Miracle-dz/UniFAR-FTUs huggingface dataset:
Program Slicing and Execution Tracing for Differential Testing at Adobe Analytics

This paper reports on the use of program slicing concepts and partial execution tracing at Adobe Analytics to address a major limitation of differential testing - namely, how to deal with the large numbers of differences typically produced by this regression testing technique. Manual verification, typically used to verify detected differences, is tedious, time-consuming and error-prone. This severely limits the volume of testing that can be done and thereby reduces adoption of differential testing. It is hoped that, by sharing this experience, researchers with expertise in program slicing might be motivated to help solve some of the issues and limitations encountered during this novel application of slicing to a real-world industrial problem.
An updated checklist of the birds of Rio Grande do Norte, Brazil, with comments on new, rare, and unconfirmed species

Summary. We present a detailed bird list for the north-east Brazilian state of Rio Grande do Norte. This is the first inventory of the avifauna of the state that complies with strict criteria as to its compilation and documentation. To achieve this, we reviewed all records published for the state, as well as records in several online databases and museum collections. Our consolidated list is enhanced by our own unpublished records, and encompasses 425 species, 391 of them based on available specified physical evidence. The list includes 12 taxa not previously documented in the state and 35 documented taxa that are considered nationally or globally threatened. Other noteworthy records include three documented range extensions of 1,000 km or more and the first proven breeding by three species in far north-eastern Brazil. The rather diverse avifauna of Rio Grande do Norte reflects its location at the juxtaposition of three major domains: Atlantic Forest, Caatinga, Cerrado, and their ecotones, bordered by a marine environment.
Context influences how individuals with misophonia respond to sounds

Misophonia is a newly researched condition in which specific sounds cause an intense, aversive response in individuals, characterized by negative emotions and autonomic arousal. Although virtually any sound can become a misophonic “trigger,” the most common sounds appear to be bodily sounds related to chewing and eating as well as other repetitive sounds. An intriguing aspect of misophonia is the fact that many misophonic individuals report that they are triggered more, or even only, by sounds produced by specific individuals, and less, or not at all, by sounds produced by animals (although there are always exceptions). In general, anecdotal evidence suggests that misophonic triggers involve a combination of sound stimuli and contextual cues. The aversive stimulus is more than just a sound and can be thought of as a Gestalt of features which includes sound as a necessary component as well as additional contextual information. In this study, we explore how contextual information influences misophonic responses to human chewing, as well as sonically similar sounds produced by non-human sources. The current study revealed that the exact same sound can be perceived as being much more or less aversive depending on the contextual information presented alongside the auditory information. The results of this study provide a foundation for potential cognitive based therapies.
Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak that started in China at the end of 2019 has rapidly spread to become pandemic. Several investigational vaccines that have already been tested in animals and humans were able to induce neutralizing antibodies against the SARS-CoV-2 spike (S) protein, however protection and long-term efficacy in humans remain to be demonstrated. We have investigated if a virus-like particle (VLP) derived from Moloney murine leukemia virus (MLV) could be engineered to become a candidate SARS-CoV-2 vaccine amenable to mass production. First, we showed that a codon optimized version of the S protein could migrate efficiently to the cell membrane. However, efficient production of infectious viral particles was only achieved with stable expression of a shorter version of S in its C-terminal domain (ΔS) in 293 cells that express MLV Gag-Pol (293GP). The incorporation of ΔS was 15-times more efficient into VLPs as compared to the full-length version, and that was not due to steric interference between the S cytoplasmic tail and the MLV capsid. Indeed, a similar result was also observed with extracellular vesicles released from parental 293 and 293GP cells. The amount of ΔS incorporated into VLPs released from producer cells was robust, with an estimated 1.25 μg/ml S2 equivalent (S is comprised of S1 and S2). Thus, a scalable platform that has the potential for production of pan-coronavirus VLP vaccines has been established. The resulting nanoparticles could potentially be used alone or as a boost for other immunization strategies for COVID-19. IMPORTANCE Several candidate COVID-19 vaccines have already been tested in humans, but their protective effect and long-term efficacy are uncertain. Therefore, it is necessary to continue developing new vaccine strategies that could be more potent and/or that would be easier to manufacture in large-scale. Virus-like particle (VLP) vaccines are considered highly immunogenic and have been successfully developed for human papilloma virus as well as hepatitis and influenza viruses. In this study, we report the generation of a robust Moloney murine leukemia virus platform that produces VLPs containing the spike of SARS-CoV-2. This vaccine platform that is compatible with lyophilization could simplify storage and distribution logistics immensely.
An Engineered Genetic Circuit for Lactose Intolerance Alleviation Coupled with Gut Microbiota Recovery

