Miracle-dz/UniFAR-FTUs huggingface dataset:
Causes and Consequences of Spatial Within-Host Viral Spread

The spread of viral pathogens both between and within hosts is inherently a spatial process. While the spatial aspects of viral spread at the epidemiological level have been increasingly well characterized, the spatial aspects of viral spread within infected hosts are still understudied. Here, with a focus on influenza A viruses (IAVs), we first review experimental studies that have shed light on the mechanisms and spatial dynamics of viral spread within hosts. These studies provide strong empirical evidence for highly localized IAV spread within hosts. Since mathematical and computational within-host models have been increasingly used to gain a quantitative understanding of observed viral dynamic patterns, we then review the (relatively few) computational modeling studies that have shed light on possible factors that structure the dynamics of spatial within-host IAV spread. These factors include the dispersal distance of virions, the localization of the immune response, and heterogeneity in host cell phenotypes across the respiratory tract. While informative, we find in these studies a striking absence of theoretical expectations of how spatial dynamics may impact the dynamics of viral populations. To mitigate this, we turn to the extensive ecological and evolutionary literature on range expansions to provide informed theoretical expectations. We find that factors such as the type of density dependence, the frequency of long-distance dispersal, specific life history characteristics, and the extent of spatial heterogeneity are critical factors affecting the speed of population spread and the genetic composition of spatially expanding populations. For each factor that we identified in the theoretical literature, we draw parallels to its analog in viral populations. We end by discussing current knowledge gaps related to the spatial component of within-host IAV spread and the potential for within-host spatial considerations to inform the development of disease control strategies.
Platonic quasicrystal for flatlens focusing of flexural waves

Negative refraction and flat lens focusing of elastic waves has been recently demonstrated experimentally, though restricted to periodic structures where dispersion relations are readily available for prediction and design of superlenses. This is not possible anymore when considering quasiperiodic structures. Here we demonstrate quasicrystal platonic superlensing of elastic waves in perforated metallic thin plates, opening new possibilities for applications of quasi-periodic structures in elastic waves.
High protein diet is of benefit for patients with type 2 diabetes

Abstract Currently, the prevalence of type 2 diabetes is still increasing worldwide and has become a major public health burden. This meta-analysis was performed to further assess high protein (HP) diet on body weight, glycemic control, and cardiovascular disease risk factors in type 2 diabetes. A literature search was conducted in PubMed and Embase databases up to June 2018. The pooled standard mean difference (SMD) and the corresponding 95% confidence interval (CI) were calculated using RevMan 5.3 software. In total, 18 randomized control trials involving 1099 adults with type 2 diabetes were included. Pooled results indicated that HP diet could not significantly affect blood pressure of patients with type 2 diabetes, compared with low protein (LP) diet. However, the overall analyses showed the significant effect of HP diet on triglycerides reduction (SMD = −0.20, 95% CI = −0.35 to −0.05, P = .01) in patients with type 2 diabetes, compared with LP diet. Subgroup analyses showed that the ratio of energy from fat and carbohydrate in diet could affect the effect of HP diet on weight and triglyceride. HP diet could be indicated to obtain beneficial results in weight loss and lipid metabolism.
Replication-Competent NYVAC-KC Yields Improved Immunogenicity to HIV-1 Antigens in Rhesus Macaques Compared to Nonreplicating NYVAC

