecular Pathogenesis

Osteoarthritis (OA) is the most prevalent joint disease in older people and is characterized by the progressive destruction of articular cartilage, synovial inflammation, changes in subchondral bone and peri-articular muscle, and pain. Because our understanding of the aetiopathogenesis of OA remains incomplete, we haven’t discovered a cure for OA yet. This review appraises novel therapeutics based on recent progress in our understanding of the molecular pathogenesis of OA, including pro-inflammatory and pro-catabolic mediators and the relevant signalling mechanisms. The changes in subchondral bone and peri-articular muscle accompanying cartilage damage are also reviewed.
An interest-driven routing algorithm in disruption-tolerant networking based social networks

With wide applications of intelligent handset devices, social networks have received more and more attentions. Currently, Disruption-Tolerant Networking provides a feasible content-distribution solution for a mobile device-dependent social network through its store-and-forward mechanism. This article puts forward an interest-driven routing algorithm for a Disruption-Tolerant Networking social networks, in which those nodes with similar interests are grouped into a same community to achieve reliable and resource-efficient forwarding of messages. In particular, each local node carrying a message will forward it by selecting the next-hop nodes with stronger Community Social Strength in the candidate node set with partial overlapped interests. On the other side, if the local node does not find a next-hop node with partially equivalent interests, the message will be forwarded to a next-hop node with a stronger Perceived Social Strength. Through the simulation experiments, the proposed routing algorithm could effectively improve the message delivery rate, average hop-count and load, compared with Epidemic and Prophet routing algorithms.
Robotic agents used to help teach social skills to children with Autism: The third generation

This paper reports on the cross-collaborative efforts between computer science, special education and mechanical engineering on some of the robotic platforms used in therapeutic environments, and our investigation of using robots as educationally useful interventions to improve social interactions for individuals with Autism Spectrum Disorders (ASD). Development of a third generation robotic agent is described which uses an approach to treatment as an educational intervention based on Socially Assistive Robotics (SAR), direct instruction pedagogy, the use of social scripts, and our investigative process of using Lego® NXT platforms.
Can community care workers deliver a falls prevention exercise program? A feasibility study

Background Almost half of older people receiving community care fall each year and this rate has not improved in the last decade. Falls prevention programs targeted at this group are uncommon, and expensively delivered by university trained allied health professionals. Purpose To investigate the feasibility of community care workers delivering a falls prevention exercise program to older clients, at low or medium risk of falling, as part of an existing service provision. Patients and methods Community care workers from 10 community care organizations participated in the training for, and delivery to their clients of, an 8-week evidence-based falls prevention exercise program. Community care workers included assessment staff (responsible for identifying the need for community care services through completing an assessment) and support workers (responsible for providing support in the home). Clients were surveyed anonymously at the completion of the intervention and workers participated in a semi-structured interview. Results Twenty-five community care workers participated in the study. The falls prevention program was delivered to 29 clients, with an average age of 82.7 (SD: 8.72) years and consisting of 65.5% female. The intervention was delivered safely with no adverse events recorded, and the eligibility and assessment tools were completed by the majority of community care workers (93.1%). Assessment staff found it difficult to find time to deliver the intervention. Support workers were able to complete the intervention within their current service delivery period, with the initial assessment taking a small amount of additional time. Support workers reported enjoying the additional responsibility afforded by delivering the falls prevention program and seeing changes in their clients. The majority of clients (82%) reported enjoying the exercises, with 59% reporting that they felt it made a positive change in their health. Clients completed the exercises on average 4.8 (SD: 2.2) days per week. Conclusion Community care workers who have completed appropriate training are able to deliver a falls prevention exercise program to their clients as part of their current services. Further research is required to determine whether the program reduces the rate of falls for community care clients and whether integration of a falls prevention program into an existing service is cost-effective.
Silent atrial fibrillation: epidemiology, diagnosis, and clinical impact