Background Lactose malabsorption occurs in around 68% of the world populations, causing lactose intolerance (LI) symptoms such as abdominal pain, bloating and diarrhoea. To alleviate LI, previous studies mainly focused on strengthening intestinal β-galactosidase activity but neglected the inconspicuous colon pH drop caused by gut microbes’ fermentation on non-hydrolysed lactose. The colon pH drop will reduce intestinal β-galactosidase activity and influence the intestinal homeostasis. Results Here, we synthesized a tri-stable-switch circuit equipped with high β-galactosidase activity and pH rescue ability. This circuit can switch in functionality between expression of β-galactosidase and expression of l-lactate dehydrogenase in respond to intestinal lactose signal and intestinal pH signal. We confirmed the circuit functionality was efficient using 12-hrs in vitro culture at a range of pH levels, as well as 6-hrs in vivo simulations in mice colon. Moreover, another 21-days mice trial indicated that this circuit can recover lactose-effected gut microbiota of mice to the status (enterotypes) similar to that of mice without lactose intake. Conclusions Taken together, the tri-stable-switch circuit can serve as a promising prototype for LI symptoms relief, especially by flexibly adapting to environmental variation, stabilizing colon pH and restoring gut microbiota.
Towards an Investigation of Embodiment Time in Virtual Reality

Virtual Reality (VR) allows us to embody any possible appearance using avatars. Previous work found that the visual appearance of an avatar can affect the user’s behavior – a phenomenon known as the Proteus effect. The illusory feeling of owning a virtual avatar – the body ownership illusion – modulates the Proteus effect. Prior investigations revealed that the time of how long users embody an avatar can affect the extent of the body ownership illusion, however, it is currently unknown whether and how behavioral changes caused by the Proteus effect are moderated by the embodiment time. Therefore, we are planning to conduct a study with 30 participants where we induce the Proteus effect using avatars of different perceived ages to evaluate the effect of embodiment time on walking speed. We hypothesize that the longer users embody an elderly avatar, the slower they will walk in VR. In this proposal, we suggest a study design to evaluate the effect of embodiment time on the body ownership illusion and behavioral changes caused by the Proteus effect in VR.
Uncovering clinical risk factors and prediction of severe COVID-19: A machine learning approach based on UK Biobank data