Though the RV144 phase III clinical trial showed promise that an effective vaccine against HIV-1 is possible, a successful vaccine will require improvement over the vaccine candidate (ALVAC) used in the RV144 study. With that goal in mind, we have tested in nonhuman primates an attenuated but replication-competent vector, NYVAC-KC, in direct comparison to its parental vector, NYVAC, which is replication restricted in human cells, similar to the ALVAC vector used in RV144. We have utilized a prime-boost regimen for administration of the vaccine candidate that is similar to the one used in the RV144 study. The results of this study indicate that a replication-competent poxvirus vector may improve upon the effectiveness of the RV144 clinical trial vaccine candidate. ABSTRACT As part of the continuing effort to develop an effective HIV vaccine, we generated a poxviral vaccine vector (previously described) designed to improve on the results of the RV144 phase III clinical trial. The construct, NYVAC-KC, is a replication-competent, attenuated recombinant of the vaccinia virus strain NYVAC. NYVAC is a vector that has been used in many previous clinical studies but is replication deficient. Here, we report a side-by-side comparison of replication-restricted NYVAC and replication-competent NYVAC-KC in a nonhuman primate study, which utilized a prime-boost regimen similar to that of RV144. NYVAC-C and NYVAC-C-KC express the HIV-1 antigens gp140, and Gag/Gag-Pol-Nef-derived virus-like particles (VLPs) from clade C and were used as the prime, with recombinant virus plus envelope protein used as the boost. In nearly every T and B cell immune assay against HIV-1, including neutralization and antibody binding, NYVAC-C-KC induced a greater immune response than NYVAC-C, indicating that replication competence in a poxvirus may improve upon the modestly successful regimen used in the RV144 clinical trial. IMPORTANCE Though the RV144 phase III clinical trial showed promise that an effective vaccine against HIV-1 is possible, a successful vaccine will require improvement over the vaccine candidate (ALVAC) used in the RV144 study. With that goal in mind, we have tested in nonhuman primates an attenuated but replication-competent vector, NYVAC-KC, in direct comparison to its parental vector, NYVAC, which is replication restricted in human cells, similar to the ALVAC vector used in RV144. We have utilized a prime-boost regimen for administration of the vaccine candidate that is similar to the one used in the RV144 study. The results of this study indicate that a replication-competent poxvirus vector may improve upon the effectiveness of the RV144 clinical trial vaccine candidate.
Utilization of a Strongly Inducible DDI2 Promoter to Control Gene Expression in Saccharomyces cerevisiae

Regulating target gene expression is a common method in yeast research. In Saccharomyces cerevisiae, there are several widely used regulated expression systems, such as the GAL and Tet-off systems. However, all current expression systems possess some intrinsic deficiencies. We have previously reported that the DDI2 gene can be induced to very high levels upon cyanamide or methyl methanesulfonate treatment. Here we report the construction of gene expression systems based on the DDI2 promoter in both single- and multi-copy plasmids. Using GFP as a reporter gene, it was demonstrated that the target gene expression could be increased by up to 2,000-fold at the transcriptional level by utilizing the above systems. In addition, a DDI2-based construct was created for promoter shuffling in the budding yeast genome to control endogenous gene expression. Overall, this study offers a set of convenient and highly efficient experimental tools to control target gene expression in budding yeast.
Temperature-Dependent Surface Charge and Flashover Behaviors of Oil-Paper Insulation Under Impulse With Superimposed DC Voltage

Oil-paper insulation will inevitably endure impulse voltage with a superimposed dc voltage (superimposed voltage) because of introduced lightning or switching, which can induce charge accumulation and trigger flashover during the operation of a converter transformer. Temperature rise is also a nonnegligible factor that can significantly influence the performances of oil-paper insulation. This paper aims to reveal the effects of ambient temperature and superimposed voltage on surface charge and flashover behaviors in an oil-paper insulation system. Surface potential decay (SPD) experiments were performed under superimposed voltage with various polarity and amplitude combinations and at the temperature ranging from 20 °C to 80 °C. The results show that the initial surface potential and decay rate increase as the amplitude of the impulse voltage increases at 20 °C. The initial surface potential declines, and the process of SPD is accelerated at higher temperatures because of the increased concentration of shallow traps. Subsequently, flashover tests were conducted under superimposed voltage. It is found that flashover occurs after applying superimposed voltages even with a rather low dc voltage. In addition, the dc voltage component is primarily responsible for flashover. Weibull results also indicate that it is prone to trigger flashover at higher temperatures, because thermal excitation helps more carriers to escape from deep traps and participate in the process of flashover. Accordingly, the insulation characteristics of oil-paper system can be significantly influenced by superimposed voltage and temperature, which should draw great concern among the power grid.
PENGEMBANGAN MEDIA SCRAPBOOK PADA PEMBELAJARAN IPA