Silent or subclinical asymptomatic atrial fibrillation (SAF) has currently gained wide interest in the epidemiologic, neurologic, and cardiovascular communities. It is well known that the electrophysiological and mechanical effects of symptomatic and silent atrial fibrillation (AF) are the same. It is probable that because “AF begets AF,” progression from paroxysmal to persistent or permanent AF might be more rapid in patients with long‐term unrecognized and untreated SAF, because no treatment is sought by or provided to such patients. Moreover, SAF is common and has significant clinical implications. The clinical consequences of SAF, which include emboli (silent or symptomatic), heart failure, and early mortality, are of paramount importance. Consequently, SAF should be considered in estimating the prevalence of the disease and its impact on morbidity, mortality, and quality of life. Several diagnostic methods of arrhythmia detection utilizing the surface electrocardiogram (ECG), subcutaneous ECG, or intracardiac devices have been utilized to seek meaningful arrhythmic markers of SAF. Whereas a wide range of clinical risk factors of SAF have been validated in the literature, there is an ongoing search for those arrhythmic risk factors that precisely identify and prognosticate outcome events in diverse populations at risk of SAF. Modern diagnostic modalities for the identification of SAF exist, but should be further explored, validated, and tailored to each patient needs. The scientific community should undertake the clinical challenge of identifying and treating SAF.
Staingan: Stain Style Transfer for Digital Histological Images

Digitized Histological diagnosis is in increasing demand. However, color variations due to various factors are imposing obstacles to the diagnosis process. The problem of stain color variations is a well-defined problem with many proposed solutions. Most of these solutions are highly dependent on a reference template slide. We propose a deep-learning solution inspired by CycleGANs that is trained end-to-end, eliminating the need for an expert to pick a representative reference slide. Our approach showed superior results quantitatively and qualitatively against the state of the art methods (10% improvement visually using SSIM). We further validated our method on a clinical use-case, namely Breast Cancer tumor classification, showing a 12% increase in AUC. The code is made publicly available 1.1https://github.com/xtarx/StainGAN
Prognostic and predictive value of EGFR and EGFR-ligands in blood of breast cancer patients: a systematic review

Abstract Epidermal growth factor receptor (EGFR) serves as a co-target for dual/pan-EGFR-inhibitors in breast cancer. Findings suggest that EGFR and EGFR-ligands are involved in resistance towards certain breast cancer treatments. The aim is to explore the validity of EGFR and EGFR-ligands in blood as prognostic and predictive biomarkers in breast cancer. The systematic review was conducted in accordance to the PRISMA guidelines. Literature searches were conducted to identify publications exploring correlations between EGFR/EGFR-ligands in serum/plasma of breast cancer patients and prognostic/predictive outcome measures. Sixteen publications were eligible for inclusion. Twelve studies evaluated EGFR, whereas five studies evaluated one or more of the EGFR-ligands. Current evidence indicates associations between low baseline serum-EGFR and shorter survival or reduced response to treatment in patients with advanced breast cancer, especially in patients with estrogen and/or progesterone receptor positive tumors. The prognostic and predictive value of EGFR and EGFR-ligands in blood has only been investigated in highly selected subsets of breast cancer patients and most studies were small. This is the first systematic review evaluating the utility of EGFR and EGFR-ligands as predictive and prognostic biomarkers in blood in breast cancer. Further exploration in large well-designed studies is needed.
Preparation of Starch Nanoparticles via High-Energy Ball Milling

Nano-sized starch particles were prepared from potato starch via high-energy ball milling, which is a purely physical method. Scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, differential scanning calorimetry, and viscometer were used to analyze the morphology and characteristics of the as-prepared nanoparticles. Spherical particles with an average size of approximately 120 nm were obtained after grinding the samples for 90 min, and the particles were free from any contamination. The particle surface was rough with a plush-like feature, and the adsorption ability was six times higher than that of native starch. Thus, the nano-sized starch particles can be used as a good embedding medium in biomedical and chemical materials.
Prevalence of Different Head-Neck Positions in Horses Shown at Dressage Competitions and Their Relation to Conflict Behaviour and Performance Marks