Background: COVID-19 is a major public health concern. Given the extent of the pandemic, it is urgent to identify risk factors associated with severe disease. Accurate prediction of those at risk of developing severe infections is also important clinically. Methods: Based on the UK Biobank (UKBB data), we built machine learning(ML) models to predict the risk of developing severe or fatal infections, and to evaluate the major risk factors involved. We first restricted the analysis to infected subjects, then performed analysis at a population level, considering those with no known infections as controls. Hospitalization was used as a proxy for severity. Totally 93 clinical variables (collected prior to the COVID-19 outbreak) covering demographic variables, comorbidities, blood measurements (e.g. hematological/liver and renal function/metabolic parameters etc.), anthropometric measures and other risk factors (e.g. smoking/drinking habits) were included as predictors. XGboost (gradient boosted trees) was used for prediction and predictive performance was assessed by cross-validation. Variable importance was quantified by Shapley values and accuracy gain. Shapley dependency and interaction plots were used to evaluate the pattern of relationship between risk factors and outcomes. Results: A total of 1191 severe and 358 fatal cases were identified. For the analysis among infected individuals (N=1747), our prediction model achieved AUCs of 0.668 and 0.712 for severe and fatal infections respectively. Since only pre-diagnostic clinical data were available, the main objective of this analysis was to identify baseline risk factors. The top five contributing factors for severity were age, waist-hip ratio(WHR), HbA1c, number of drugs taken(cnt_tx) and gamma-glutamyl transferase levels. For prediction of mortality, the top features were age, systolic blood pressure, waist circumference (WC), urea and WHR. In subsequent analyses involving the whole UKBB population (N for controls=489987), the corresponding AUCs for severity and fatality were 0.669 and 0.749. The same top five risk factors were identified for both outcomes, namely age, cnt_tx, WC, WHR and cystatin C. We also uncovered other features of potential relevance, including testosterone, IGF-1 levels, red cell distribution width (RDW) and lymphocyte percentage. Conclusions: We identified a number of baseline clinical risk factors for severe/fatal infection by an ML approach. For example, age, central obesity, impaired renal function, multi-comorbidities and cardiometabolic abnormalities may predispose to poorer outcomes. The presented prediction models may be useful at a population level to help identify those susceptible to developing severe/fatal infections, hence facilitating targeted prevention strategies. Further replications in independent cohorts are required to verify our findings.
DNA methylation patterns and disease activity in a longitudinal cohort of lupus patients

Epigenetic dysregulation is implicated in the pathogenesis of lupus. We performed a longitudinal analysis to assess changes in DNA methylation in lupus granulocytes over 4 years of follow up and across disease activity levels using 229 patient samples. We demonstrate that DNA methylation profiles in lupus are influenced by ancestry-specific genetic variants and are highly stable over time. DNA methylation levels in two CpG sites correlated significantly with changes in lupus disease activity. Progressive demethylation in SNX18 was observed with increasing disease activity in African-American patients. Importantly, demethylation of a CpG site located within GALNT18 was associated with the development of active lupus nephritis. Differentially methylated genes between African-American and European-American lupus patients include type I interferon-response genes such as IRF7 and IFI44, and genes related to the NFkB pathway. TREML4, which plays a vital role in toll-like receptor signaling, was hypomethylated in African-American patients and demonstrated a strong cis-meQTL association.
An improved method to estimate the effective reproduction number of the COVID-19 pandemic: lessons from its application in Greece

Introduction: Monitoring the time-varying effective reproduction number Rt is crucial for assessing the evolution of the COVID-19 pandemic. We present an improved method to estimate Rt and its application to routine surveillance data from Greece. Methods: Our method extends that of Cori et al (2013), adding Bayesian imputation of missing symptom onset dates, imputation of infection times using an external estimate of the incubation period, and an adjustment for reporting delay. To facilitate its use, we provide an R software package named "bayEStim". We applied the method to COVID-19 surveillance data from Greece, and examined the resulting Rt estimates in relation to control measures applied, in order to assess their effectiveness. We also associated Rt, as a measure of transmissibility, to population mobility as recorded in Google data and to ambient temperature. We used a serial interval between 4 and 7.5 days, and a median incubation period of 5.1 days. Results: In Greece Rt fell rapidly as the first control measures were introduced, dropping below 1 at least a week before a full lockdown came into effect. In mid-July Rt started increasing again, as increased mobility associated with tourism activity was observed. Each 10% of increase in relative mobility increased Rt by 8.1% (95% CrI 6.1-10.2%), whereas each unit celsius of temperature increase decreased Rt by 4.6% (95% CrI 5.4-13.7%). Conclusions: Mobility patterns significantly affect Rt. Most of the reduction in COVID-19 transmissibility in Greece occurred already before the lockdown, likely as a result of decreased population mobility. Lower viral transmissibility in summer does not appear sufficient to counterbalance the increased mobility due to tourism. Monitoring Rt is an essential component of COVID-19 surveillance, and it is crucial for correctly assessing the effect of control measures.
Texture Classification Using Local Neighbor Differences