In particular learning in natural science subjects, there are still a number of students who concentrate less on science, even less interested in the learning process, with the problem the researchers conducted research on scrapbook development in science learning. It is expected that with the development of these media students can be motivated and more enthusiastic in learning. The object and subject of this research are third grade students of elementary school. The data of this research are the results of media validation by material experts, media experts, and practitioners and the siwa III response to the developed media. This research uses Research and Development (R & D) research methodology and Borg and Gall development model. Media relevance is obtained from assessment by media experts and material experts. Based on the results of scrapbook media development research in science learning, the media developed proved valid based on the results of media validation by experts and practitioners. Learning media can also be accepted by students as evidenced by student responses taken by questionnaire responses used by researchers. Keywords: Development, Media, Scrapbook
Prognostic Dynamic Nomogram Integrated with Inflammation-Based Factors for Non-Small Cell Lung Cancer Patients with Chronic Hepatitis B Viral Infection

Chronic inflammation plays an important role in tumor progression. The aim of this study was to develop an effective predictive dynamic nomogram integrated with inflammation-based factors to predict overall survival (OS) of non-small cell lung cancer (NSCLC) patients with chronic hepatitis B viral (HBV) infection. We retrospectively analyzed NSCLC patients with HBV infection from Sun Yat-sen University Cancer Center between 2008 and 2010. Univariate and multivariate Cox survival analyses were performed to identify prognostic factors associated with OS of patients. All of the independent prognostic factors were utilized to build the dynamic nomogram. The predictive accuracy of the dynamic nomogram was evaluated concordance index (C-index), decision curve analysis and were compared with previous reported model and traditional TNM staging system. According to the total points (TPS) by dynamic nomogram, we further stratified patients into different risk groups. A total of 203 patients were included. Multivariate Cox analysis showed TNM stage (P = 0.019), treatment (P < 0.001), C-reactive protein (P = 0.020) and platelet (P = 0.012) were independent prognostic factors of OS. The dynamic nomogram was established by involving all the factors above. The C-index of dynamic nomogram for predicting OS was 0.76 (95%CI: 0.72-0.80), which was statistically higher than that of traditional TNM staging system (0.70, 95%CI: 0.66-0.74, P<0.001). Decision curve analysis demonstrated that the dynamic nomogram was better than the TNM staging system. The predictive accuracy of the current model keeping almost the same accuracy as previous one. Based on the total points (TPS) of dynamic nomogram, we divided the patients into 3 subgroups: low risk (TPS ≤ 107), intermediate risk (107< TPS ≤ 149), and high risk (TPS > 149). The differences of OS rates were significant in the subgroups. We propose a novel dynamic nomogram model based on inflammatory prognostic factors that is highly predictive of OS in NSCLC patients with HBV infection and outperforms the traditional TNM staging system.
Machine Learning Models Comparison for Bitcoin Price Prediction

In recent years, Bitcoin is the most valuable in the cryptocurrency market. However, prices of Bitcoin have highly fluctuated which make them very difficult to predict. Hence, this research aims to discover the most efficient and highest accuracy model to predict Bitcoin prices from various machine learning algorithms. By using 1-minute interval trading data on the Bitcoin exchange website named bitstamp from January 1, 2012 to January 8, 2018, some different regression models with scikit-Iearn and Keras libraries had experimented. The best results showed that the Mean Squared Error (MSE) was as low as 0.00002 and the R-Square (R2) was as high as 99.2%.
Privacy-preserving Recommender Systems Facilitated By The Machine Learning Approach