Much controversy exists among riders, and in particular among those practicing dressage, regarding what can be considered an “appropriate” Head-Neck-Position (HNP). The objective was to assess the prevalence of different HNPs in the field, the behavioural reactions of horses during warm-up and competition rides in relation to HNP and the relation between HNP and marks achieved in the competition. Horses (n = 171) were selected during dressage competitions according to their HNP (3 categories based on the degree of flexion), and their behaviour was recorded during 3 minutes each of riding in the warm-up area and in the competition. Scans were carried out on an additional 355 horses every 15 minutes to determine the proportion of each HNP in the warm-up area. Sixty-nine percent of the 355 horses were ridden with their nasal planes behind the vertical in the warm-up area, 19% were ridden at or behind the vertical and only 12% were ridden with their nasal plane in front of the vertical. Horses carrying their nasal plane behind the vertical exhibited significantly (P<0.0001) more conflict behaviours than horses with their nose held in front of the vertical. Horses were commonly presented with a less flexed HNP during competition compared to warm-up (P<0.05). A HNP behind the vertical was penalised with lower marks in the lower (P = 0.0434) but not in the higher (P = 0.9629) competition levels. Horses in higher classes showed more (P = 0.0015) conflict behaviour than those in lower classes. In conclusion, dressage horses are commonly ridden during warm-up for competitions with their nasal plane behind the vertical, and this posture seems to cause significantly more conflict behaviour than HNPs in front of the vertical.
In Vitro Enhancement of Respiratory Syncytial Virus Infection by Maternal Antibodies Does Not Explain Disease Severity in Infants

ABSTRACT Respiratory syncytial virus (RSV) is the leading cause of severe respiratory illness in infants. At this young age, infants typically depend on maternally transferred antibodies (matAbs) and their innate immune system for protection against infections. RSV-specific matAbs are thought to protect from severe illness, yet severe RSV disease occurs mainly below 6 months of age, when neutralizing matAb levels are present. To investigate this discrepancy, we asked if disease severity is related to antibody properties other than neutralization. Some antibody effector functions are mediated via their Fc binding region. However, it has been shown that this binding may lead to antibody-dependent enhancement (ADE) of infection or reduction of neutralization, both possibly leading to more disease. In this study, we first showed that high levels of ADE of RSV infection occur in monocytic THP-1 cells in the presence of RSV antibodies and that neutralization by these antibodies was reduced in Vero cells when they were transduced with Fc gamma receptors. We then demonstrated that antibodies from cotton rats with formalin-inactivated (FI)-RSV-induced pulmonary pathology were capable of causing ADE. Human matAbs also caused ADE and were less neutralizing in vitro in cells that carry Fc receptors. However, these effects were unrelated to disease severity because they were seen both in uninfected controls and in infants hospitalized with different levels of RSV disease severity. We conclude that ADE and reduction of neutralization are unlikely to be involved in RSV disease in infants with neutralizing matAbs. IMPORTANCE It is unclear why severity of RSV disease peaks at the age when infants have neutralizing levels of maternal antibodies. Additionally, the exact reason for FI-RSV-induced enhanced disease, as seen in the 1960s vaccine trials, is still unclear. We hypothesized that antibodies present under either of these conditions could contribute to disease severity. Antibodies can have effects that may lead to more disease instead of protection. We investigated two of those effects: antibody-dependent enhancement of infection (ADE) and neutralization reduction. We show that ADE occurs in vitro with antibodies from FI-RSV-immunized RSV-infected cotton rats. Moreover, passively acquired maternal antibodies from infants had the capacity to induce ADE and reduction of neutralization. However, no clear association with disease severity was seen, ruling out that these properties explain disease in the presence of maternal antibodies. Our data contribute to a better understanding of the impact of antibodies on RSV disease in infants.