This paper proposes texture descriptor for texture classification called Local Neighbor Differences (LND). LND is a high discriminating texture descriptor and also robust to illumination changes. The proposed descriptor utilizes the sign of differences between surrounding pixels in a local neighborhood. The differences of those pixels are thresholded to form an 8-bit binary codeword. The decimal values of these 8-bit code words are computed and they are called LND values. A histogram of the resulting LND values is created and used as feature to describe the texture information of an image. Experimental results, with respect to texture classification accuracies using OUTEX_TC_00001 test suite has been performed. The results show that LND outperforms LBP method, with average classification accuracies of 92.3% whereas that of local binary patterns (LBP) is 90.7%
ZnO-based multifunctional nanocomposites to inhibit progression and metastasis of melanoma by eliciting antitumor immunity via immunogenic cell death

Rationale: The development of a highly effective and tumor-specific therapeutic strategy, which can act against the primary tumor and also condition the host immune system to eliminate distant tumors, remains a clinical challenge. Methods: Herein, we demonstrate a facile yet versatile ZnO-capping and Doxorubicin (DOX)-loaded multifunctional nanocomposite (AuNP@mSiO2@DOX-ZnO) that integrates photothermal properties of gold nanoparticles (NPs), pH-responsive properties and preferential selectivity to tumor cells of ZnO QDs and chemotherapeutic agent into a single NP. The photothermal performance, pH-triggered release and preferential phagocytic ability were assessed. The induced anti-tumor immunity was determined by analyzing immune cell profile in tumor in vivo and molecular mechanism were identified by detecting expression of immunogenic cell death (ICD) markers in vitro. Moreover, mice models of unilateral and bilateral subcutaneous melanoma and lung metastasis were established to evaluate the antitumor effects. Results: As an efficient drug carrier, ZnO-capped NPs guarantee a high DOX payload and an in vitro, efficient release of at pH 5.0. In murine melanoma models, the nanocomposite can significantly inhibit tumor growth for a short period upon low-power laser irradiation. Importantly, ZnO NPs not only demonstrate preferential selectivity for melanoma cells but can also induce ICD. Meanwhile, AuNP@mSiO2-based photothermal therapy (PTT) and DOX are directly cytotoxic towards cancer cells and demonstrate an elevated ICD effect. The induced ICD promotes maturation of dendritic cells, further stimulating the infiltration of effector T cells into tumor sites, preventing tumor growth and distant lung metastases. Conclusions: This study highlights the novel mechanism of ZnO-triggered anti-tumor immunity via inducing ICD. Additionally, we shed light on the multifunctionality of nanocomposites in delivering localized skin tumor therapy as well as inhibiting metastatic growth, which holds great promise in clinical applications.
Aggression Identification in Posts - two machine learning approache

Social media have changed the way people communicate. One of the aspects is cyber-aggression and interpersonal aggression that can be catalyzed by perceived anonymity. Automatically monitoring user-generated content in order to help moderating it is thus a hot topic. In this paper, we present and evaluate two supervised machine learning models to identify aggressive content and the level of aggressiveness. The ﬁrst model uses random forest and linear regression while the second model uses deep learning techniques.
Improvement of Cell Proliferation and Antioxidant Activity of Silymarin in Hair Follicles Dermal Papillae Isolated from the Human Scalp: Comparison with Vitamin C Effects

Introduction: Nowadays, hair loss is becoming a major problem for a large number of people. The main factors affecting hair growth include racial, gender, genetics, and hormonal. Furthermore, environment, physiology, and nutrition are the tools that are affecting hair growth. Materials and Methods: This article analyses the effects of silymarin and Vitamin C on the proliferation of dermal papilla cells (DPCs), COX2, inducible nitric oxide synthase (iNOS), total anti-oxidant capacity (TAC), and reactive oxygen species (ROS). The DPCs of the hair follicle treated by 50 and 100 μM of silymarin and 100 μM of Vitamin C on days 2, 7, and 14. Results: A comparatively effect of silymarin and Vitamin C demonstrated that Vitamin C is more effective in the stimulation of dermal papillae in cell culture. Furthermore, the stimulation effects of silymarin are attributed to its antioxidant activity of the cells. Conclusion: The overall result shows that cell proliferation and TAC significantly increased. However, iNOS, ROS, and COX2 levels were decreased.
Clinical application of mesenchymal stem cells for cartilage regeneration