Recommender systems, which play a critical role in e-business services, are closely linked to our daily life. For example, companies such as Youtube and Amazon are always trying to secure their profit by estimating personalized user preferences and recommending the most relevant items (e.g., products, news, etc.) to each user from a large number of candidates. State-of-the-art recommender systems are often built on-top of collaborative filtering techniques, of which the accuracy performance relies on precisely modeling user-item interactions by analyzing massive user historical data, such as browsing history, purchasing records, locations and so on. Generally,more data can lead tomore accurate estimations andmore commercial strategies, as such, service providers have incentives to collect and use more user data. On the one hand, recommender systems bring more income to service providers and more convenience to users; on the other hand, the user data can be abused, arising immediate privacy risks to the public. Therefore, how to preserve privacy while enjoying recommendation services becomes an increasingly important topic to both the research community and commercial practitioners. The privacy concerns can be disparate when constructing recommender systems or providing recommendation services under different scenarios. One scenario is that, a service provider wishes to protect its data privacy from the inference attack, a technique aims to infer more information (e.g., whether a record is
Transforaminal lumbar interbody fusion with expandable cages: Radiological and clinical results of banana-shaped and straight implants

Purpose: Expandable titanium transforaminal lumbar interbody fusion (TLIF) devices are a relatively new group of implants allowing restoration of lumbar lordosis (LL) and thus improvement of sagittal alignment. The purpose of our study is to compare clinical and radiological results of two different expandable TLIF devices. Materials and Methods: In a retrospective study, patients who underwent TLIF surgery with a banana-shaped or straight TLIF cage in our spine center were analyzed. Primary outcome was change of disc height (DH), segmental lordosis angle (SLA), and lumbar lordotic angle (LLA). Moreover, basic patients parameters and cage subsidence were evaluated. Results: Sixty-one patients were studied (33 banana-shaped and 28 straight cages). DH changed in the banana group from 4.8 mm (standard deviation SD 2.5) to 10.4 (SD 2.4) and in the straight cage group from 6.2 mm (SD 2.5) to 9.6 mm (SD 1.7). The difference was statistically significant (P = 0.03). In addition, SLA correction was higher in the banana group with 5.8° (SD 5.0)–3.7° (SD 3.6), but not significant. LLA improved in the straight group with 5.2 (SD 6.4) compared to 3.7° (SD 5.8) in the banana group. We found subsidence in four patients (6.6%) in the banana-shaped group and nine cases (14.8%) in the other group. Conclusions: Expandable titanium implants show similar improvements in restoring segmental and global lordosis. Banana-shaped expandable cages offer higher potency restoring the intervertebral DH and show less rates of subsidence compared to straight expandable cages.
Natural Environment Benchmarks for Reinforcement Learning

While current benchmark reinforcement learning (RL) tasks have been useful to drive progress in the field, they are in many ways poor substitutes for learning with real-world data. By testing increasingly complex RL algorithms on low-complexity simulation environments, we often end up with brittle RL policies that generalize poorly beyond the very specific domain. To combat this, we propose three new families of benchmark RL domains that contain some of the complexity of the natural world, while still supporting fast and extensive data acquisition. The proposed domains also permit a characterization of generalization through fair train/test separation, and easy comparison and replication of results. Through this work, we challenge the RL research community to develop more robust algorithms that meet high standards of evaluation.
Holistic cognitive and neural processes: a fNIRS-hyperscanning study on interpersonal sensorimotor synchronization

Abstract Interpersonal sensorimotor synchronization (interpersonal SMS) is the foundation of complex human social interaction. Previous studies primarily focused on the individual cognitive processes of interpersonal SMS. However, all individuals compose an entire interaction system with emerged holistic properties during interpersonal SMS. Therefore, we proposed the `holistic cognitive and neural processes’ of interpersonal SMS and defined quantitative measurements that included Holistic Correction Gain (HCG), Holistic Timekeeper Variance (HTV) and Holistic Motor Variance (HMV) based on linear error correction model and inter‐brain couplings obtained by hyperscanning technique. We performed a joint‐tapping experiment including bidirectional and unidirectional conditions using functional near‐infrared spectroscopy (fNIRS) hyperscanning to evaluate effects of these holistic processes on synchronization performance. We found that the dyads’ performance highly correlated with the integrated effect of holistic cognitive processes in both conditions. Each holistic cognitive process played different roles in interpersonal SMS. HCG was critical to maintain synchronization. HTV related to mentalizing others’ behavior. Holistic neural process, the inter‐brain coupling of right prefrontal cortex (PFC), was significantly different between bidirectional and unidirectional conditions, which suggested the existence of neural markers at holistic level in interpersonal SMS.
Flexor Tendon Injuries and Repairs: A Single Centre Experience.

BACKGROUND Although flexor tendon injuries cause significant morbidities and socio-economic implications, there have been limited data on patient demographics, injury characteristics and surgical details. The aim of this study is to describe our experience in flexor tendon injuries and repairs. METHODS We performed a retrospective study of all digital flexor tendon injuries that were repaired from January 2011 to December 2014. The collected data included patient demographics, injury characteristics and surgical details. RESULTS A total of 214 patients, 308 digits with 446 flexor tendon repairs were identified. We found that males, non-residents, and 20-29 age group were most prone to flexor tendon injuries. Cleaners, labourers and related occupations were the most vulnerable. The mechanism of injury was usually work-related and mostly caused by glass. Most injuries involve both flexor digitorum profundus and flexor digitorum superficialis tendons. Concomitant digital nerve and vessel injuries were common. Most patients suffered zone 2 laceration of a single digit of the non-dominant hand. Most patients underwent procedures that lasted 1 to 2 hours, including multiple flexor tendon repairs, microsurgical repairs and other interventions. CONCLUSIONS This study is the largest study on patient demographics, injury characteristics and surgical details on flexor tendon injuries and repairs. It could be used to plan resources and policies for the management and prevention of flexor tendon injuries.
Analysis and Experiment of Equilateral Triangular Uniaxial-Anisotropic Dielectric Resonator Antennas

The design procedure of a uniaxial anisotropic equilateral triangular dielectric resonator antenna (ETDRA) is presented for the first time. The uniaxial material is realized by a periodic stack of sheets of two dissimilar materials with different dielectric constants. It is proven that the increase of the boresight gain and impedance bandwidth of the ETDRA is possible by using the uniaxial material for the antenna prism. The gain improvement is due to the increase in the sidewall radiations and the bandwidth enhancement is owing to the lowering of the effective permittivity of the structure. The fabricated anisotropic ETDRA offers an impedance bandwidth of 27.7% between 3.025 and 4 GHz with a measured gain above 8 dB. The simulation results agree well with the experimental ones.
Exploring the Validity of the Perceived Restorativeness Soundscape Scale: A Psycholinguistic Approach

Soundscapes affect people's health and well-being and contribute to the perception of environments as restorative. This paper continues the validation process of a previously developed Perceived Restorativeness Soundscape Scale (PRSS). The study takes a novel methodological approach to explore the PRSS face and construct validity by examining the qualitative reasons for participants' numerical responses to the PRSS items. The structure and framing of items are first examined, to produce 44 items which are assessed on a seven-point Likert agreement scale, followed by a free format justification. Ten English speaking participants completed the PRSS interpretation questionnaire in two cafes in Montréal, Canada. Interpretation of participant free format responses led to six themes, which related to either the individual (personal attributes, personal outcomes), the environment (physical environment attributes, soundscape design) or an interaction of the two (behavior setting, normality, and typicality). The themes are discussed in relation to each Attention Restoration Theory (ART) component, namely Fascination, Being-Away, Compatibility, and Extent. The paper concludes by discussing the face and construct validity of the PRSS, as well as the wider methodological and theoretical implications for soundscape and attention restoration research, including the terminology importance in items measuring ART components and the value of all four components in assessing perceived restorativeness.