Cartilage has the ability to transmit and distribute loads, providing lubrication in the diarthrodial joints. Risk factors including age, gender, genetics, nutrition and bone density may predispose to osteoarthritis (OA) and cartilage defect formation. Appropriate treatment include sufficient rest and medical therapy. Intra-articular injections such as steroids, platelet-rich plasma, visco-supplementation and mesenchymal stem cells (MSCs) injections present as alternative options for non-operative treatments. For cartilage defects, microfracture (MF), osteochondral autograft transplantation (OAT) and autologous chondrocyte implantation (ACI) are the most common treatment procedures. MSCs have been identified as an ideal cell source for OA therapy because they are easily expanded in culture, generally non-tumorigenic, and can be readily obtained from patients. It may be harvested from bone marrow (BMSCs), adipose tissue (ADSCs), synovium (SDSCs) or peripheral blood. BMSCs features the most common source of stem cells, and infrapatellar fat pad (IPFP) is another popular stem cell source. A phase 1 clinical study entitled “Treatment of Knee OA with Autologous Mesenchymal Stromal Cell Product (RegStem®)” was conducted in Taiwan and utilized 5 × 107 IPFP-MSCs in the study for OA therapy. Most of the existing clinical studies have shown that patients receiving MSCs treatment have improved clinical outcome, such as Visual Analogue Scale, International Knee Documentation Committee and Western Ontario and McMaster Universities Arthritis Index (WOMAC) score. Some studies have also found an improvement in cartilage volume by Magnetic Resonance Imaging evaluation. Furthermore, MSCs can also be used for cartilage defect treatment. Clinical outcomes such as IKDC, Lysholm, and Tegner scores showed significant improvement when the cartilage defects were repaired and regenerated by several millions of stem cells. A 10-year follow-up clinical research indicated that there was no apparent increased tumor formation risk when BMSCs were used for cartilage defect treatment. Page 2 of 12 Chen et al. Plast Aesthet Res 2020;7:49 I http://dx.doi. org/10.20517/2347-9264.2020. 28 In addition, a BMSCs/collagen gel composite for cartilage repair clinical trial in Taiwan was conducted in 2008, and results suggested that there was an improvement in IKDC and MRI score at 9-years of follow-up. It appears that the use of MSCs for OA and cartilage defect treatment may be a promising method.
Studies in Stream Life in Tributaries of the Welsh Dee

This study attempts to investigate the fauna of some streams of the Dee river system in Wales, with reference to seasonal variation, food cycles and the available food for the fish population. The field work, apart from preliminary summer samples, extended from September I946 to July I947, and involved quantitative studies of the lithophilic fauna in two streams, the Ceirw and the Merddwr, amplified by general collections from various habitats. The gut contents of many forms were investigated and considered in relation to mode of feeding and the'constitution of the microscopic planktonic and benthic fauna and flora. Many of the earlier investigations on the benthic fauna of running waters, both continental and American, are cited by Carpenter (1928) and by Welch (I935). In Britain, the main general surveys of unpolluted waters are those of Carpenter (I 927), Percival & Whitehead (I 929, I930), Butcher, Longwell & Pentelow (I937) and Jones (94I, I943, I948). Edmonds (I939, unpublished) made an extensive study of the plankton of the Dee, and some observations on the benthos. The chief seasonal quantitative surveys deal with the fauna of a chalk stream (Whitehead, I935), and of submerged mosses (Frost, 1942). Neill (1938) discusses the fauna of the Scottish Don quantitatively in relation to the food of brown trout. The food of salmon parr has been considered in relation to available fauna of the Eden and Thuirso (Allen, 194I) and the Welsh Dee (Carpenter, I940). 2. METHODS